6:59 AM 7/24/2020 - "3.4% of dogs and 3.9% of cats had measurable SARS-CoV-2 neutralizing antibody titers" - Evidence of exposure to SARS-CoV-2 in cats and dogs from households in Italy
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Your dog has many ways of communicating with you - here are 50 things they do and what it means.
6:59 AM 7/24/2020
The researchers say that pets are unlikely to be an important route of viral spread, but when animals are present at high density, as on mink breeding farms, the virus may spread from animals to humans more readily...
“This is the largest study to investigate SARS-CoV-2 in companion animals to date. We found that companion animals living in areas of high human infection can become infected...
The evidence supports the ability of dogs and cats to seroconvert when living as pets in a COVID-19 positive household and in regions with high burden of human disease...
reverse transmission is probable, with 3-4% of a large number of domestic pets showing antibodies to the infection, though no virus was recovered from any animal... https://www.https://www.
- No animals tested PCR positive. However, 3.4% of dogs and 3.9% of cats had measurable SARS-CoV-2 neutralizing antibody titers
Evidence of exposure to SARS-CoV-2 in cats and dogs from households in Italy https://www.biorxiv.org/content/10.1101/2020.07.21.214346v1 … - Michael Novakhov RetweetedTrump has demonstrated that it is possible to hollow out and manipulate even the institutions of the United States to serve one individual’s personal interests, writes @justicemalala https://wapo.st/3jzqbeY
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- The researchers say that pets are unlikely to be an important route of viral spread, but when animals are present at high density, as on mink breeding farms, the virus may spread from animals to humans more readily.https://www.news-medical.net/news/20200724/Pets-Show-Antibodies-to-SARS-CoV-2-in-Italian-Study.aspx …
- “This is the largest study to investigate SARS-CoV-2 in companion animals to date. We found that companion animals living in areas of high human infection can become infected.”https://www.news-medical.net/news/20200724/Pets-Show-Antibodies-to-SARS-CoV-2-in-Italian-Study.aspx …
- The evidence supports the ability of dogs and cats to seroconvert when living as pets in a COVID-19 positive household and in regions with high burden of human disease.https://www.news-medical.net/news/20200724/Pets-Show-Antibodies-to-SARS-CoV-2-in-Italian-Study.aspx …
- reverse transmission is probable, with 3-4% of a large number of domestic pets showing antibodies to the infection, though no virus was recovered from any animal.https://www.news-medical.net/news/20200724/Pets-Show-Antibodies-to-SARS-CoV-2-in-Italian-Study.aspx …
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Scientists determine the origin and transmission rates of SARS-CoV-2 strains https://www.news-medical.net/news/20200724/Scientists-determine-the-origin-and-transmission-rates-of-SARS-CoV-2-strains.aspx … - Michael Novakhov Retweeted#PopeFrancis writes a letter to a young man with disabilities after he completes the Camino de Santiago pilgrimage.http://ow.ly/EIuH30r0gEO
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Covid-19-Review: 4:09 PM 7/23/2020 - Integrating Genomics into Publ... https://covid-19-review.blogspot.com/2020/07/409-pm-7232020-integrating-genomics.html?spref=tw … - Integrating Genomics into Public Health Surveillance: Ushering in a New Era of Precision Public Health | | Blogs | CDC https://blogs.cdc.gov/genomics/2017/07/19/integrating-genomics/ … via @CDCgov
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Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California https://science.sciencemag.org/content/early/2020/06/05/science.abb9263 … - Michael Novakhov RetweetedWuhan family rushes to take coronavirus tests after finding a dead bat in their half-eaten pork soup https://trib.al/7KOGo31
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| Evidence of exposure to SARS-CoV-2 in cats and dogs from households in Italy | bioRxiv | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Evidence of exposure to SARS-CoV-2 in cats and dogs from households in Italy
View ORCID ProfileE.I. Patterson, G. Elia, A. Grassi, A. Giordano, C. Desario, M. Medardo, S.L. Smith, E.R. Anderson, T. Prince, G.T. Patterson, E. Lorusso, M.S. Lucente, G. Lanave, S. Lauzi, U. Bonfanti, A. Stranieri, V. Martella, F. Solari Basano, V.R. Barrs, A.D. Radford, U. Agrimi, View ORCID ProfileG. L. Hughes, S. Paltrinieri, View ORCID ProfileN. Decaro
doi: <a href="https://doi.org/10.1101/2020.07.21.214346" rel="nofollow">https://doi.org/10.1101/2020.07.21.214346</a>
This article is a preprint and has not been certified by peer review [what does this mean?].
AbstractSARS-CoV-2 originated in animals and is now easily transmitted between people. Sporadic detection of natural cases in animals alongside successful experimental infections of pets, such as cats, ferrets and dogs, raises questions about the susceptibility of animals under natural conditions of pet ownership. Here we report a large-scale study to assess SARS-CoV-2 infection in over 500 companion animals living in northern Italy, sampled at a time of frequent human infection. No animals tested PCR positive. However, 3.4% of dogs and 3.9% of cats had measurable SARS-CoV-2 neutralizing antibody titers, with dogs from COVID-19 positive households being significantly more likely to test positive than those from COVID-19 negative households. Understanding risk factors associated with this and their potential to infect other species requires urgent investigation.
One Sentence Summary SARS-CoV-2 antibodies in pets from Italy.
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| Pets Show Antibodies to SARS-CoV-2 in Italian Study | ||||||||||||||||||||||||||||||||||||||||||||||||||||
The current COVID-19 pandemic is caused by the SARS-CoV-2 coronavirus, which is thought to have originated in animals. This jumped species barriers to infect humans and is now showing rapid and easy transmission between them.
