Barcelona COVID-19 wastewater study - GS | 7:11 AM 6/28/2020 - The Barcelona COVID-19 discovery questions prevailing assumptions - Michael Novakhov - SharedNewsLinks℠: "This study suggests that the story behind COVID-19 may not be as clear or as simple as initially thought. Science must lead the way in determining its origin, which may challenge our popular assumptions and reasoning. The precise origin of COVID-19 is not scientifically certain." | SARS-CoV-2 has been evolving for at least 7 years
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Barcelona COVID-19 wastewater study - GS
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7:11 AM 6/28/2020 - The Barcelona COVID-19 discovery questions prevailing assumptions - Michael Novakhov - SharedNewsLinks℠ | InBrief |
SARS-CoV-2 has been evolving for at least 7 years
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Anderson - Calgary University study: Sars-Cov-2 existed for at least from 2013 and is originally and specifically targeted at humans - GS
Sars-Cov-2 existed for at least from 2013 and is originally and specifically targeted at humans: Anderson - Calgary University and Petrovsky - Flinders University studies - GS
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Articles:
In silico comparison of spike protein-ACE2 binding affinities across species; significance for the possible origin of the SARS-CoV-2 virus
Detailed phylogenetic analysis of SARS-CoV-2 reveals latent capacity to bind human ACE2 receptor
Michael Novakhov - SharedNewsLinks  | ||||||||
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| The Barcelona COVID-19 discovery questions prevailing assumptions - CGTN | ||||||||
Coronavirus. /VCG
Coronavirus. /VCG
Editor's note: Tom Fowdy is a British political and international relations analyst and a graduate of Durham and Oxford universities. He writes on topics pertaining to China, the DPRK, Britain and the U.S. The article reflects the author's opinions, and not necessarily the views of CGTN.
On Saturday, news emerged that Spanish virologists had discovered purported traces of the COVID-19 virus in samples of Barcelona wastewater that were collected in March 2019. The team at the University of Barcelona had been testing sewage since April in order to identify new potential outbreaks of the virus and subsequently found what they believe to be its genome from that a sample over a year ago.
"The levels of SARS-CoV-2 were low but were positive," scientist Albert Bosch told the media. Although more testing is needed to ensure the result is not a false positive, the finding was nevertheless described as "suggestive" and has been submitted for peer review.
Scientifically, there is no comprehensive answer concerning its development. Certain actors, however, have sought to pinpoint the virus directly to make certain cultural and political points. This study suggests that the story behind COVID-19 may not be as clear or as simple as initially thought. Science must lead the way in determining its origin, which may challenge our popular assumptions and reasoning. The precise origin of COVID-19 is not scientifically certain. What experts know is that the genome behind the virus is of a zoonotic origin, which at some point crossed the species barrier via an unknown intermediate host and mutated into something contagious to humans.
However, the circumstances as to how it specifically emerged are yet to be determined and remain a mystery on a scientific and research level. While the development of a cluster of cases at the Huanan Seafood Market in Wuhan has received repeated attention as the purported point and time of origin, this is also not established scientific consensus.
Prof. Stephen Turner, head of the department of microbiology at Melbourne's Monash University, told The Guardian back in April: "I don't think it's conclusive by any means," while Donna Lu, writing in the New Scientist magazine the same month, also highlighted the mysteries regarding the certainty of its precise origin.
Medical workers pay a silent tribute to martyrs who died in the fight against the novel coronavirus disease (COVID-19) outbreak and compatriots who died of the disease, at Huoshenshan Hospital in Wuhan, central China's Hubei Province, April 4, 2020. /Xinhua
Medical workers pay a silent tribute to martyrs who died in the fight against the novel coronavirus disease (COVID-19) outbreak and compatriots who died of the disease, at Huoshenshan Hospital in Wuhan, central China's Hubei Province, April 4, 2020. /Xinhua
The rest of course is all political narrative, with the "China virus" line having been hammered by politicians, media outlets and other non-scientific actors who have sought to weaponize a stigmatic blame game against the country and thrive on culturalist and ideological tropes to draw pre-determined conclusions.
The public, of course, always wants immediate, simple answers and in general lacks the patience, rationality, foresight and perspective of professional scientists. As a result, the new Barcelona findings are suggestive in reminding us that the prevailing public "ideas" concerning the virus are not helpful or informative at all. The potential presence of virus genomes existing a year previously in Spain does not of course give us new conclusions or consensus regarding the origins of COVID-19, it does not mean it "originated" there merely by having a presence, but by showing it at an earlier location, at an earlier time, serves to question the prevailing public logic across the world. In this case, the development serves to remind the world that we cannot be armchair experts in virology and we do not know as much about the virus as we think. Because what is a very simple and straightforward word, "virus," for the public, is in fact an extremely complex and often immeasurable subject for actual scientists. Thus, understanding and mapping out COVID-19 is a timely process of discovery, which, owing to the mood and emotions of the public, may not always tell people the "stories" that they have assumed or even want to hear. This is why a scientific determination must come before a political one. (If you want to contribute and have specific expertise, please contact us at opinions@cgtn.com.) | ||||||||
| SARS-CoV-2 has been evolving for at least 7 years | ||||||||
The current COVID-19 pandemic demonstrates the vast unknown of virology, which continues to challenge the ability of humanity to remain healthy when faced with pathogens. While most known microbes have restricted affinity for specific species, continuing to adapt with the host species, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has crossed over from an unknown animal reservoir, like the preceding SARS and MERS coronaviruses, to infect human cells. Such viruses are typically more readily infective and cause more severe disease, as they have not yet adapted fully to the target host.
.jpg "Novel Coronavirus SARS-CoV-2 Colorized scanning electron micrograph of an apoptotic cell (green) heavily infected with SARS-COV-2 virus particles (purple), isolated from a patient sample. Image captured at the NIAID Integrated Research Facility (IRF) in Fort Detrick, Maryland. Credit: NIAID") Novel Coronavirus SARS-CoV-2 Colorized scanning electron micrograph of an apoptotic cell (green) heavily infected with SARS-COV-2 virus particles (purple), isolated from a patient sample. Image captured at the NIAID Integrated Research Facility (IRF) in Fort Detrick, Maryland. Credit: NIAIDAcquiring Potential for Human InfectionThe burning question is how novel viruses acquire the ability to recognize, bind to and enter human cells for the first time whether this is dependent only on viral proteins recognizing host cell proteins, or adaptations in other viral processes that allow replication in a human host.This issue is discussed by researchers at the University of Calgary in a new study published on the preprint server bioRxiv* in June 2020. The spike protein is the most well known of the SARS-CoV-2 proteins, and its binding to ACE2 receptors on the host cell is responsible for viral entry into the target cell. The human ACE2 (hACE2) has some rare variants which make the host more vulnerable to infection. Similarly, the spike protein of this virus has a greater affinity for the receptor than the previous SARS virus, which is another possible explanation for the increased infective potential of the current virus. The Study: Origin of ACE2 Binding AffinityThe current study examines the origin of this spike protein variant with its affinity for hACE2, using molecular dynamics (MD) simulations along with sequence reconstruction to identify the adaptation pathway of the virus. The result is a preliminary phylogenetic analysis that agrees with earlier studies the virus is 96% similar to the bat coronavirus (RaTG13) genome and 90% similar to the Pangolin-CoV genome.The next step was to carry out a more detailed analysis of 479 sequences collected from December 30, 2019, to March 20, 2020, where they found 16 variants. Of these, 11 were missense mutations occurring in 5% or more of cases, and each had its own phylogenetic route. The researchers then tried to recreate the ancestral sequence for the spike-RBD region, so that they could identify the important mutations that specifically drive its recent adaptation to the human host. They reconstructed the hypothetical common ancestor spike-RBD sequence for all human SARS-CoV-2 cases, called N1, and for the common ancestor with the closest animal virus, called N2. N1 is identical to the sequence in the SARS-CoV-2 reference sequence, but the N0 sequence is unique, which shows that this virus has originated uniquely. The two differ at 4 positions. The ancestral protein gave rise to various descendants, one of which is the RaTG13. Since this was around in 2013, the researchers conclude that the ancestral strain existed as early as that year, at least. In other words, the N0-N1 branch has been evolving for at least 7 years. Ancestral Sequence Had Higher Binding AffinityWhat are the functional differences between N0 and current spike-RBD sequences? The researchers used MD simulations of the spike-RBD-hACE2 complex, beginning with the X-ray crystal structures. The