New Bat Coronavirus 94.5% Identical to COVID-19

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New Bat Coronavirus 94.5% Identical to COVID-19 Jun 11, 2021 20:03:26 GMT

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Post by Admin on Jun 11, 2021 20:03:26 GMT

Researchers in China and Australia have reported the discovery of novel bat coronaviruses that further reveal the diversity and complex evolutionary history of these viruses.

In early 2020, the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the causative agent of the coronavirus disease 2019 (COVID-19) outbreak that first began in Wuhan, China, in late December 2019.

A combination of genome sequencing and sampling studies then identified a number of SARS-CoV-2-related coronaviruses in wildlife species that together pointed to underestimation of the phylogenetic and genomic diversity of coronaviruses.

Now, Weifeng Shi from Shandong First Medical University & Shandong Academy of Medical Sciences in Taian, China and colleagues have conducted a meta-transcriptomic analysis of samples collected from 23 bat species in Yunnan province in China during 2019 and 2020.

“Our study highlights both the remarkable diversity of bat viruses at the local scale and that relatives of SARS-CoV-2 and SARS-CoV circulate in wildlife species in a broad geographic region of Southeast Asia and southern China,” says the team.

“These data will help guide surveillance efforts to determine the origins of SARS-CoV-2 and other pathogenic coronaviruses.”

A pre-print version of the research paper is available on the bioRxiv* server, while the article undergoes peer review:
www.biorxiv.org/content/10.1101/2021.03.08.434390v1

Bats are well-known hosts of coronaviruses
Bats are well-established hosts to a broad range of viruses that are known to cause severe disease in humans, including the Hendra virus, Ebola virus and, most notably, coronaviruses.

Four of the seven known human coronaviruses have zoonotic origins. These include the SARS-CoV virus responsible for the 2002 to 2004 SARS outbreak and the Middle East respiratory coronavirus (MERS-CoV) responsible for numerous outbreaks of severe respiratory illness across the Middle East since 2012.

Sampling information and detection of SARS-CoV-2-like viruses in individual bat fecal samples. (A) Sample numbers of different bat species captured live in Yunnan province from May 2019 to November 2020. (B) Numbers of samples collected from different time points (orange column - feces; green - oral swab; light purple - urine). The numbers of individual bats are shown with black dots and relate to the y-axis. The associated numbers are in the form sample numbers/number of individual bats. (C) Identification of SARS-CoV-2-like virus positive samples using qPCR.

Although bats are the most likely hosts of these coronaviruses, their emergence in humans has also sometimes involved “intermediate” hosts such as the palm civet (in the case of SARS-CoV) and dromedary camels (MERS-CoV).

In early 2020, the novel SARS-CoV-2 virus was identified as the causative agent of a pneumonia outbreak in Wuhan, China, that quickly turned into a global pandemic.

A combination of retrospective genome sequencing and sampling studies identified a number of SARS-CoV-2-related coronaviruses in wildlife species.

These included the RaTG13 virus found in the Rhinolophus affinis bat, which is the closest known relative of SARS-CoV-2 across the viral genome as a whole.

SARS-CoV-2-related viruses have also been identified in various other Rhinolophid bats, including R. shameli bats sampled in Cambodia, R. cornutus bats sampled in Japan, and R. acuminatus bats sampled in Thailand.

“Collectively, these studies indicate that bats across a broad swathe of Asia harbor coronaviruses that are closely related to SARS-CoV-2 and that the phylogenetic and genomic diversity of these viruses has likely been underestimated” says Shi and the team.

The team obtained novel coronavirus genomes
From these data, the researchers assembled 24 full-length novel coronavirus genomes, including four genomes related to SARS-CoV-2 and three related to SARS-CoV.

Notably, one of these novel bat coronaviruses – RpYN06 – exhibited 94.5% sequence identity to SARS-CoV-2 across the whole genome. Furthermore, in some individual genes (ORF1ab, ORF7a, ORF8, N, and ORF10), RpYN06 was the closest relative of SARS-CoV-2 identified to date.

However, at the genomic scale, low sequence identity in the spike gene made RpYN06 the second closest relative of SARS-CoV-2, next to RaTG13. The spike protein is the main structure SARS-CoV-2 uses to bind to and infect host cells.

Differences in the overall sequence of the spike gene
The researchers say that although several SARS-CoV-2-like viruses have previously been identified in different wildlife species, none are highly similar (>95% ) in the overall sequence identity of the spike gene.

Indeed, while the other three SARS-CoV-2-related viruses identified here were almost identical in sequence, the spike protein sequences formed an independent lineage that was separated from known sarbecoviruses by a relatively long branch. Sarbecovirus is a viral subgenus or the coronaviruses that SARS-CoV-2 and SARS-CoV belong to.

“Collectively, these results highlight the extremely high, and likely underestimated, genetic diversity of the sarbecovirus spike proteins, which likely reflects their adaptive flexibility,” writes Shi and colleagues.

The researchers say studies have previously shown that host switching of coronaviruses among bats is a frequent occurrence.