 A new study* shows that reverse transmission is probable, with 3-4% of a large number of domestic pets showing antibodies to the infection, though no virus was recovered from any animal. Almost from the beginning, there have been reports that the virus can infect pet cats and dogs, with some animals showing symptoms of infection. Though these fears were initially decried, sporadic cases continue to be reported. In these pets, the respiratory or fecal specimens, or both, have tested positive for the virus by reverse transcriptase polymerase chain testing (RT-PCR). Specific antibodies against the virus have also been detected in pet sera. Targeted experiments also show that dogs are not easily infected and mostly develop an asymptomatic infection, with low viral titers being shed. On the other hand, cats show respiratory infection and shed high titers of the virus, and spread it to other animals as well. The study: testing pets for SARS-CoV-2The current study aimed at a more wide-scale testing of animal infection in their natural farm or home conditions. The researchers carried out a comprehensive survey of dogs and cats in Italy, from March to May 2020, in families with cases of COVID-19 or families living in severely affected areas.Their own vets tested all the animals in the study during routine visits, including over 900 dogs and over 500 cats. The samples were from nasopharyngeal, oropharyngeal or other severely affected areas in humans, or from other convenient sites. This yielded approximately 300 and 180 oropharyngeal swabs, 180 and 80 nasal samples, and 55 and 30 rectal swabs from dogs and cats, respectively. Altogether, there were 1420 swabs, including around 40 dogs and cats each that were symptomatic at the time of sampling, and about 60 dogs and cats each from families that had one or more positive cases. However, all were negative on PCR, including those living in households with confirmed cases of COVID-19 and those with and without respiratory symptoms. This suggests the animals were not actively infected at that time. Serologic testingSerum samples from around 190 and 60 dogs and cats were available along with the full history and location, and 200 and 90 cats approximately, lacking history but with known locations.The virus was tested for by RT-PCR targeting the viral nucleoprotein and envelope protein antigens. Plaque neutralization assays for neutralizing antibodies were also carried out to find the highest dilution at which the plaque number was reduced by 80%. This revealed the presence of specific neutralizing antibodies in 13 dogs and 6 cats, amounting to about 3% and 4% each. The titers detected ranged from 1:20 to 1:160 and from 1:40 to 1:1280 in dogs and cats, respectively. None of these animals were symptomatic at the time of testing. COVID-19-positive household distributionThe break up among the dogs was as follows: 6/47 dogs and 1/22 cats from COVID-19 positive households, 1/7 dogs from households suspected to be positive, and 2/133 dogs, and 1/38 cats, from households negative for COVID-19.This means that in households confirmed or suspected to have at least one case, 13% to 14% of dogs were antibody positive, as compared to 5% of cats in only confirmed positive households. In negative households, this dropped to approximately 2% of animals, whether dogs or cats. Age- and sex-stratified distributionWhen stratified by age, they found that of 423 animals of known age, none were infected among the animals below one year. About 7%, 3% and 3% of animals aged 1-3 years, 4-7 years and 8 years or more were positive.Some important associations were made. When there were 10 or more samples available, the human case count was strongly and positively correlated with the positive tests in dogs, and also with cats, but to a smaller and less significant extent. Community sampling in humans yielded a comparable seropositivity percentage at a similar period in Europe. The evidence supports the ability of dogs and cats to seroconvert when living as pets in a COVID-19 positive household and in regions with high burden of human disease. The greater tendency of dogs to develop neutralizing antibodies may reflect the greater susceptibility of dogs to the infection. More male than female dogs were infected, which may be due to the physiological differences in the sexes. This is different from humans, where infection rates are similar in both even though the disease severity is greater in males. Implications and importanceThe researchers point out, This is the largest study to investigate SARS-CoV-2 in companion animals to date. We found that companion animals living in areas of high human infection can become infected.As often seen in humans, none of the animals below one year of age developed infection as assessed by PCR. This agrees with earlier research findings, and also indicates that older animals should be used in experimental studies, since otherwise the true susceptibility of the animal model may not be detected. All animals tested positive by PCR, despite the significant percentage of seroconversion. This may mean that viral shedding is very short-lived in pet animals. This has been observed in studies showing that shedding in cats ceases by 10 days following experimental infection, and neutralizing antibodies are detected by 13 days. In dogs, fecal samples showed the presence of the virus at up to 6 days post infection, but oropharyngeal swabs were negative. The study notes that a natural infection in a Pomeranian, among the earliest reported, was associated with positive viral RNA in nasal swabs for 13 days, albeit at low levels, but not in fecal or rectal specimens. This may indicate variation in shedding pattern between animals. Moreover, in another experimental animal study, half the dogs who were infected had demonstrable antibodies by 14 days. This indicates the difficulty in SARS-CoV-2 detection whether in humans or animals. In the current study, the period that elapsed from infection to seroconversion is unknown. Even if the time of sampling was known, there could well have been delays in sampling due to the difficulty of visiting the vet during the period of lockdown. Therefore, the researchers advise that pets also be sampled to understand the true incidence of infection and viral shedding in the household and the community. The researchers say that pets are unlikely to be an important route of viral spread, but when animals are present at high density, as on mink breeding farms, the virus may spread from animals to humans more readily. Once the human-to-human spread is terminated, contact tracing will become more important. At that point, serologic surveys of pets may help provide a broad picture of the changing disease conditions within the community and an early warning of any transmission route left open. *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.