model showed that the free binding energy for this complex decreased as N0 changed to N1. Thus, this actually reduced the binding affinity both in the simulations and in vitro.However, two of the changes were associated with more significant decreases than the other. This shows that the N0 strain had, unexpectedly, greater binding affinity than the N1 strain. This is the first study to show that the common ancestor of both SARS-CoV-2 and the RaTG13 had the ability to bind to the ACE2 receptor in humans. Other Molecular Changes Key to InfectivityThe implications are that firstly, the binding affinity of the spike-RBD to hACE2 is not the primary driver of the highly infectious nature of the current virus since the ancestral virus was capable of doing this too. Secondly, the researchers suggest that this virus was, even then, able to bind tightly to the receptor. Therefore, this was not sufficient to produce the currently observed ability to spread rapidly and widely among humans. Instead, this must be due to another set of mutations in the viral genome.Yet another implication is that the current virus may not have jumped to humans from an animal origin at all because its affinity for hACE2 was not a recently acquired molecular trait. This may mean that the ability to infect human cells was present over a more extended period in the past, but produced less obvious or fewer clinical symptoms which passed unnoticed. Another alternative was that it affected only a small number of people, allowing it to remain under the public health radar.  Characterization of SARS-CoV-2 Spike-RBD functional evolution. A. Table of MM/PBSA binding energies between receptor binding domains of SARS-CoV2 evolutionary constructs and hACE2 receptor (note that lower energy indicates tighter binding). Blue cells indicate the presence of the ancestral (N0) state and green cells (with an x) indicate the presence of the SARS-CoV-2 state (N1) at a given position. Two values are present for constructs with an ancestral (N0) state at position 498 (which reflect the ambiguity of its ancestral reconstruction), corresponding to h498 and y498 from left to right. Energies are shown as the mean of three replicate simulations with SEM indicated in parenthesis. B. The relative effect of changes in the SARS-CoV-2 receptor-binding domain from ancestral (N0) to SARS-CoV-2 (N1) state on MM/PBSA binding energies. Size of spheres indicates the relative magnitude, with red spheres indicating decreased binding affinity and blue indicating increased binding affinity. Values are averaged for h498 and y498 states (both raw values shown in parentheses). C. Schematic of two possible evolutionary scenarios stemming from the observed evolutionary SARS-CoV-2 Spike-RBD function. In Scenario 1, it is postulated that a zoonotic ancestral SARS-CoV-2 strain possessed the ability to effectively bind hACE2 but was unable to effectively enter human cells, requiring the presence of subsequent mutations to infect humans. In Scenario 2, an ancestral SARS-CoV-2 strain was actively infecting humans prior to the outbreak at low levels, thus escaping public health detection until subsequent mutations lead to increased infectivity and/or severity.Future ResearchThese possibilities can only be tested by a broad-spectrum approach to sequencing all coronavirus strains in human populations, as this will reveal the presence of closely related viruses if such are present.The current study is an in silico study, and further validation of these findings is necessary using combinatorial libraries which can be screened to map functionalities to the genomic regions of the virus. This will help understand how the virus evolved in the most recent past. The researchers conclude: It appears that the SARS-CoV-2 Spike-RBD did not recently evolve binding affinity to a human-specific protein. Instead, that function appears to have been latent, making it clear that the evolution of this disease along with so many other aspects of its etiology is more complex than expected. *Important NoticebioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information. | ||||||||
| Disease X-19 News Review In Brief - 11:41 AM 6/27/2020: SARS-CoV-2 has been evolving for at least 7 years | ||||||||
Disease X-19 News Review In Brief - 11:41 AM 6/27/2020
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| 9:42 AM 6/27/2020 - SARS-CoV-2 has been evolving for at least 7 years: "We used detailed phylogenetic analysis, ancestral sequence reconstruction, and molecular dynamics simulations to examine the Spike-RBDs functional evolution, finding to our surprise that it has likely possessed high affinity for human cell targets since at least 2013." | ||||||||
 9:42 AM 6/27/2020 "We used detailed phylogenetic analysis, ancestral sequence reconstruction, and molecular dynamics simulations to examine the Spike-RBDs functional evolution, finding to our surprise that it has likely possessed high affinity for human cell targets since at least 2013." Detailed phylogenetic analysis of SARS-CoV-2 reveals latent capacity to bind human ACE2 receptor
Erin Brintnell, Mehul Gupta, Dave W Anderson
doi: <a href="https://doi.org/10.1101/2020.06.22.165787" rel="nofollow">https://doi.org/10.1101/2020.06.22.165787</a>
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This article is a preprint and has not been certified by peer review [what does this mean?].
SARS-CoV-2 has been evolving for at least 7 years https://news.knowledia.com/AU/en/articles/sars-cov-2-has-been-evolving-for-at-least-7-years-a376631e4f1f43879dbf4720405fc94a26b7eafe
SARS-CoV-2 Traces Detected in Barcelona Waste Water From March 2019 | Technology Networks
Study Suggests Coronavirus Emerged In Spain Much Earlier Than Thought - The New York Times https://www.nytimes.com/2020/06/26/health/coronavirus-spain.html
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| SARS-CoV-2 has been evolving for at least 7 years | ||||||||
The current COVID-19 pandemic demonstrates the vast unknown of virology, which continues to challenge the ability of humanity to remain healthy when faced with pathogens. While most known microbes have restricted affinity for specific species, continuing to adapt with the host species, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has crossed over from an unknown animal reservoir, like the preceding SARS and MERS coronaviruses, to infect human cells. Such viruses are typically more readily infective and cause more severe disease, as they have not yet adapted fully to the target host. Novel Coronavirus SARS-CoV-2 Colorized scanning electron micrograph of an apoptotic cell (green) heavily infected with SARS-COV-2 virus particles (purple), isolated from a patient sample. Image captured at the NIAID Integrated Research Facility (IRF) in Fort Detrick, Maryland. Credit: NIAID Acquiring Potential for Human Infection This issue is discussed by researchers at the University of Calgary in a new study published on the preprint server bioRxiv* in June 2020. The spike protein is the most well known of the SARS-CoV-2 proteins, and its binding to ACE2 receptors on the host cell is responsible for viral entry into the target cell. The human ACE2 (hACE2) has some rare variants which make the host more vulnerable to infection. Similarly, the spike protein of this virus has a greater affinity for the receptor than the previous SARS virus, which is another possible explanation for the increased infective potential of the current virus. The Study: Origin of ACE2 Binding Affinity The current study examines the origin of this spike protein variant with its affinity for hACE2, using molecular dynamics (MD) simulations along with sequence reconstruction to identify the adaptation pathway of the virus. The result is a preliminary phylogenetic analysis that agrees with earlier studies the virus is 96% similar to the bat coronavirus (RaTG13) genome and 90% similar to the Pangolin-CoV genome. The next step was to carry out a more detailed analysis of 479 sequences collected from December 30, 2019, to March 20, 2020, where they found 16 variants. Of these, 11 were missense mutations occurring in 5% or more of cases, and each had its own phylogenetic route. The researchers then tried to recreate the ancestral sequence for the spike-RBD region, so that they could identify the important mutations that specifically drive its recent adaptation to the human host. They reconstructed the hypothetical common ancestor spike-RBD sequence for all human SARS-CoV-2 cases, called N1, and for the common ancestor with the closest animal virus, called N2. N1 is identical to the sequence in the SARS-CoV-2 reference sequence, but the N0 sequence is unique, which shows that this virus has originated uniquely. The two differ at 4 positions. The ancestral protein gave rise to various descendants, one of which is the RaTG13. Since this was around in 2013, the researchers conclude that the ancestral strain existed as early as that year, at least. In other words, the N0-N1 branch has been evolving for at least 7 years. Ancestral Sequence Had Higher Binding Affinity What are the functional differences between N0 and current spike-RBD sequences? The researchers used MD simulations of the spike-RBD-hACE2 complex, beginning with the X-ray crystal structures. The model showed that the free binding energy for this complex decreased as N0 changed to N1. Thus, this actually reduced the binding affinity both in the simulations and in vitro. However, two of the changes were associated with more significant decreases than the other. This shows that the N0 strain had, unexpectedly, greater binding affinity than the N1 strain. This is the first study to show that the common ancestor of both SARS-CoV-2 and the RaTG13 Read full article | ||||||||
| Detailed phylogenetic analysis of SARS-CoV-2 reveals latent capacity to bind human ACE2 receptor | bioRxiv | ||||||||
Detailed phylogenetic analysis of SARS-CoV-2 reveals latent capacity to bind human ACE2 receptor
Erin Brintnell, Mehul Gupta, Dave W Anderson
doi: <a href="https://doi.org/10.1101/2020.06.22.165787" rel="nofollow">https://doi.org/10.1101/2020.06.22.165787</a>
This article is a preprint and has not been certified by peer review [what does this mean?].