“That individual bat species can harbor multiple viruses increases the difficulty in resolving the origins of SARS-CoV-2 and other pathogenic coronaviruses,” they add.

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New Bat Coronavirus 94.5% Identical to COVID-19 Jun 12, 2021 4:01:41 GMT

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Post by Admin on Jun 12, 2021 4:01:41 GMT

At least 47,000 wild animals were illegally sold in markets across Wuhan before the COVID-19 pandemic, a study found, adding fuel to the fierce debate over the origins of the pandemic.

The study filled important gaps in our knowledge about the circumstances around some of the earliest known human cases of the coronavirus that emerged in the central Chinese city in late 2019. It provided the most detailed picture yet of the trade of live wild animals that could have spread the virus to people.

Researchers found that 38 mammal, reptile, and bird species were sold in four markets in Wuhan between May 2017 and November 2019. The animals included raccoon dogs, civets, and minks, which scientists previously identified as possible intermediate hosts that spread the virus from a bat to the human population.

The study, published in peer-reviewed journal Scientific Reports on June 7, was authored by researchers affiliated with China West Normal University, University of Oxford and the University of British Columbia. They happened to be conducting monthly surveys of 17 wild animal shops across Wuhan to look into potential animal sources of a pathogen unrelated to the novel coronavirus.

Scientists have yet to find the missing links between bats, the likely original host of SARS-CoV-2, and the first human cases. SARS-CoV-2 is the name of the virus that causes COVID-19.

A direct infection by bats in Wuhan is deemed unlikely because the city is far from their natural habitats, and the study said bats were not sold in the Wuhan markets it surveyed, including the Huanan seafood market.

A WHO-China joint mission to Wuhan earlier this year said the coronavirus likely jumped to humans through an intermediate host in a natural spillover event, although the head of WHO said all hypotheses remained on the table.

Some virologists have cited the study as further evidence that animals capable of carrying SARS-CoV-2 were actively traded in the city’s markets in poor hygiene conditions and could have passed the virus on to people and triggered the pandemic that has killed more than 3.7 million people worldwide.

Others, including those who believe that the virus spilled from a lab in Wuhan, have argued that the paper ruled out pangolins as an intermediate host of the virus, since the researchers did not find those animals at the markets.

Angela Rasmussen, a virologist with the University of Saskatchewan in Canada, who was not involved with the study, said the research strengthened the possibility of the natural emergence of SARS-CoV-2 by showing that some animals susceptible to the novel coronavirus were present in Wuhan.

“It puts the animals in Wuhan and makes a compelling hypothesis,” Rasmussen told VICE World News, although she said it was “not proof.”

“To give proof, we would have to actually sequence and isolate a virus that is very much like SARS-CoV-2 from one of these animals.”

Previously, the WHO-China joint report identified only snakes, salamanders, and crocodiles as being sold as live animals in the Huanan seafood market in Wuhan, which 28 percent of the first confirmed COVID-19 patients had exposure to. The news media previously reported that plenty of live animals were sold in the market, but the WHO-China joint mission called those reports unverified. Instead, it cited local authorities’ assertion that no illegal trade in wildlife took place in the market, a claim that the newly-published study suggests was false.

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New Bat Coronavirus 94.5% Identical to COVID-19 Oct 21, 2021 19:28:27 GMT

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Post by Admin on Oct 21, 2021 19:28:27 GMT

A top NIH official admitted in a Wednesday letter that U.S. taxpayers funded gain-of-function research on bat coronaviruses in Wuhan and revealed that EcoHealth Alliance, the U.S. non-profit that funneled NIH money to the Wuhan Institute of Virology, was not transparent about the work it was doing.

In the letter to Representative James Comer (R., Ky.), Lawrence A. Tabak of the NIH cites a “limited experiment” that was conducted to test if “spike proteins from naturally occurring bat coronaviruses circulating in China were capable of binding to the human ACE2 receptor in a mouse model.” The laboratory mice infected with the modified bat virus “became sicker” than those infected with the unmodified bat virus.

The revelation vindicates Republican senator Rand Paul, who got into heated exchanges with National Institute of Allergy and Infectious Disease director Anthony Fauci during his May and July testimonials before Congress over the gain-of-function question. At the second hearing, Paul accused Fauci of misleading Congress by denying that the U.S. had funded gain-of-function projects at the Wuhan Institute of Virology.

Gain-of-function research involves extracting viruses from animals and artificially engineering them in a laboratory to make them more transmissible or deadly to humans.

In keeping with Fauci’s refusal to use “gain-of-function,” Tabak avoids the term, though the work he described matches its commonplace definition precisely.

A previously unpublished EcoHealth grant proposal filed with NIAID, obtained by The Intercept, had already exposed that $599,000 of the total grant to the Wuhan Institute of Virology was for research designed to make viruses more dangerous and/or infectious.

Dr. Richard Ebright, biosafety expert and professor of chemistry and chemical biology at Rutgers University, had previously rebutted Fauci’s claim that the NIH “has not ever and does not now fund gain of function research in the Wuhan Institute of Virology [WIV]” as “demonstrably false.”