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| Google Alert - Sars Cov-2 and Animals: Pets Show Antibodies to SARS-CoV-2 in Italian Study | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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| Voice of America - English: Turkey Appoints Hagia Sophia Mosque Imams | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Three imams were named Thursday to lead prayers at Turkeys Hagia Sophia mosque, a day before the countrys president joins hundreds of worshippers inside the national landmark that was recently designated a mosque. Ali Erbas, head of Turkeys religious authority, announced the appointments of Mehmet Boynukalin, a professor of Islamic Law at Istanbuls Marmara University; Ferruh Mustuer and Bunjamin Topcuoglu, imams at two other Istanbul mosques. Erbas also named five muezzins, officials who make the Muslim call to prayer. In a July 10 decree that stirred international opposition, Turkish President Recep Tayyip Erdogan declared the nearly 1,500-year-old structure a mosque after a top Turkish court ruled the buildings earlier conversion into a museum was illegal. The sixth century UNESCO-listed site was initially an Orthodox Christian cathedral that became a mosque following the Ottoman conquest of Istanbul in 1453. It was made into a museum in 1934 by modern Turkeys founding statesmen, Mustafa Kemal Ataturk. Following Erdogans decree this month, Pope Francis said he was very pained, and the World Council of Churches expressed grief and dismay. Greeces culture ministry described the decision as an open provocation to the civilized world, and the U.S. State Department was disappointed. Though mosaics depicting Christian figures in the Hagia Sophia will be covered during Muslim prayers, Erdogan said the mosque would be open to all, locals and foreigners, Muslims and non-Muslims. As many as 17,000 security personnel will be on duty for the mosques first prayers on Friday.  | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| FOX News: Confirmed coronavirus cases in the US top 4 million | ||||||||||||||||||||||||||||||||||||||||||||||||||||
The number of confirmed coronavirus cases in the United States exceeded 4 million on Thursday.   | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| 4:09 PM 7/23/2020 - Integrating Genomics into Public Health Surveillance: Ushering in a New Era of Precision Public Health | | Blogs | CDC | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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| Genomics and epidemiological surveillance | Nature Reviews Microbiology | ||||||||||||||||||||||||||||||||||||||||||||||||||||
This months Genome Watch highlights how genomic surveillance can provide important information for identifying and tracking emerging pathogens such as SARS-CoV-2.
The timely detection and surveillance of infectious diseases and responses to pandemics are crucial but challenging. Whole-genome sequencing (WGS) is a common tool for pathogen identification and tracking, establishing transmission routes and outbreak control.
At the turn of 2019/20, Wu et al1 used metagenomic RNA sequencing to identify the aetiology of an at this point unknown respiratory disease in a single patient in Wuhan, China, where several cases of severe respiratory infections have been reported. The authors identified the potential causative pathogen as a new coronavirus by reconstructing the viral genome from the bronchoalveolar lavage fluid sample of the patient. In early January 2020, the viral genome sequence was released, which facilitated the development of rapid molecular diagnostics assays worldwide. Subsequently, the virus (now known as SARS-CoV-2, which causes the ongoing coronavirus disease 2019 (COVID-19) pandemic) rapidly spread globally, and there has been an immediate effort to study viral transmission and evolution using WGS. For example, SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance (SPHERES) in the United States and the COVID-19 Genomics UK2 (COG-UK) in the United Kingdom.
Credit: Philip Patenall/Springer Nature Limited
The latter consortium was launched in March 2020 as a nationwide genomic surveillance network that aims to track viral transmission, identify viral mutations and integrate viral data with health data2. By June 2020, the consortium sequenced >20,000 SARS-CoV-2 genomes and defined transmission lineages based on phylogeny. Open data sharing and standardized lineage definitions (Global Initiative on Sharing All Influenza Data (GISAID)) were established to enable global efforts in detecting emerging lineages and mutations that are relevant for outbreak control and vaccine development on an international level3. By the end of June 2020, >57,000 SARS-CoV-2 genomes from around 100 different countries have been deposited in the GISAID database. To overcome the challenge in data analysis and interpretation, user-friendly web-based applications were designed for linage assignment (Pangolin COVID-19 Lineage Assigner) and to interactively visualize the circulating lineages on national and international scales (for example, Microreact and Nextstrain).
The international effort towards open data sharing is of major scientific benefit, enabling monitoring of SARS-CoV-2 evolution in nearly real time and on a global level. Korber et al.4 developed a bioinformatics pipeline to track changes in the SARS-CoV-2 spike glycoprotein, which mediates host cell entry and is a key vaccine target. The pipeline monitors changes in the amino acid sequence of spike over time to identify variants that are concomitantly increasing in frequency in different geographic locations. The analysis, which was enabled by data from GISAID, suggested that a SARS-CoV-2 variant carrying a particular spike mutation (D614G) became globally dominant over a period of one month. Comparison of different regions revealed consistent patterns of the D614 variant replacing a previously established G614 variant, which might be indicative of potential positive selection. The viral genome data were linked with patient clinical information, which showed that the G614 variant might be associated with potentially higher viral loads but not with disease severity. Updated data and current global counts of the spike 614 variants are available in the COVID-19 Viral Genome Analysis Pipeline.
Genomic surveillance can generate a rich source of information for tracking pathogen transmission and evolution on both national and international levels. More importantly, the recent application of genomics in surveillance of COVID-19 highlighted its usefulness in the nearly real-time response to a public health crisis.
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| 2:05 PM 7/23/2020 - News - covid-19 origins: "Inside the Global Quest to Trace..." | ||||||||||||||||||||||||||||||||||||||||||||||||||||
 News - covid-19 origins - GS - 2:05 PM 7/23/2020 Michael Novakhov - SharedNewsLinks - Latest Post
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| 2:05 PM 7/23/2020 - News - covid-19 origins: "Inside the Global Quest to Trace..." | ||||||||||||||||||||||||||||||||||||||||||||||||||||
News - covid-19 origins - GS - 2:05 PM 7/23/2020 Michael Novakhov - SharedNewsLinks - Latest Post Michael Novakhov - SharedNewsLinks Where Did Coronavirus Originate? Inside the Hunt to Find Out | Time Michael_Novakhov shared this story . Inside the Global Quest to Trace the Origins of COVID-19and Predict Where It Will Go Next Artwork by Brea Souders for TIME; | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| Where Did Coronavirus Originate? Inside the Hunt to Find Out | Time | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Inside the Global Quest to Trace the Origins of COVID-19and Predict Where It Will Go Next
July 23, 2020 6:15 AM EDT
It wasnt greed, or curiosity, that made Li Rusheng grab his shotgun and enter Shitou Cave. It was about survival. During Mao-era collectivization of the early 1970s, food was so scarce in the emerald valleys of southwestern Chinas Yunnan province that farmers like Li could expect to eat meat only once a yearif they were lucky. So, craving protein, Li and his friends would sneak into the cave to hunt the creatures they could hear squeaking and fluttering inside: bats.