AbstractSARS-CoV-2 is a once-in-a-century pandemic, having emerged suddenly as a highly infectious viral pathogen. Previous phylogenetic analyses show its closest known evolutionary relative to be a virus isolated from bats (RaTG13), with a common assumption that SARS-CoV-2 evolved from a zoonotic ancestor via recent genetic changes (likely in the Spike protein receptor binding domain or RBD) that enabled it to infect humans. We used detailed phylogenetic analysis, ancestral sequence reconstruction, and molecular dynamics simulations to examine the Spike-RBDs functional evolution, finding to our surprise that it has likely possessed high affinity for human cell targets since at least 2013.Main TextViral pathogens are a continuous and evolving challenge for human populations.1,2 Most known viruses maintain species-specific infectivity, often co-evolving with their host to mirror animal species trees.3,4 While less common, the emergence of novel viral pathogens is of particular interest because they often exhibit abnormal degrees of infectivity and/or virulence,5 having not evolved to a natural selection balance with their new host.6 Viruses of animal origin include periodic Ebola outbreaks,7 the 1918 Spanish Flu,8 and most recently, SARS-CoV-2, the viral agent that causes COVID-19.9 In these cases, viruses spread through human populations after evolving to cross the species barrier.10 Yet, many questions remain for viruses of non-human origin: How do they acquire the ability to infect humans? Is it wholly dependent on recognition (a function typically mediated by protein-protein binding between viral capsid and target host cell), or must there be changes in other viral replication mechanisms as well? And specifically focusing on SARS-Cov-2, did it evolve to infect humans via many evolutionary changes or only a few? Was it dependent on a key functional shift in its ability to bind human cells, or is there evidence that other genomic changes were needed for it to acquire its strikingly high degree of infectivity? Answering these questions is critical if we are to understand both the origin of specific viruses, such as SARS-CoV-2, as well as the capacity of animal viruses to evolve human infectivity.SARS-CoV-2 emerged in late 201911 and has high infectivity, spreading rapidly around the world, causing a global health emergency.12 A member of the Coronaviridae family of polymorphic, enveloped, single stranded RNA viruses,13 it is thought that SARS-CoV-2 evolved from a zoonotic origin,14,15 owing to its clear evolutionary relationship with coronaviruses that have been isolated from animals16 (its closest known evolutionary relative is the bat coronavirus, RaTG131720 and the second-closest known relative is a pangolin coronavirus, Pangolin-CoV).21 While most of the SARS-CoV-2 genome is most similar to the RaTG13 genome, some genomic regions, including the Spike glycoprotein Receptor Binding Domain (RBD) (which mediates viral entry into host cells), have greater sequence similarity to the Pangolin-CoV homolog,22 prompting some to suggest SARS-CoV-2 may be the product of recombination during co-infection.2124 The Spike protein is a key component of the SARS-CoV-2 infection pathway.25 Knockout and overexpression studies have demonstrated that binding of the Spike-RBD to human angiotensin converting enzyme 2 (hACE2) mediates cellular entry of SARS-CoV-2.2630 The protein sequence of this surface receptor is variable, with particular rare variants increasing patient susceptibility to SARS-CoV-2 infection.31 The SARS-CoV-2 Spike protein has been shown to bind the hACE2 receptor with greater affinity than the SARS-CoV-1 homolog, which has been suggested as a possible explanation for its greater infectivity.29 Additionally, many other related coronaviruses have been shown to be unable to bind hACE2 with sufficient affinity to support infection, raising the possibility that high hACE2 is a recently acquired trait for SARS-CoV-2.3234 Given this, a critical question remains to be answered: How and when did the SARS-CoV-2 Spike protein evolve its relatively higher affinity for the hACE2? With this question in mind, we set out to robustly characterize the evolutionary changes that accompanied the emergence of SARS-CoV-2, and that distinguish it from its closest zoonotic relatives. We focused on the evolution of the Spike-RBD by leveraging its known evolutionary relationships to other animal and human viruses and employed ancestral sequence reconstruction in conjunction with molecular dynamics simulations to identify biochemical and biophysical changes that enhanced Spike binding to the hACE2 receptor. Our initial phylogenetic analysis utilized whole viral genomic data, and generally supports prior studies conclusions, finding similar levels of nucleotide identity to the RaTG13 genome (96.0% sequence identity) and the Pangolin-CoV genome (90.0% sequence identity) (Supplementary Figure 1A).21,29 We next quantified the degree of evolutionary diversification that has occurred during SARS-CoV-2s global spread. We performed an in-depth analysis of 479 sequences collected between December 30, 2019 and March 20, 2020, and observe 16 polymorphisms, including 11 missense mutations present in >5% of infections (Supplemental Table 1), each mapping to unique phylogenetic branches (Figure 1A). One monophyletic clade was primarily isolated within the United States and Canada, and is defined by two synapomorphic missense mutations: c.17848A>G and c.28134C>T.35 Since these occur in one of the most variable parts of the coronavirus genome, it is likely that its distribution is due to a founder effect and that it does not confer an evolutionary advantage.36 It is also worth noting that neither appears in the Spike protein-coding region, making it unlikely to impact hACE2 affinity.
Supplementary Figure 1: Phylogenetic reconstruction of family that includes SARS-CoV-2.
Phylogenies were constructed using whole genome sequencing data from a series of known coronaviruses. The two closest relatives to SARS-CoV-2 are highlighted in red and sequence identities are specified. A. Displays phylogeny of 25 whole genomes of related coronaviruses represented as a horizontal cladogram, with sequence identities compared to RaTG13 and Pangolin CoV genomes specified. B. Phylogenetic reconstruction of 127 RdRp sequences represented as a circular cladogram, including a larger number of related coronavirus sequences.
View this table:
Supplementary Table 1: Frequency of genomic variants across SARS-CoV-2 infections.
Each noted variant that differs from the SARS-CoV-2 reference genome sequence is compiled, counted, and its frequency across human infections measured here is indicated, as well as the type of polymorphism and its potential impact on a protein-coding sequence.
Figure 1: Detailed examination of SARS-CoV-2 evolution.
A. Cladogram illustrating location-dependent evolution of the SARS-CoV-2 full genome following viral infection (December 30, 2019 - March 20, 2020). Distinct mutations (present in >5% of the examined sequences) are coloured and statistically significant clades (Bayes value > 0.9) are highlighted with black circles. B. Cladogram illustrating the last common ancestor all SARS-CoV-2 Spike-RBDs (N1) and of SARS-CoV-2 and the RaTG13 Spike-RBD (N0). C. Structural representation of the four mutations in the Spike-RBD (ribbon diagram) relative to the ACE2 receptor (Space filling model) that differ between N0 to N1. Stick models show the mutations in their N1 state. D. Alignment of the of the Spike-RBD of SARS-CoV-2 and its ancestors for both protein (top) and DNA (bottom). Black boxes highlight the four mutations that differ from N0 to N1.
View this table:
Supplementary Table 2: Statistical confidence of ancestral sequence reconstructions for positions that vary between N0 and N1.
Ancestral sequence reconstruction was assessed via computed posterior probability for each reconstructed state at each position in the sequence. The posterior probability for each reconstructed state at the four key positions that vary between N0 and N1 is shown, as calculated by two independent software packages (FastML and GRASP).
View this table:
Supplementary Table 3: Sources of all SARS-CoV-2 genome sequences.
Each genome sequence analyzed from SARS-CoV-2 infection cases are detailed according to geographic region of origin, as well as potentially relevant patient meta-data.
Supplementary Figure 2: RMSD of simulation data used for energy calculations.
Root-mean-square deviation (RMSD) is shown for simulation window that was used to calculate complex binding energy. Note that the Spike-RBD maintains a consistent stable configuration at the interface with hACE2, suggesting our energy calculations can be safely compared across simulations and that higher random stochasticity should not be a confounding factor.
Figure 2: Characterization of SARS-CoV-2 Spike-RBD functional evolution.
A. Table of MM/PBSA binding energies between receptor binding domains of SARS-CoV2 evolutionary constructs and hACE2 receptor (note that lower energy indicates tighter binding). Blue cells indicate the presence of the ancestral (N0) state and green cells (with an x) indicate the presence of the SARS-CoV-2 state (N1) at a given position. Two values are present for constructs with an ancestral (N0) state at position 498 (which reflect the ambiguity of its ancestral reconstruction), corresponding to h498 and y498 from left to right. Energies are shown as the mean of three replicate simulations with SEM indicated in parenthesis. B. Relative effect of changes in SARS-CoV-2 receptor binding domain from ancestral (N0) to SARS-CoV-2 (N1) state on MM/PBSA binding energies. Size of spheres indicate the relative magnitude, with red spheres indicating decreased binding affinity and blue indicating increased binding affinity. Values are averaged for h498 and y498 states (both raw values shown in parentheses). C. Schematic of two possible evolutionary scenarios stemming from the observed evolutionary SARS-CoV-2 Spike-RBD function. In Scenario 1, it is postulated that a zoonotic ancestral SARS-CoV-2 strain possessed the ability to effectively bind hACE2 but was unable to effectively enter human cells, requiring the presence of subsequent mutations to infect humans. In Scenario 2, an ancestral SARS-CoV-2 strain was actively infecting humans prior to the outbreak at low levels, thus escaping public health detection until subsequent mutations lead to increased infectivity and/or severity.