Li would creep into the gloom and fire blindly at the vaulted ceiling, picking up any quarry that fell to the ground, while his companions held nets over the mouth of the cave to snare fleeing bats. They cooked them in the traditional manner of Yunnans ethnic Yi people: boiled to remove hair and skin, gutted and fried. Theyd be small ones, fat ones, says Li, now 81, sitting on a wall overlooking fields of tobacco seedlings. The meat is very tender. But Ive not been in that cave for over 30 years now, he adds, shaking his head wistfully. They were very hard times. China today bears little resemblance to the impoverished nation of Lis youth. Since Deng Xiaoping embraced market reforms in 1979, the Middle Kingdom has gone from strength to strength. Today it is the worlds No. 2 economy and top trading nation. It has more billionaires than the U.S. and more high-speed rail than the rest of the world combined. Under current strongman President Xi Jinping, China has embarked on a campaign to regain center place in the world. Farmers like Li no longer have to hunt bats to survive. Dubbed RaTG13, Shis virus has a 96.2% similarity with the virus that has claimed some 600,000 lives across the world, including more than 140,000 in the U.S. Shis discovery indicates COVID-19 likely originated in batsas do rabies, Ebola, SARS, MERS, Nipah and many other deadly viruses. But how did this virus travel from a bat colony to the city of Wuhan, where the coronavirus outbreak was first documented? And from there, how did it silently creep along motorways and flight routes to kill nurses in Italy, farmers in Brazil, retirees in Seattle? How this virus entered the human population to wreak such a devastating toll is the foremost issue of global scientific concern today. The search for patient zeroor the index case, the first human COVID-19 infectionmatters. Not because any fault or blame lies with this individual, but because discovering how the pathogen entered the human population, and tracing how it flourished, will help the science and public-health communities better understand the pandemic and how to prevent similar or worse ones in the future. On top of the millions of lives that hang in the balance, Cambridge University puts at $82 trillion across five years the cost to the global economy of the current pandemic. The human race can ill afford another. The provenance of COVID-19 is not only a scientific question. The Trump Administration also regards it as a political cudgel against Beijing. As the U.S. has failed to control outbreaks of the coronavirus and its economy founders, President Donald Trump has deflected blame onto China. Trump and senior Administration figures have dubbed COVID-19 the China virus and Wuhan virus. Secretary of State Mike Pompeo said there was enormous evidence the virus had escaped from Shis lab in the city. (He has yet to share any hard evidence.) This is the worst attack weve ever had on our country. This is worse than Pearl Harbor. This is worse than the World Trade Center, Trump said in May of the pandemic, pointing the finger at China. In response, Chinese Foreign Minister Wang Yi accused the U.S. President of trying to foment a new cold war through lies and conspiracy theories. The origin of the virus is clearly a touchy subject. Nevertheless, the world desperately needs it broached. Australia and the E.U. have joined Washingtons calls for a thorough investigation into the cause of the outbreak. On May 18, Xi responded to pressure to express support for global research by scientists on the source and transmission routes of the virus overseen by the World Health Organization. Partisan bickering and nationalism threaten to eclipse the invaluable scientific work required to find the true source of the virus. Time is of the essence; a SARS vaccine was within touching distance when research that could have proved invaluable today was discontinued as the crisis abated. Once this pandemic settles down, were going to have a small window of opportunity to put in place infrastructure to prevent it from ever happening again, says Dr. Maureen Miller, a Columbia University epidemiologist. The search for the viruss origins must begin behind the squat blue-shuttered stalls at Wuhans Huanan seafood market, where the outbreak of viral pneumonia we now know as COVID-19 was first discovered in mid-December. One of the first cases was a trader named Wei Guixian, 57, who worked in the market every day, selling shrimp out of huge buckets. In mid-December she developed a fever she thought was a seasonal flu, she told state-run Shanghai-based the Paper. A week later, she was drifting in and out of consciousness in a hospital ward. Of the first 41 patients hospitalized in Wuhan, 13 had no connection to the marketplace, including the very first recorded case. That doesnt necessarily excuse the market as the initial point of zoonotic jump, thoughwe dont know yet for certain how many COVID-19 cases are asymptomatic, but research suggests it could be as high as 80%. And, even if Huanan market wasnt where the virus first infected humans, it certainly played a huge role as an incubator of transmission. At a Jan. 26 press conference, the Hong Kong Centre for Health Protection revealed 33 of 585 environmental samples taken after the market was shut Jan. 1 tested positive for the virus. Of these, 31 were taken in the western section where wildlife was sold. In May, China acceded to demands for an independent inquiry after more than 100 countries supported a resolution drafted by the E.U. Still, President Xi insists it must be comprehensivelooking not just at China but also at how other nations responded to the WHOs warningsand cannot begin until after the pandemic has subsided. The principles of objectivity and fairness need to be upheld, Xi told the World Health Assembly. (Notably, inquiries into the 2009 H1N1 swine flu pandemic and 2014 West African Ebola outbreak began before the crises had abated.) According to past investigations protocols, teams are composed of independent public-health experts and former WHO staff appointed by the WHO based on member states recommendations. At a practical level, however, any probe within China relies on cooperation from Beijing, and its uncertain whether the U.S. will accept the findings of a body Trump has slammed for severely mismanaging and covering up the spread of the coronavirus. 