If this is the case that this viral lineage possessed the ability to bind hACE2 with high affinity for at least the past 7 years (Figure 1B) then why did it not emerge as a public health issue until recently? One possibility is that binding hACE2 by the Spike-RBD is not sufficient, on its own, to infect humans, and that other molecular components first needed to acquire new functions to do so. A second possibility is that this virus may have been capable of infecting human cells for a longer period of time in the past, but that its ancestral form either presented with far fewer symptoms (making it less disruptive and/or noticeable to those infected), or that it was far less infectious (thereby impacting only a small number of people), in either case escaping the notice of public health monitoring (Figure 2C). To test this, a broad and concerted effort to sequence the range of coronaviruses across human populations would need to be conducted, in order to test whether a closely related virus may also be circulating.4345 Naturally, as an in silico study, these results should be interpreted with some caution. Insofar as they can be validated, however, they are largely consistent with direct functional measurements in the lab.42 Ideally, combinatorial libraries could be constructed46,47 and functionally screened48 in order to glean more detailed insights into the molecular mechanisms underlying the recent evolution of this virus. Predicting the emergence of highly infectious and virulent diseases, while difficult, is vital for human population health.49 To do so, however, we must take steps to understand how pandemic diseases such as SARS-Cov2 emerged as they did, and to understand if and when they acquired the novel molecular functions that enabled their infectivity. In this case, it appears that the SARS-Cov2 Spike-RBD did not recently evolve binding affinity to a human-specific protein. Instead, that function appears to have been latent, making it clear that the evolution of this disease along with so many other aspects of its etiology is more complex than expected. Supplementary MethodsConfirmation of SARS-CoV-2 genome evolutionA phylogenetic analysis of 26 viral genomes was performed to confirm known SARS_CoV_2 ancestors. 24 known enzootic and endemic viruses and the SARS-CoV-2 reference genome and the Pangolin-CoV genome were downloaded from the National Center for Biotechnology Information (NCBI)50 and Lam et al.21 respectfully. Selected sequences were aligned using the Multiple Alignment using Fast Fourier Transform Version 7 (MAFFT) FFT-NS-2 algorithm. 51,52 MAFFT default parameters were used in our alignment, meaning gap penalties were assigned a value of 1.53. PhyML 3.0 was employed to construct a phylogeny of aligned genomes. 53,54 Bayes values 0.90 were considered statistically significant. The output tree was visualized using the online tool, Interactive Tree of Life (iTOL), and statistically significant clades were examined to validate current knowledge surrounding SARS-CoV-2 evolution.55We isolated the RbRp domain from the SARS-CoV-2 reference genome using the Basic Local Alignment Search Tool (BLAST).56 First, we performed a tblastn search of the SARS-CoV-2 RbRp reference domain published on NCBI using a BLOSUM 62 matrix, a gap opening penalty of 11 and a gap extension penalty of 1.50 We then used the output of this query to find the specific location of the RbRp domain in the nucleotide SARS-CoV-2 reference genome and isolated this portion of the genome for our analysis. Next, we employed BLASTn to isolate the RbRp domain from the pangolin coronavirus and the RaTG13 coronavirus. In this alignment, we used the gap opening penalty of 0 and gap extension penalty of 2.5. We also downloaded the 127 RbRp bat coronavirus sequences published by Joffrin et al.15 Isolated RbRp sequences were aligned using the MAFFT G-INS-I algorithm.51,52 Gap opening and extension penalties were the same as previously described. Finally, we created a phylogeny of the aligned sequences using PhyML 3.0. 53,54 The tree was visualized using iTOL and statistically significant clades were examined.55 Identification of geographic differences in SARS-CoV-2 sequencesTo identify geographic and time dependent differences in the SARS-CoV-2 viral genome, we performed a phylogenetic analysis of 479 SARS-CoV-2 sequences obtained from GISAID (Supplementary Table 3).57,58 We arbitrarily selected one sequence per day per country from December 30, 2019 to March 25, 2020. We also included the RaTG13 reference genome and the Pangolin-CoV genome published by Lam et al. in our analysis. 21,50 Selected sequences were aligned, as previously described, using the MAFFT FFT-NS-2 alignment algorithm.51,52 A consensus sequence was constructed from the 479 aligned SARS-CoV-2 sequences using the online tool MSAViewer.59 We validated our consensus sequence by cross referencing the sequence to the SARS-CoV-2 reference genome published by NCBI.50 Following, validation we uploaded the consensus sequence to the online cloud-based informatics platform, Benchling, and extracted the ORFs (<a href="http://benchling.com" rel="nofollow">benchling.com</a>).To determine common SNPs within the 479 SARS-CoV-2 sequences, the consensus ORFs were aligned using Nucleotide BLAST.56 By default, our analysis used a gap opening penalty of 5, a gap extension penalty of 2 and a mismatch penalty of 3. SNPs were extracted from the BLAST output using the Java module BlastNToSnp (http://dx.doi.org/10.6084/m9.figshare.1425030). We then selected for SNPs present in >5% of the sequences and inputted the SNPs into Benchling to determine whether the SNPs caused silent or missense mutations in the ORFs (<a href="http://benchling.com" rel="nofollow">benchling.com</a>). PhyML 3.0 was employed to construct a phylogenetic tree of the 479 aligned SARS-CoV-2 genomes, the RaTG13 genome and the Pangolin-CoV genome, 53,54 which was visualized using iTOL.55 Ancestral sequence reconstruction of spike glycoprotein receptor binding domainnBLASTx, run using a BLOSUM 62 matrix, a gap opening penalty of 11 and a gap extension penalty of 1, was employed to extract the Spike glycoprotein from the 479 SARS-CoV-2 sequences and the Pangolin-CoV genome.56 Additional, Spike sequences, including the RaTG13 Spike protein, were obtained directly from NCBI.50 Protein sequences were initially aligned using the Multiple Sequence Alignment by Log-Expectation (MUSCLE) program.60 The optimal parameters for phylogenetic reconstruction analysis were taken from the best-fit evolutionary model selected using the Akaike Information Criterion (AIC) implemented in the PROTTEST3 software,61 and were inferred to be the Jones-Taylor-Thornton (JTT) model62 with gamma-distributed among-site rate variation and empirical state frequencies. Phylogeny was inferred from these alignments using the RaXML v8.2.9 software63 and results were visualized using FigTree v1.4.4 (https://github.com/rambaut/figtree/releases). Ancestral sequence reconstruction was performed with the FastML software64 and further validated independently using the Graphical Representation of Ancestral Sequence Predictions (GRASP) software.65 Statistical confidence in each positions reconstructed state for each ancestor determined from posterior probability; any reconstructed positions with less than 95% posterior probability was considered ambiguous, and alternate states were also tested.Mutagenesis of ancestral proteinsTo understand the evolutionary importance of sequence changes observed between ancestral, zoonotic, and SARS-CoV-2 spike protein sequences, in silico mutagenesis and binding energy studies were performed. A previously constructed x-ray crystallography structure for the complex between the receptor binding domain (RBD) of the SARS-CoV-2 spike protein and the human hACE2 receptor were obtained from RCSB (accession number 6M0J). Utilizing PyMOL mutagenesis wizard, 66 the four missense mutations (R346t, A372t, Q498h or Q498y, H519n) identified between the N0 and N1 sequences were introduced into the SARS-CoV-2 RBD sequence, replicating the sequence of the putative ancestral zoonotic (N0) sequence. In addition to the N1 and N0 structures, additional structures were developed in a similar fashion, selectively including each of the 4 mutations to represent all of the possible combinations that these mutations may have existed throughout evolutionary timeMolecular dynamics simulation of Spike-RBD-hACE2 interactionsMolecular interactions were characterized with molecular dynamics simulations using Gromacs, TIP3P waters and CHARM07 force-field parameters for proteins. For each condition, three replicate 10 ns simulations were run, starting from crystal structures or structural models. Historical mutations were introduced and energy-minimized before MD simulation. Each system was solvated in a cubic box with a 10 Å margin, then neutralized and brought to 150 mM ionic strength with sodium and chloride ions. This was followed by energy minimization to remove clashes, assignment of initial velocities from a Maxwell distribution, and 1 ns of solvent equilibration in which the positions of heavy protein and DNA atoms were restrained. Production runs were 50 ns, with the initial 10 ns excluded as burn-in. The trajectory time step was 2 fs, and final analyses were performed on frames taken every 12.5 ps. We used TIP3P waters and the CHARM07 FF03 parameters for proteins, as implemented in GROMACS 4.5.5.67 Analyses were performed using VMD 1.9.1.68 GROMACS output was uploaded into Visual Molecular Dynamics (VMD) for Root-Mean Squared Deviation (RMSD) Analysis using the RMSD trajectory tool (ref). After discovering large deviations in RMSD values for the full RBD, which we attributed to noise at the ends of the RBD, we isolated our analysis to residues 397 to 512 of the RBD.Measurement of binding energiesNext, we measured the binding energies between residues 397 to 512 and the ACE2 receptor using g_mmpbsa, a program which employs Molecular mechanics PoissonBoltzmann surface area (MMPBSA) calculations to determine binding energy. Van der Waal forces, polar solvation energy, apolar solvation energy and SASA energy were calculated every 0.25 ns using a gridspace of 0.5 and a solute dielectric constant of 2. The output of the three replicates was amalgamated and binding energy was calculated using the bootstrap analysis (n = 2000 bootstraps) published by Kumari et al.40,41 We then characterize the genetic effect of each mutation (on average) and assessed whether there were any statistically significant epistatic interactions using established methods.46,47References
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| 7:44 AM 6/27/2020 - Michael Novakhov - SharedNewsLinks: CDC says there may be 10 times more coronavirus infections than reported in the US | ||||||||
 7:44 AM 6/27/2020 Michael Novakhov - SharedNewsLinks | InBrief | - - TWEETS BY MIKENOV | In Brief | _____________________________________________________________________ | ||||||||
| CDC says there may be 10 times more coronavirus infections than reported in the US BGR | ||||||||
The novel coronavirus infection is anything but contained in several hot spots around the world, including several US states that have registered record figures after reopening. President Trump has often said that the increased number of testing leads to a higher caseload, advocating in all seriousness for a reduction in tests. That approach will not deal with the underlying problem. The virus is spreading in communities faster than before now that lockdown measures have been lifted. Furthermore, resistance to wearing face masks could further increase the risk of transmission of the deadly disease. New estimates from the CDC indicate that the coronavirus has infected 10 times more Americans than confirmed so far via testing. The forecast comes from Director Robert Redfield, and its based on data from a COVID-19 antibody screening program. Even without the surges in Texas, Florida, California, and other states, officials did not have a complete picture of the COVID-19 epidemic in the US. A lack of testing made it impossible to test all suspected patients in the first months of the outbreak. Issues with antibody tests can further prevent the accurate collection of data. Knowing exactly how many people were infected is a crucial detail for planning future measures, whether its lockdowns, opening economies, or vaccination campaigns. An accurate caseload figure would also benefit researchers, as it would provide more accurate data about the number of people who are asymptomatic and the real mortality rate. As of Friday morning, more than 2.5 million Americans have been diagnosed. If the CDC estimates are accurate, then the actual number of people who were infected so far is 25 million. So far, nearly 127,000 thousand patients have died in the US. This virus causes so much asymptomatic infection, Redfield said on Thursday, via The Hill. We probably recognized about 10 percent of the outbreak. The director explained that serological surveys were collected for coronavirus tests as well as other reasons, like blood donations and laboratory tests. They showed that between 5% and 8% of Americans have contracted the virus. The CDC data seems to be in line with other regions. In mid-May, Spanish researchers published a study showing that the countrys real COVID-19 caseload may be at around 5% of the population, or 2,350,000 cases. At the time, Spain had over 272,000 confirmed cases, a tenth of which were fatal. Spain was the COVID-19 epicenter of Europe for a while, but managed to flatten the curve significantly. Both datasets indicate there shouldnt be any talk of herd immunity in either country. An incredibly high percentage of a population needs to be infected or immunized with a vaccine for the spread to be reduced. Unlike the Spanish study, Redfield did not provide the full data, and theres always a chance the estimate isnt accurate. Issues with antibody tests, as well as a recent finding that said antibodies can disappear three months after recovery, may alter results in antibody studies. This outbreak is not over. This pandemic is not over. The most powerful tool that we have, powerful weapon, is social distancing, Redfield said. We have responsibility to practice the social mitigation strategies to protect the vulnerable, to protect the elderly. The CDC is monitoring the situation in about 20 states where 100 CDC staffers are helping authorities deal with the surge in cases. Were not talking about a second wave right now, were still in the first wave. And that first wave is taking different shapes, Redfield said. The CDC updated its COVID-19 symptoms list in mid-May. On Thursday, the CDC also updated the list of medical conditions that can pose a severe risk of developing COVID-19 complications or dying.  | ||||||||
| Is there any truth behind the Covid-19 conspiracy theories? | ||||||||
Icke talks less about lizards and the Illuminati nowadays. Its all Covid (which doesnt exist), Bill Gates and 5G theories that have seen him falling foul of the major social media channels in the process. His official YouTube channel, with around 900,000 subscribers, was removed in May due to continued violation of its policies on transmitting information about Covid-19. Facebook removed his official page from its platform a few days earlier.
But he has become London Reals biggest attraction. The platform has live-streamed four interviews with Icke. The first, in March, drew the biggest audience in the channels history, and went on to receive six million views on YouTube. The third, in May, streamed live in contrived high drama from what Rose describes as the London Real secret bunker, was watched by over one million viewers. Watching Icke, bristling with bulging-eyed, messianic self-righteousness and indignation, expound his theories, unchallenged, over the course of three hours, is by turns excruciating, baffling and exhausting. His claims include that Bill Gates has purchased the entire global medical system. Another is that nano-technology chips in vaccines will transform us all into synthetic biological humans that will be unable to procreate. Behind it all is the cult. George Soros is a puppet of the cult. So is the Pope. And Mark Zuckerberg. The Covid pandemic, in fact, everything mass migration, climate change, transgenderism have all been manipulated by the cult in order to control and enslave us. It is the most complete architecture of paranoia and delusion it would be possible to imagine. And who are this cult? Icke is maddeningly unspecific. But in a separate video called Who Controls the World, he reveals that its a handful of people that you can probably get on 10 fingers, a global network of ultra-Zionist groups that answer to Israel. Of course! Who else would it be? Icke, who in the past has spoken of his disdain for the unquestioning, pathetic mainstream media did not respond to numerous requests for an interview. Rose claims that the audience for his third interview with Icke was the largest live stream of a human conversation in history by far. From that you can conclude a few things that people are idiots; or you can say that people arent as stupid as we thought they were, that they can digest a nuanced conversation and make up their own minds. He says he does not personally subscribe to Ickes views of a cult conspiring to rule the world. I dont consider myself a conspiracy theorist. Im a freedom of speech advocate, and besides David Icke I dont think Ive had anyone on my show that anyone would call a conspiracy theorist. My opinion isnt the point. The point is, you should have the right to hear these ideas and right now you dont. Rose claims that as a result of giving a platform to Icke and others, London Real has suffered very sophisticated malicious attacks on our technology platform [he does not specify by whom]; that he has been shadow-banned (the act of blocking followers from seeing a users content without the user knowing) on Instagram and warned that any mention of Covid-19, 5G or vaccines on his YouTube postings would lead to a real problem in putting London Real content on the platform. He denies that he is giving a voice to people who have no medical or scientific credibility and who are peddling potentially harmful misinformation. Who decides these things? Who are the gatekeepers here? These digital platforms [like YouTube] are essential to freedom of information, but if they decide youve violated their policies, whatever they want to stop they can stop. For Daniel Freeman, the consequences of giving the likes of Mikovits and Icke a platform are clearly shown in the results of the Oxford University survey. There is an underlying mistrust of official accounts, and a scepticism towards science, that is extraordinarily worrying, he says. We need evidence-based strategies for countering the spread of these sorts of theories. But its also the erosion of the trust in experts that needs to be built up again. Because this is exactly the moment we need to rely on them. But the insidiousness of conspiracy theories goes deeper still. There is some irony in the fact that theories which purport to tell the truth about hidden organisations plotting to rule the world by fear, actually cultivate precisely that fear and paranoia themselves the belief that everything we are told is designed to deceive and enslave us, that the world as we know it is a lie and fundamentally evil. There can be no more harmful conspiracy theory than that. Five of todays weirdest conspiracy theoriesActors were used in the video of George Floyds deathThe death of George Floyd in Minneapolis for which white police officer Derek Chauvin has been charged ignited demonstrations around the world, with over 50 countries participating in the Black Lives Matter protests. And with it has come a wealth of conspiracy theories, the main one being that everyone involved, including Floyd himself, are actors. Specifically, its what is dubbed a false flag conspiracy, when an incident is staged by a group who want a reason to retaliate against the person or group theyll later accuse of the attack.Pokemon Go is a government spying programme | ||||||||
| How the Coronavirus Short-Circuits the Immune System | ||||||||
At the beginning of the pandemic, the coronavirus looked to be another respiratory illness. But the virus has turned out to affect not just the lungs, but the kidneys, the heart and the circulatory system even, somehow, our senses of smell and taste.
Now researchers have discovered yet another unpleasant surprise. In many patients hospitalized with the coronavirus, the immune system is threatened by a depletion of certain essential cells, suggesting eerie parallels with H.I.V. The findings suggest that a popular treatment to tamp down the immune system in severely ill patients may help a few, but could harm many others. The research offers clues about why very few children get sick when they are infected, and hints that a cocktail of drugs may be needed to bring the coronavirus under control, as is the case with H.I.V. Growing research points to very complex immunological signatures of the virus, said Dr. John Wherry, an immunologist at the University of Pennsylvania whose lab is taking a detailed look at the immune systems of Covid-19 patients.
In May, Dr. Wherry and his colleagues posted online a paper showing a range of immune system defects in severely ill patients, including a loss of virus-fighting T cells in parts of the body.