Artwork by Brea Souders for TIME; Shutterstock (3)
Mistakes do happen. The last known case of small-pox leaked from a U.K. laboratory in 1978. SARS has leaked from Chinese laboratories on at least two occasions, while U.S. scientists have been responsible for mishandlings of various pathogens, including Ebola. There are only around 70 bsl-4 laboratories in 30 countries. Suspicions regarding the nature of research under way inside the Wuhan laboratory persist. According to one leading virologist, who asked to remain anonymous for fear of jeopardizing funding and professional relationships, Were you to ask me wheres the most likely place in the world for a naturally occurring bat coronavirus to escape from a laboratory, Wuhan would be in the top 10. Still, neither the WHO nor the Five Eyes intelligence networkcomprising the U.S., U.K., Canada, Australia and New Zealandhas found evidence that COVID-19 originated from Shis lab. Canberra has even distanced itself from a U.S.-authored dossier that sought to convince the Australian public that the Five Eyes network had intelligence of a Chinese cover-up. (It appeared to rely exclusively on open-source material.) Meanwhile, scientific peers have rallied to defend Shi from suspicion. She is everything a senior scientist should be, says Miller, who has collaborated with Shi on various studies. The Wuhan Institute of Virology did not respond to requests for comment. Available evidence suggests COVID-19 leaped from wild animal to human. Tracing exactly how is crucial. It enables governments to install safeguards regarding animal husbandry and butchery to prevent any repeat. SARS, for example, originated in bats and then infected a palm civet, a catlike mammal native to South and Southeast Asia. The animal was then sold at a wet marketwhere fresh meat, fish and sometimes live animals are soldin Guangdong, from which it jumped to humans. In the wake of that outbreak, which claimed at least 774 lives worldwide, palm civets were banned from sale or consumption in China. Bats may have been the initial reservoir for SARS-CoV-2, but its likely that there was an intermediary before it got to humans, and thats where the possibilities grow. Bats share Shitou Cave with starlings, for one, and at least one large white owl nests in its upper reaches. Herds of black and white goats graze the dusty shrub all around the cave opening, while the Yi ethnic group traditionally rear and eat dogs. Bat guano is also traditionally prized as a fertilizer on crops. That COVID-19 originated in bats and then jumped to humans via a pangolin intermediary is now the most likely hypothesis, according to multiple studies (although some virologists disagree). Up to 2.7 million of the scaly mammals have been plucked from the wild across Asia and Africa for consumption mostly in China, where many people believe their scales can treat everything from rheumatoid arthritis to inflammation. Their meat is also highly prized for its supposed health benefits. On Feb. 24, China announced a permanent ban on wildlife consumption and trade, scratching out an industry that employs 14 million people and is worth $74 billion, according to a 2017 report commissioned by the Chinese Academy of Engineering. Its again extremely sensitive. President Xi is an ardent supporter of TCM and has promoted its use globally. The total value of Chinas TCM industry was expected to reach $420 billion by the end of this year, according to a 2016 white paper by Chinas State Council. And rather than raising the possibility that misuse of TCM sparked the outbreak, Chinese state media has laudedwithout evidencethe critical role TCM has played in the treatment of COVID-19 patients. In an apparent attempt to head off criticism related to the pandemic, draft legislation was published in late May to ban any individual or organization from defaming or making false or exaggerated claims about TCM. Cracking down on the illicit animal trade would go a long way toward preventing future outbreaks. But as demand for meat grows across increasingly affluent Asia, Africa and Latin America, the potential for viruses to spill over into human populations will only increase. It probably wasnt blind luck that Li and his friends didnt get sick from their hunting expeditions in Shitou Cave. Research by Columbias Miller with WIVs Shi, published in 2017, found that local people were naturally resistant to SARS-like viruses. Examining their lifestyle habits and antibodies can help deduce both mitigating factors and possible therapies, while pinpointing which viruses are particularly prone to infecting humans, potentially allowing scientists to design vaccines in advance. They are the canaries in the coal mine, says Miller. The page signaled the first confirmed U.S. case of COVID-19. The patient was a Washington State resident who had recently returned from visiting family in Wuhan, where the disease was spreading rapidly. Aware of his higher risk, and concerned when he developed a fever, the 35-year-old (who wishes to remain anonymous) visited an urgent-care center where he told health care providers about his travel history. They notified the state health department, which in turn helped the care center send a sample for testing to the Centers for Disease Control and Prevention (CDC) in Atlantaat the time, the only labs running COVID-19 tests. When the test was positive, CDC scientists recommended the patient be hospitalized for observation. And Diazs team was paged. A trained ambulance team arrived at the mans home, moved him into a specially designed mobile isolation unit, and drove 20 minutes to Providence Regional. There, the patient couldnt see who greeted him; everyone assigned to his care was garbed in layers of personal protective equipment. Once in his room, he spoke to medical staff only through a tele-health robot equipped with a screen that displayed their faces, transmitted from just outside the room. A nurse carefully swabbed the back of his nose and pharynx for a sample of the virus that had brought him to the hospital. Not only was he the first confirmed case of COVID-19 in the U.S., he was also the first in the country to have his virus genetically sequenced. As the index patient in the U.S., his sequence, named WA1 (Washington 1), served as the seed from which experts would ultimately trace the genetic tree describing SARS-CoV-2s path from person to person across communities, countries and the globe, as it mutated and either died out or moved on with renewed vigor to infect more people. Genetic sequencing is a powerful tool to combat viruses fondness for mutating. Viruses are exploitative and unscrupulous; they dont even bother investing in any of their own machinery to reproduce. Instead, they rely on host cells to do thatbut it comes at a price. This copying process is sloppy, and often leads to mistakes, or mutations. But viruses can sometimes take advantage of even that; some mutations can by chance make the virus more effective at spreading undetected from host to host. SARS-CoV-2 seems to have landed on at least one such suite of genetic changes, since those infected can spread the virus even if they dont have any symptoms. Since the first SARS-CoV-2 genome was published and made publicly available online in January, scientists have mapped the genomes of over 70,000 (and counting) samples of the virus, from patients in China, the U.S., the E.U., Brazil and South Africa, among others. They deposited those sequences into the Global Initiative on Sharing All Influenza Data (GISAID), a publicly available genetic database created in 2008 initially to store and share influenza genomes. During the coronavirus pandemic, it has quickly pivoted to become a clearinghouse for tracking the genetics of SARS-CoV-2, enabling scientists to map the viruss march across continents and detail its multipronged attack on the world. We have genomes from researchers and public-health labs from all over the world on six continents, says Joel Wertheim, associate professor of medicine at University of California, San Diego. It provides us with unique insight and confidence that other types of