In a separate study, the investigators identified three patterns of immune defects, and concluded that T cells and B cells, which help orchestrate the immune response, were inactive in roughly 30 percent of the 71 Covid-19 patients they examined. None of the papers have yet been published or peer reviewed. Researchers in China have reported a similar depletion of T cells in critically ill patients, Dr. Wherry noted. But the emerging data could be difficult to interpret, he said like a Rorschach test. Research with severely ill Covid-19 patients is fraught with difficulties, noted Dr. Carl June, an immunologist at the University of Pennsylvania who was not involved with the work. It is hard to separate the effects of simply being critically ill and in an I.C.U., which can cause havoc on your immune system, he said. What is missing is a control population infected with another severe virus, like influenza.
One of the more detailed studies, published as a preprint and under review at Nature Medicine, was conducted by Dr. Adrian Hayday, an immunologist at Kings College London.
He and his colleagues compared 63 Covid-19 patients at St. Thomass Hospital in London to 55 healthy people, some of whom had recovered from coronavirus infections.
Dr. Hayday and his colleagues began with the assumption that the patients would generate a profound immune response to the coronavirus. That is why most people recover from infections with few, if any, symptoms.
But those who get very sick from the virus could have immune systems that become impaired because they overreact, as happens in sepsis patients. Alternately, the scientists hypothesized, these patients could have immune systems that struggle mightily, but fail to respond adequately to the virus. One of the most striking aberrations in Covid-19 patients, the investigators found, was a marked increase in levels of a molecule called IP10, which sends T cells to areas of the body where they are needed. Ordinarily, IP10 levels are only briefly elevated while T cells are dispatched. But in Covid-19 patients as was the case in patients with SARS and MERS, also caused by coronaviruses IP10 levels go up and stay up.
That may create chaotic signaling in the body: Its like Usain Bolt hearing the starting gun and starting to run, Dr. Hayday said, referring to the Olympic sprinter. Then someone keeps firing the starting gun over and over. What would he do? Hed stop, confused and disoriented.
The result is that the body may be signaling T cells almost at random, confusing the immune response. Some T cells are prepared to destroy the viruses but seem undermined, behaving aberrantly. Many T cells apparently die, and so the bodys reserves are depleted particularly in those over age 40, in whom the thymus gland, the organ that generates new T cells, has become less efficient. Some patients are severely affected by coronavirus infections because their immune systems respond too vigorously to the virus. The result, a so-called cytokine storm, also has been seen in cancer patients treated with drugs that supercharge T cells to attack tumors. These overreactions can be quelled with medications that block a molecule called IL-6, another organizer of immune cells. But these drugs have not been markedly effective in most Covid-19 patients, and for good reason, Dr. Hayday said. There clearly are some patients where IL-6 is elevated, and so suppressing it may help, he explained. But the core goal should be to restore and resurrect the immune system, not suppress it. The new research may help answer another pressing question: Why is it so rare for a child to get sick from the coronavirus? Children have highly active thymus glands, the source of new T cells. That may allow them to stay ahead of the virus, making new T cells faster than the virus can destroy them. In older adults, the thymus does not function as well.
The emerging picture indicates that the model for H.I.V. treatment, a cocktail of antiviral drugs, may be a good bet both for those with mild illnesses and those who are severely ill.
Some experts have wondered if antiviral treatment makes sense for severely ill Covid-19 patients, if their main affliction is an immune system overreaction. But if the virus directly causes the immune system to malfunction, Dr. Hayday said, then an antiviral makes sense and perhaps even more than one, since its important to stop the infection before it depletes T cells and harms other parts of the immune system. I have not lost one ounce of my optimism, Dr. Hayday said. Even without a vaccine, he foresees Covid-19 becoming a manageable disease, controlled by drugs that act directly against the virus. A vaccine would be great, he said. But with the logistics of its global rollout being so challenging, its comforting to think we may not depend on one. | ||||||||
| Study Suggests Coronavirus Emerged In Spain Much Earlier Than Thought | ||||||||
In a study not yet published in a journal, scientists have reported that the new coronavirus was present in wastewater in Barcelona, Spain in March 2019, a finding that, if confirmed, would show that the pathogen had emerged much earlier than previously thought.
But independent experts who reviewed the findings said they doubted the claim. The study was flawed, they said, and other lines of evidence strongly suggest the virus emerged in China late last year. Up until now, the earliest evidence of the virus anywhere in the world has been from December 2019 in China and it was only known to have hit mainland Spain in February 2020. Barcelona is a city that is frequented by Chinese people, in tourism and business, so probably this happened also elsewhere, and probably at the same time, said the lead author, Albert Bosch, a professor in the Department of Microbiology of the University of Barcelona who has been studying viruses in wastewater for more than 40 years.
Several experts not involved in the research pointed out problems with the new study, which has not yet been subjected to the critical review by outside experts that occurs before publication in a scientific journal. They suggested that the tests might very well have produced false positives because of contamination or improper storage of the samples.
I dont trust the results, said Irene Xagoraraki, an environmental engineer at Michigan State University. Researchers at the University of Barcelona posted their findings online on June 13. Most of their report described research on wastewater treatments from early 2020. The surprising finding about March 2019 was only mentioned briefly at the end of the report. The research gained more attention when the university issued a news release on Friday. For months, scientists have been struggling to assemble clues about the origin of the new coronavirus. The earliest official reports came from the city of Wuhan in China in December 2019. Researchers have studied the mutations that have arisen in coronavirus samples collected from across the world since then and have estimated on the basis of their findings that the samples shared a common ancestor that dated to late 2019.
More evidence for the origin of the novel coronavirus has come from other viruses that scientists have found in animals. The closest relatives to the coronavirus infect bats in China.
Because the virus can be shed in feces, researchers have begun examining wastewater to detect the pathogens genes. In Europe, Australia and the United States, researchers discovered rising levels of the viruss genes in wastewater days before confirmed cases began to arise. These discoveries have led a number of researchers to examine frozen wastewater samples from earlier periods, seeking evidence of the viruss presence before anyone knew to look for it. Last week, Italian researchers reported finding the virus in Milan and Turin on December 18, two months before northern Italy was besieged by Covid-19 cases. Separately, in Spain, Dr. Bosch and his colleagues began taking weekly samples of wastewater from two of Barcelonas treatment plants in April. They found the virus in these samples, prompting them to look back at earlier samples. The researchers found the virus in a number of samples from early 2020, in the months before the pandemic struck Spain.
Dr. Bosch found it plausible that the virus could appear in March but not show up in more recent samples.
Respiratory viruses usually have peaks around this time of the year, Dr. Bosch said. Probably the virus then disappeared. But Dr. Xagoraraki noted that the researchers used tests that search for bits of three different genes. The only tests that came back positive were for a gene called RdRp. One of the other tests, for a gene called N, is known to be more sensitive. It should have shown a signal as well, Dr. Xagoraraki said. It was possible that the positive results were the result of contamination from other samples that did have the virus, Dr. Xagoraraki said. She also doubted whether the delicate coronavirus could have survived for over a year without the sample having been put in a deep freeze. If the samples were not stored in -80 degrees, you cant trust the results, she said. Gertjan Medema of the KWR Water Research Institute in the Netherlands said that the study came from a knowledgeable research team, and so should be taken seriously. But, he added, they need to confirm this finding in multiple ways. Dr. Bosch said that his team would not be able to repeat the experiments in the positive sample from March 2019 because it was depleted during the first test. We proved it from this sample but we cannot repeat it, he said. But contamination was unlikely, he said. The way we work, when there is contamination, we notice it. Another way to confirm the finding would be to search through stored samples of blood from patients in Barcelona hospitals in March 2019. If the virus were circulating, even briefly, in Spain, some people would most likely have been hospitalized complaining of flulike symptoms. [Like the Science Times page on Facebook. | Sign up for the Science Times newsletter.] | ||||||||
| SARS-CoV-2 Traces Detected in Barcelona Waste Water From March 2019 | ||||||||
Please note, the study from University of Barcelona is a preprint and as such has not undergone peer review yet.
COVID-19 was announced in Wuhan (China) in early December in 2019 and it would reach every place worldwide later, including Europe. The first case in Europe was announced in France in late January 2020. This chronology on the evolution of the disease can change according to a study led by the University of Barcelona, in collaboration with Aigües de Barcelona. Researchers detected the presence of the virus that caused the disease in samples of waste water in Barcelona, collected in March 12, 2019. These results, sent to a high impact journal and published in the archive medRxiv, suggest the infection was present before knowing about any case of COVID-19 in any part of the world. This study, which counts on the participation of the researchers of theGroup on Enteric Virus of the UB Gemma Chavarria Miró, Eduard Anfruns Estrada and Susana Guix, led by Rosa Maria Pintó and Albert Bosch, is part of the project on sentinel surveillance of SARS-CoV-2. This initiative is coordinated by this research group, in collaboration with Aigües de Barcelona and funded by the REVEAL project, from the company SUEZ, in order to detect the virus in waste waters and adopt immediate measures considering future COVID-19 outbreaks. An early detection tool Although COVID-19 is a respiratory disease, researchers proved there are large quantities of the coronavirus genome in the excrements that reach waste waters. This situation made the waste water-based epidemiology a potential tool for an early detection of the circulation of the virus among population, especially considering the important presence of asymptomatic people, especially considering the important presence of asymptomatic and asymptomatic people who transmit the virus. As part of the sentinel surveillance project, and after April 13, the researchers analysed weekly the obtained samples in two big water treatment plants in Barcelona. The levels of the SARS-CoV-2 genome coincided with the evolution of COVID-19 cases in the population, notes Albert Bosch, professor at the Faculty of Biology of the UB and coordinator of the study. COVID-19 cases hidden by the flu Later, researchers analysed frozen samples from previous months to the systematic sampling, which revealed the growing apparition of SARS-CoV-2 genome between early January and early March in 2020, bringing the chronology of the coronavirus arrival in Spain even earlier: the presence of the virus was detected in January 15, 41 days before the announcement of the first case of COVID-19, which was announced on February 25. According to the researchers, these results show the validity of the surveillance of waste waters to anticipate cases, specially considering the significant contribution of the asymptomatic and pre-symptomatic carriers in the spreading of the virus. Those infected with COVID-19 could have been diagnosed with flu in primary care by mistake, contributing to the community transmission before the public health took measures, notes Albert Bosch, also president of the Spanish Society of Virology. See also: Dutch Study Indicates Value of Sewage Monitoring for SARS-CoV-2 Tracking In the specific case of Barcelona the virologist continues, having detected the SARS-CoV-2 spread a month before could have improved the response to the pandemic. Analysis of frozen samples from 2018 and 2019 These results encouraged the researchers to analyse some frozen samples between January 2018 and December 2019, with the shocking results of the presence of SARS-CoV-2 genome in March 2019, before any notification of COVID-19 cases in the world. All samples were negatives regarding the SARS-CoV-2 genome presence except for March 12, 2019, in which the levels of SARS-CoV-2 were low but were positive, using two different targets, says the researcher. Barcelona receives many visitors for both tourist and professional reasons, continues Bosch, and it is possible for a similar situation to have taken place in other parts of the world, and since most of the COVID-19 cases show a similar symptomatology to the flu, those cases could have been disguised as an undiagnosed flu. Models in the SARS-CoV-2 epidemiological surveillance The Group on Enteric Viruses is also in charge of the scientific coordination of a project on the SARS-CoV-2 sentinel surveillance in waste waters in Spain, funded by the Spanish Ministry for Ecological Transition and Demographic Challenge. This task counts on the participation of two groups from CSIC, the Institute of Agrochemistry and Food Technology (IATA-CSIC) and the Centre of Edafology and Applied Biology of Segura (CEBAS), as well as a group from the University of Santiago de Compostela. Moreover, together with the research group Microbiology of Water related to the Health (MARS) of the UB, led by Anicet Blanch, coordinates the surveillance of the same virus in Spanish waters. Last, this group also takes part in a monitoring project on the presence of SARS-CoV-2 in waste waters in the entrance of Catalan treatment plants, funded by the Catalan Water Agency and coordinated by the Catalan Institute for Water Research (ICRA). Another participant in this project is the Research Group on Virus, bacteria and protozoans of water interest in and food (VIRBAP) of the UB. Reference: The study has been submitted for peer-review and is currently published as a preprint in the archive medRxiv. This article has been republished from the following materials. Note: material may have been edited for length and content. For further information, please contact the cited source. | ||||||||
| More virus cases in Seoul as new clusters emerge | ||||||||
Posted: Jun 26, 2020 5:43 AM EDT Updated: Jun 27, 2020 6:33 AM EDTBy The Associated Press
SEOUL, South Korea - South Korea has reported 51 more confirmed coronavirus cases as new clusters emerge in the densely populated Seoul area where people have been increasingly venturing out despite government warnings against complacency. Thirty-five of the new cases are in the capital region, which is at the center of a COVID-19 resurgence threatening to erase earlier gains against the virus. Authorities are struggling to trace contacts and predict infection routes as new clusters pop up. Hundreds of infections have been linked to nightspots, church gatherings, restaurants and low-income workers who couldnt afford to stay home. Officials are resisting calls to reimpose stronger social distancing guidelines, concerned about hurting the economy. ___ HERES WHAT YOU NEED TO KNOW ABOUT THE VIRUS OUTBREAK: - Virus taking stronger hold in US, other populated countries - Governors who quickly reopened backpedal as virus surges - After waves of COVID deaths, care homes face legal reckoning - Hospitals in the capital of Venezuelas main oil-producing state are filled with coronavirus patients and dozens of health workers have been infected, witnesses said this week in the first reports of the pandemic overwhelming the countrys debilitated health care system. - While Indias leaders have promised coronavirus testing and care for all who need it, regardless of income, treatment options are as stratified and unequal as the country itself. - U.S. officials estimate that 20 million Americans have been infected with the coronavirus since it first arrived in the United States, with millions never knowing they had it. Thursdays estimate is roughly 10 times the 2.3 million cases that have been confirmed in the U.S. - A government whistleblower ousted from a top scientific job alleges that the Trump administration is intensifying its campaign to punish him for revealing shortcomings in the U.S. coronavirus response. ___ Follow all of AP's pandemic coverage at http://apnews.com/VirusOutbreak and <a href="https://apnews.com/UnderstandingtheOutbreak" rel="nofollow">https://apnews.com/UnderstandingtheOutbreak</a> ___ HERES WHAT ELSE IS HAPPENING: BEIJING - China has reported an uptick in new coronavirus cases a day after national health authorities said they expected an outbreak in Beijing to be brought under control soon. The National Health Commission said Saturday that 21 more cases had been confirmed nationwide in the latest 24-hour period, including 17 in the nations capital. City officials have temporarily shut a huge wholesale food market where the virus spread widely, re-closed schools and locked down some neighborhoods. Anyone leaving Beijing is required to have a negative virus test result within the previous seven days. Many Chinese are traveling during a four-day holiday weekend that ends Sunday. China has reported 83,483 cases and 4,634 deaths in the pandemic. It does not include in the numbers people who test positive but don't show symptoms. ___ CANBERRA, Australia - Australian health officials are expecting more cases of COVID-19 as hundreds of nationals return from overseas to begin mandatory quarantine. About 300 people are due to arrive in Adelaide this weekend from Mumbai, India, while hundreds are expected to follow from South America and Indonesia. People in hotel quarantine will be tested for the coronavirus at the start and end of their 14-day isolation. South Australia state Health Minister Stephen Wade says he is preparing for about 5% to 10% of returnees being infected, as was the case when people arrived from Indonesia in other states. Melbourne reported 30 new cases Friday, continuing a run of double-digit increases that has more than tripled Victoria states active cases to 183 in just over a week. In all, Australia has had 104 COVID-19 deaths and nearly 7,600 confirmed cases. ___ AUSTIN, Texas - Texas has surpassed 5,000 hospitalized coronavirus patients for the first time as Gov. Greg Abbott continues a dramatic retreat in his aggressive reopening of Americas second-biggest state. In Houston, county officials Friday elevated a public threat warning system to the highest level. Harris County Judge Lina Hidalgo said We never brought the curve all the way down. We only flattened it. Hospitalizations in Texas, reported by state health officials, have now skyrocketed more than threefold over the past month. New records are set daily, and Abbott has brought back a ban on elective surgeries to free up beds. His latest orders shuttered bars indefinitely and ordered restaurants dining rooms to scale back on seating customers. ___ RANCHO CORDOVA, Calif. - Gov. Gavin Newsom said Friday that he wants an agricultural Southern California county to reimpose stay-home orders amid a surge in positive coronavirus tests there and through much of the state. Imperial County, with a population of 175,000 people on the states border with Mexico, has been the slowest in the state to reopen amid continued high positivity rates, which have averaged 23% in the last week, compared with 5.7% statewide. The Imperial Valley, which provides many of the vegetables in U.S. supermarkets in the winter, lies across the border from Mexicali, a sprawling industrial city of 1 million people that has enormous influence on its economy and culture. Newsom said San Francisco is also pausing plans to reopen businesses that were expected to open Monday, such as hair salons, museums and outdoor bars. ___ NEW YORK - A federal judge has