epidemiological data just cannot supply. Relying on the GISAID sequences, Nextstrain has become a virtual watering hole for scientistsand increasingly public-health officialswho want to view trends and patterns in the viruss genetic changes that can help inform decisions about how to manage infections. If genetic sequencing is the new language for managing infectious-disease outbreaks, then the mutations that viruses generate are its alphabet. If paired with information on how infected patients fare in terms of their symptoms and the severity of their illness, genomic surveillance could reveal useful clues about which strains of virus are linked to more severe disease. It might shed light on the mystery of why certain victims of the virus are spared lengthy hospital stays and life-threatening illness. As nations start to reopen, and before a vaccine is widely available, such genetic intel could help health care providers to better plan for when and where they will need intensive-care facilities to treat new cases in their community. Genetic information is also critical to developing the most effective drugs and vaccines. Knowing the sequence of SARS-CoV-2 enabled Moderna Thera-peutics to produce a shot ready for human testing in record time: just two months from when the genetic sequence of SARS-CoV-2 was first posted. Even after a vaccine is approved and distributed, continuing to track genetic changes in SARS-CoV-2 to ensure its not mutating to resist vaccine-induced immunity will be critical. The data collected by Nextstrain will be crucial to help vaccine researchers tackle mutations, potentially for years to come. Already, the group advises the WHO on the best genetic targets for the annual flu shot, and it plans to do the same for COVID-19. We can track the areas of the virus targeted by the vaccine, and check the mutations, says Emma Hodcroft from the University of Basel, who co-developed Nextstrain. We can predict how disruptive those mutations are to the vaccine or not and tell whether the vaccines need an update. After Diazs patient tested positive for SARS-CoV-2, Washington State public-health officials diligently traced the places the patient had been and the people hed come in contact with. He had taken a ride-share from the airport, gone to work and enjoyed lunch at a seafood restaurant near his office with colleagues. But because so little was known about the virus at the time, these contact tracers were focusing mostly on people with symptoms of illnessand at the time, none of the patients contacts reported them. The genetics, however, told a different story. Seattle happened to have launched a program in 2018 to track flu cases by collecting samples from patients in hospitals and doctors offices, sites on college campuses, homeless shelters, the citys major international airport and even from volunteers with symptoms who agreed to swab their nasal passages at home. Those that were positive for influenza and other respiratory illnesses had their samples genetically sequenced to trace the diseases spread in the community. As COVID-19 began to emerge in the Seattle area at the end of February, Bedford and his colleagues began testing samples collected in this program for SARS-CoV-2, regardless of whether people reported symptoms or travel to China, then the worlds hot spot for the virus. Thats how they found WA2, the first case in Washington that wasnt travel-related. By comparing samples from WA1, WA2 and other COVID-19 cases, they figured out that SARS-CoV-2 was circulating widely in the community in February. If that community-based sequencing work had been conducted earlier, theres a good chance it might have picked up cases of COVID-19 that traditional disease-tracking methods, which at the time focused only on travel history and symptoms, missed. That would have helped officials make decisions about a lockdown sooner, and might have helped to limit spread of the virus. SARS-CoV-2 moves quickly but mutates relatively slowly, for a virusgenerating only about two mutations every month in its genome. For drug and vaccine developers, it means the virus can still evade new treatments designed to hobble it. Those same changes serve as passport stamps for its global trek through the worlds population, laying out the itinerary of the viruss journey for geneticists like Bedford. The cases in the initial Seattle cluster, he says, appear to have all been connected, through a single introduction directly from China to the U.S. in mid- to late January. Until the end of February, most instances of SARS-CoV-2 in the U.S. piggybacked on unwitting travelers from China. But as the pandemic continued, that changed. Bedfords team began to see mutations in samples from Seattle that matched samples from people in Europe and the U.S.s East Coast. At the beginning we could kind of draw a direct line from viruses circulating in China to viruses circulating in the Seattle area, says Bedford. Later, we see that viruses collected from China have some mutations that were seen later in Europe, and those same mutations were seen in viruses in New York. So, we can draw another line from China to Europe to New York and then on to Seattle. The virus had begun multiple assaults into the U.S.
TIME Graphic by Emily Barone and Lon Tweeten
Bartolini, a virologist at the hospital, and her colleagues compared the genetic sequences from a sample taken from the wife to sequences posted on GISAID. The Italian researchers found it matched five other samples from patients as far-flung as France, Taiwan, the U.S. and Australia. SARS-CoV-2 was clearly already on a whirlwind tour of the planet. Not all strains of SARS-CoV-2 are equally virulent; some branches of its genetic tree are likely to grow larger and sprout further offshoots, while others terminate more quickly, says Harm van Bakel, assistant professor of genetics and genomic sciences at the Icahn School of Medicine at Mount Sinai. His team conducted the first genetic sequencing analysis of cases in New York City, which quickly became a U.S. hot spot; by March the city had seen a half a dozen or so separate introductions of SARS-CoV-2, but only two resulted in massive spread of the virus. The remainder petered out without transmitting widely. Retrospectively, theres no way to tell for sure if these two strains were simply in the right place at the right timein a particularly densely populated area of the city, for example, or in an area where people congregated and then dispersed to other parts of the cityor if they were actually more infectious. But determining the genetic code of a circulating virus early may help scientists and governments decide which strains are worth worrying about and which arent. From analyzing genetic sequences from 36 samples of patients in Northern California, Dr. Charles Chiu, professor of laboratory medicine and infectious diseases at the University of California, San Francisco, says it might have been possible to identify the major circulating strains and track how they spread if more testing were available to know who was infectedand use this information to guide quarantine and containment practices. There was a window of opportunity that if we had more testing and more contact-tracing capacities available early on, we likely would have prevented the virus from gaining a foothold at least in California, he says. Ongoing genetic sequencing can also help officials tailor narrower strategies to quell the spread of a virus. It wasnt long after Beijing reopened following two months of lockdown that infections began creeping up again in June. Sequencing of the new cases revealed that the viruses circulating at the time shared similarities with viruses found in patients in Europe, suggesting the cases were new introductions of SARS-CoV-2 and not lingering virus from the original outbreak. That helped the Chinese government decide to implement only limited lockdowns and testing of people in specific apartment blocks around a food market where the cluster of cases emerged, rather than resort to a citywide quarantine. And there are other, less obvious ways that genetic analysis of SARS-CoV-2 could help to predict surges in cases as people emerge from lockdown. Italian scientists have sampled wastewater from sewage treatment plants in northern cities where the pandemic flourished, and found evidence of SARS-CoV-2 weeks before the first cases showed up to flood the hospitals. In La Crosse, Wis., Paraic Kenny, director of the Kabara Cancer Research Institute of the Gundersen Health System, applied the same strategy in his hometown in the spring. A few weeks later, in mid-June, when cases of COVID-19 surged because of bars reopening in downtown La Crosse, Kenny compared samples from infected people with the viral genomes in his wastewater samples. They were a genetic match. The same strain of SARS-CoV-2 had been circulating in the community weeks before the cases were reported. In principle, an approach like this can be used to not just ascertain how much virus is in the community, but maybe give hospitals and public-health departments a warning of when to anticipate a surge in cases, he says. The goal is to know not just where we are today but where we will be a week or two from now. It has been 100 years since an infectious disease pushed the entire worlds population into hiding to the extent that COVID-19 has. And the primary approaches we take to combatting emerging microbes today are likewise centuries old: quarantine, hygiene and social distancing. We may never learn exactly where SARS-CoV-2 came from, and its clearly too late to prevent it from becoming a global tragedy. But extraordinary advances in scientific knowledge have given us new tools, like genetic sequencing, for a more comprehensive understanding of this virus than anyone could have imagined even a decade or two ago. These are already providing clues about how emerging viruses like SARS-CoV-2 operate and, most important, how they can be thwarted with more effective drugs and vaccines. With reporting by Jamie Ducharme/New York, Madeline Roache/London and John Walcott/Washington This appears in the August 03, 2020 issue of TIME. The Coronavirus Brief. Everything you need to know about the global spread of COVID-19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| 11:02 AM 7/23/2020 - When two or more diseases cluster, interact, and are driven by some bigger phenomenon, they are known as syndemics, says Emily Mendenhall | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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| 10:24 AM 7/23/2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Rats may be infected with Covid-19, and the dogs that hunt on them might get the infection and spread it to humans. This has to be looked in carefully and ASAP. Rodents as the potential vector of Covid-19 have to be dealt with.
Furthermore, the Coronavirus Covid-19 Infection may be just a part of the complex Disease X-19 Infection, crudely mixed as the combined biological (and possibly chemical) weapon. One of the other parts may include the Hantaviruses infections, deliberately spread through rats. The relative crudeness of this hypothetical "disease and pandemic as bioweapon" design may point, also hypothetically (and together with other observations) in the direction of the Organized Crime (TOC, Russian-Jewish Mafia). See also: Hantavirus rats in NYC - GS Michael_Novakhov shared this story from The FBI News Review.
The Satanic Temple plans to sue the state of Mississippi if its new flag i
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| Google Alert - coronavirus in new york post: Hamptons home prices skyrocket due to demand from NYC coronavirus fleers | ||||||||||||||||||||||||||||||||||||||||||||||||||||
The COVID-19 exodus has driven Hamptons real-estate prices to record ... boom times because a few big-ticket transactions can pull the number up. ... is increased demand from hordes of New Yorkers fleeing the virus epicenter. ... The study counted 1,906 Hamptons properties on the market during this ... | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| Google Alert - covid rash: Researcher: Covid-19 infection rates 5 times higher in US Prisons | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Researcher: Covid-19 infection rates 5 times higher in U.S. Prisons ... prisoners for the disease and recently found its largest rash of infections yet 89 ... | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| Google Alert - Sars-Cov-2 origins: Italy's earliest coronavirus strains not from China, new study suggests | ||||||||||||||||||||||||||||||||||||||||||||||||||||
After Milan's researchers analyzing more than 300 blood samples of COVID-19 patients and tracing the origin of the viral strains by changes in their ... | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| Google Alert - coronavirus in italy: Italy's first coronavirus strains didn't come from China, study suggests | ||||||||||||||||||||||||||||||||||||||||||||||||||||
... has suggested that the first COVID-19 variants that spread throughout Italy's Lombardy region were not from China. The non-peer-reviewed paper ... | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| 8:06 AM 7/23/2020 - Michael Novakhov - SharedNewsLinks: Hypothesis: The pathogens causing the Disease X-19 circulated in the major local epicenters areas for years (10-15) before the first clinical cases were detected and identified. | ||||||||||||||||||||||||||||||||||||||||||||||||||||
 Michael Novakhov - SharedNewsLinks - Latest Post ______________________________________________________ Michael Novakhov - SharedNewsLinks | InBrief |
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| 7:33 AM 7/23/2020 - Hypothesis: The pathogens causing the Disease X-19 circulated in the major local epicenters areas for years (10-15) before the first clinical cases were detected and identified. Besides Sars-Cov-2, they may include, hypothetically, the pathogens of the Hantaviruses Infections, African Swine Fever, and/or other infections, with or without the genomic modifications of these pathogens in a Lab. | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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| 11 mysteries about the coronavirus and COVID-19 we have yet to solve | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Six months have passed since China reported the first coronavirus cases to the World Health Organization. But evn now, what experts are still trying to understand sometimes seems to outweigh what they can say for certain. That is little surprise to any infectious-disease researcher: Highly contagious diseases can move through communities much more quickly than the methodical pace of science can produce vital answers. What we do know is that the coronavirus seems to have emerged in China as early as mid-November and has now reached 188 countries, infected more than 10.4 million people, and killed around 510,000. Population-level studies using new testing could boost case numbers about 10-fold in the US and perhaps elsewhere as well. As hospitals around the world care for COVID-19 patients with blood clots, strokes, and long-lasting respiratory failure, scientists are racing to study the coronavirus, spread life-saving information, and combat dangerous misunderstandings. Here are 11 of the biggest questions surrounding the coronavirus and COVID-19, and why answering each one is critically important. | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| 7:18 AM 7/23/2020 - The Hypothesis of the Disease X-19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||
/cdn.vox-cdn.com/uploads/chorus_asset/file/19760564/GettyImages_1204248113.jpg) The Hypothesis of the Disease X-19 7:18 AM 7/23/2020 Michael Novakhov - SharedNewsLinks - Latest Post
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| 6:27 AM 7/23/2020 - Study of Covid-19 in Lombardy, Northern Italy "revealed that a sustained community transmission was ongoing way before the first COVID-19 case found in Lombardy." | ||||||||||||||||||||||||||||||||||||||||||||||||||||
 Study of Covid-19 in Lombardy, Northern Italy "revealed that a sustained community transmission was ongoing way before the first COVID-19 case found in Lombardy."