blocked New York state from enforcing coronavirus restrictions limiting indoor religious gatherings to 25% capacity when other types of gatherings are limited to 50%. Judge Gary Sharpe acted Friday to enjoin Gov. Andrew Cuomo, New York City Mayor Bill de Blasio and Attorney General Letitia James from enforcing some of the capacity restrictions put in place by executive order to contain the spread of the virus. A spokesperson for Cuomo said the governors office will review the decision. A spokesperson for the New York City law department said city lawyers would review the ruling as well. -- NEW ORLEANS -- The number of reported COVID-19 cases in Louisiana took another large one-day jump, increasing Friday by more than 1,300 as the number of people hospitalized with the disease caused by the new coronavirus continued upward. The state reported a total of 54,769 confirmed cases as of midday. The death toll was 3,077, up by 26 from Thursday. Some of the growth in known case numbers can be attributed to increased testing. However, the number of people sick enough to be hospitalized - considered a key indicator that the virus is spreading - went up to 700. The figure is down from nearly 2,000 in April but up from a low of 542 on June 13. The increasing numbers led Gov. John Bel Edwards this week to delay plans to further lift restrictions on public gatherings and some business activity. Edwards has promised stepped up enforcement on businesses that arent complying with virus-related restrictions on capacity and requirements that employees dealing with the public wear masks. Friday marked Louisianas second one-day spike of more than 1,300 this week. ___ FORT LAUDERDALE, Fla. - Florida banned alcohol consumption at its bars after its daily confirmed coronavirus cases neared 9,000, almost double the previous record set just two days ago. The Florida agency that governs bars announced the ban on Twitter, minutes after the Department of Health reported 8,942 new confirmed cases, topping the previous record of 5,500 set Wednesday. More than 24,000 cases have been reported since Saturday, more than a fifth of the 111,724 cases confirmed since March 1. The department had not updated its death total, which still stood at 3,327. The seven-day average for positive tests dropped slightly to 13.4%, down 1 percentage point from Thursday but still triple the rate of 3.8% of June 1. State officials have attributed much of the new outbreak to young adults flocking to bars after they reopened about a month ago. ___ UNITED NATIONS - The United Nations is marking its 75th anniversary with a scaled-down event because of the COVID-19 pandemic, one of many challenges a deeply divided world must tackle along with poverty, inequality, discrimination and unending wars. U.N. Secretary-General Antonio Guterres told Fridays virtual commemoration of the signing of the U.N. Charter that global pressures are spiraling up and todays realities are as forbidding as ever. He said people continue to lose trust in political establishments and has spoken of rising populism threatening multilateralism and denounced xenophobia, racism and intolerance. Todays marches against racism were preceded by widespread protests against inequality, discrimination, corruption and lack of opportunities all over the world grievances that still need to be addressed, including with a renewed social contract, he said in a video address. Meanwhile, Guterres said, other fundamental fragilities have only grown: the climate crisis, environmental degradation, cyberattacks, nuclear proliferation, a push-back on human rights and the risk of another pandemic. He stressed the urgent need for global cooperation. One virus ... has put us on our knees, and we have not been able to fight it effectively, Guterres told reporters Thursday. Its spreading now everywhere. There was no control, no effective coordination among member states. We are divided in fighting COVID-19. ___ ROME - Italy registered 30 more deaths of people with coronavirus infections on Friday, with 16 of them in Lombardy, the northern region that continues to still have by far the highest daily tally of new confirmed cases. According to Health Ministry data, the nation confirmed 259 new cases since Thursday, raising to 239,961 the number of known coronavirus infections since Italys outbreak began in late February. Deaths now total 34,708. Authorities say the number of overall cases and deaths is certainly higher, since many without serious symptoms didnt get tested, and many died in nursing homes without being tested. Meanwhile, Premier Guiseppe Conte said Italys classrooms will be receiving students starting on Sept. 14, more than six months after the governments efforts to contain the spread of COVID-19 shuttered schools, forcing millions of students to have lessons remotely. Copyright 2020 The Associated Press. All rights reserved. This material may not be published, broadcast, rewritten or redistributed without permission. | ||||||||
| 5:56 AM 6/27/2020 - Sars-Cov-2 as bioweapon: Is there any truth behind the Covid-19 conspiracy theories? | Italy's Frontline: A Doctor's Diary shows stark reality of coronavirus crisis | Coronavirus and US Military: As COVID-19 spikes across US, troop diagnoses jump 20 percent in a week | Coronavirus and HIV: How the Coronavirus Short-Circuits the Immune System | ||||||||
 Disease X-19 as the Bio-weapon from Michael_Novakhov (3 sites): Google Alert - sars cov 2 as bioweapon: Is there any truth behind the Covid-19 conspiracy theories? 5:56 AM 6/27/2020 Coronavirus and US Military: As COVID-19 spikes across US, troop diagnoses jump 20 percent in a week
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| NY Times: Russia Offered Afghan Militants Bounties to Kill US Troops | ||||||||
U.S. intelligence has concluded that the Russian military offered bounties to Taliban-linked militants in Afghanistan to kill American troops and other coalition forces, The New York Times reported Friday. Citing officials briefed on the matter, the Times said the United States determined months ago that a Russian military intelligence unit linked to assassination attempts in Europe had offered rewards for successful attacks last year. Islamist militants, or armed criminal elements closely associated with them, are believed to have collected some bounty money, the newspaper said. The White House, the CIA and the Office of the Director of National Intelligence declined requests from Reuters for comment on the Times report. President Donald Trump has been briefed on the intelligence finding, the Times said. It said the White House had yet to authorize any steps against Russia in response to the bounties. Of the 20 Americans killed in combat in 2019, the Times said, it was not clear which deaths were under suspicion. After nearly 20 years of fighting the Taliban, the United States is looking for a way to extricate itself from Afghanistan and to achieve peace between the U.S.-backed government and the militant group, which controls swaths of the country. On February 29, the United States and the Taliban struck a deal that called for a phased U.S. troop withdrawal. U.S. troop strength in Afghanistan is down to nearly 8,600, well ahead of a schedule agreed with the Taliban, in part because of concerns about the spread of the coronavirus, U.S. and NATO officials said in late May.  | ||||||||
| 6:35 PM 6/26/2020 - Coronavirus Updates: NY reports lowest infection rate in US | ||||||||
 6:35 PM 6/26/2020 Disease X-19 News Review - from Michael Novakhov _______________________________________________
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| Google Alert - sweden herd immunity: Swedish Disease Expert Says WHO COVID-19 Warning Is 'A Total Mistake' | ||||||||
"Herd immunity occurs when enough people of a population are immune to an infectious disease, either because they've been infected and recovered ... | ||||||||
| Google Alert - covid-19 in meat plants workers: Working conditions in meat processing plants make them hotbed for COVID-19 | ||||||||
The EU Commission has been urged to take swift measures to protect workers in the meat processing sector following a major coronavirus outbreak in ... | ||||||||
| Google Alert - coronavirus in water: Spain's top researchers discover coronavirus in waste water collected on March 12, 2019 | ||||||||
... one of Spain's most prestigious universities, had detected the presence of the novel coronavirus in waste water samples collected here on March 12 ... | ||||||||
| Coronavirus: our study suggests more people have had it than previously estimated theconversation.com/coronavirus-ou | ||||||||
Coronavirus: our study suggests more people have had it than previously estimated theconversation.com/coronavirus-ou
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| Google Alert - Coronavirus and failure of US Intelligence Services: The Latest: Trump administration eyes new testing strategy for coronavirus, Fauci says | ||||||||
The latest on the coronavirus pandemic around the U.S. and the world. The Trump administration is weighing a new testing strategy as coronavirus ... | ||||||||
| 4:17 PM 6/26/2020 - Semiaquatic mammals might be intermediate hosts to spread avian influenza viruses from avian to human | Scientific Reports | ||||||||
 Were rodents and domestic animals tested for Sars-Cov-2? We currently do not fully understand how COVID-19 affects different animal species. 4:17 PM 6/26/2020 Michael Novakhov - SharedNewsLinks | InBrief | -
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| 3:49 PM 6/26/2020 - We cannot rely on natural infection to achieve herd immunity. Studies Report Rapid Loss of COVID-19 Antibodies | ||||||||
 3:49 PM 6/26/2020 TWEETS BY MIKENOV | In Brief | _____________________________________________________________________ | ||||||||
| Rat coronavirus - Wikipedia | ||||||||
Rat coronavirus, or RCV, is a strain or subspecies of Murine coronavirus that infects rats.[1] The earliest discovered strains of Rat coronavirus were Sialodacryoadenitis virus, also known as SDAV, and Parker's Rat Coronavirus (PRC). Four other substrains have since been discovered; CARS, RCV-BCMM, RCV-W and RCV-NJ.[2]
Virology[edit]The viral particles of RCV are irregular to round and about 120 to 160 nm in size. They cannot be distinguished morphologically from other members of the genus Coronavirus.The rat coronavirus is a single-stranded RNA virus with positive polarity that is approximately 27 to 33 kb long.[3] Substrains[edit]Sialodacryoadenitis virus, or SDAV affects the upper respiratory tract[4][1] and can be transmitted between individuals by direct contact and indirectly by aerosol. It causes the disease Sialodacryoadenitis, the primary symptom of which are tropism of the salivary, lachrymal and harderian glands.[5] Most infections are mild, but acute infections have high morbidity. It is spread among laboratory animals as well as in pets.Parkers rat coronavirus, or PRC and most other rat coronavirus strains cause respiratory illness.[4] Both SDAV and PRC can cause lesions in the lungs.[5] References[edit]
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