6:27 AM 7/23/2020
Hypothesis: The pathogens causing the Disease X-19 circulated in the major local epicenters areas for years (10-15) before the first clinical cases were detected and identified.
Besides Sars-Cov-2, they may include, hypothetically, the pathogens of the Hantaviruses Infections, African Swine Fever, and/or other infections, with or without the genomic modifications of these pathogens in a Lab.
The vectors may include pigs, especially industrially produced, as in the Northern areas of Italy and Spain, and various rodents: rats and mice, including the large water or river rats, such as nutrias or coypus. The unusual and very noticeable proliferation of these rodents, especially the large ones, which appear to be sick, infected, and psychotic, was observed in all mayor cities of the world. Quite often, these infections may occur in humans and animals asymptomatically.
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| Italys earliest coronavirus strains did not arrive from China, study suggests | ||||||||||||||||||||||||||||||||||||||||||||||||||||
The earliest coronavirus strains circulating in Italy did not come directly from China, according to a new study.
Researchers in Milan collected more than 300 blood samples of Covid-19 patients from the Lombardy region between February and April and traced the origin of the viral strains by changes in their genes.
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Italy was the first country in the world that put up a travel restriction barring all flights from China, but the genome sequencing suggested a transmission chain not directly involving China, said the researchers led by Professor Carlo Federico Perno of Milan University in a non-peer-reviewed paper posted on <a href="http://medRxiv.org" rel="nofollow">medRxiv.org</a> on Monday.
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Lombardy had the earliest known outbreak in the West and has accounted for more than a third of the coronavirus cases in Italy. It is Italys richest region with thriving businesses, international transport connections and densely populated urban areas.
Sars-CoV-2, the virus that causes the disease Covid-19, was isolated and sequenced by Chinese researchers in early January. It was not until February 20 that the first case of local infection was confirmed by Lombardys health authorities, but sustained community transmission was ongoing way before that date, the researchers said.
Pernos team collected blood samples from 371 patients in 12 provinces across the region. They were randomly chosen from people admitted to hospital with mild, moderate or severe symptoms. About 7 per cent of the samples failed to produce high-quality reading of the virus full genome, but the remainder still provided the largest sample base so far from the Lombardy region.
Hong Kong tops previous daily record of 108 Covid-19 cases: sources
The strains belonged to two separate lineages, each playing a dominant role in some provinces. But they did not contain viral strains isolated in the first months of the outbreak in China, said the paper.
Italy banned travellers from China on January 31, after a Chinese couple tested positive for Covid-19 in Rome. But according to a study by the Italian National Institute of Health last month, the virus had already appeared in sewage water in Milan and Turin in mid-December.
Pernos new study showed that there could have been multiple introductions of the virus to the Lombardy region. These strains formed relatively isolated clusters in separate areas. One possible direction of the source was Central Europe, where strains with similar mutations had been detected, according to the researchers.
Their calculation suggested that these entries may have happened in the second half of January, based on the assumption that the virus was mutating at a relatively constant speed although that may not have been the case.
The Italian study is one of several around the world to have found strains that were not traced to China.
In New York, the viral strains circulating in March did not come from China, which researchers said was unanticipated because government scientists had gone put extra emphasis on collecting samples in Chinese-speaking neighbourhoods.
Rather, the sequence analysis suggests probable introductions of Sars-CoV-2 from Europe, from other US locations and local introductions from within New York, said the official report of the joint research by the citys Department of Health and the US Centres for Disease Control and Prevention, released last Friday.
A study by the Pasteur Institute in Paris in May confirmed that the outbreak in France had no direct link to China. Another study by Russian government scientists identified 67 introductions into their country and found only one that related to a Chinese source.
Some other studies challenged the belief that the pandemic originated in Wuhan, where the virus was first detected in late December.
A research team led by Spains top biologists identified the virus in a waste water sample in Barcelona dated back to March last year. In the Brazilian beach town Florianopolis, drainage samples collected and stored in government research facilities in November later tested positive for the coronavirus.
Benjamin Neuman, professor and chair of biological sciences with the Texas A&M University Texarkana, said that the recent findings could be potentially a really big story but that the data would require more scrutiny.
For example, the viral strains detected in sewage samples should have their genome sequenced to determine their position in the evolutionary tree, he said.
If the sequences are indeed from that early part of the outbreak, it should resemble the earliest sequences from China, possibly with mutations that have not yet been seen, Professor Neuman said.
They should not have some of the mutations that appeared later in other parts of the world, he added.
A government epidemiologist in Beijing, who asked not to be named because they were not authorised to speak to the media, said tracing the origin of the coronavirus by its genes had limitations.
The copies preserved in poor environments such as waste water were probably compromised and unlikely to produce full genome sequences, they said. It would be difficult to estimate a strains age by mutation because a genetic change appearing later in an international database may not mean it was younger than those sequenced earlier.
A mutation could be in circulation for some time in a remote corner of the world, said the researcher. Can we say that it did not exist until sequencing?
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