6 new coronaviruses discovered in bats By Jeanna Bryner – Live Science Editor-in-Chief

6 new coronaviruses discovered in bats By Jeanna Bryner – Live Science Editor-in-Chief

6 new coronaviruses discovered in bats By Jeanna Bryner – Live Science Editor-in-Chief 754 424 VISFER

(Image: © Geza Farkas/Shutterstock)

Scientists have discovered six entirely new coronaviruses lurking in bats in Myanmar.

These viruses are in the same family as the SARS-CoV-2 virus that is currently spreading across the globe; but the researchers said the newbies aren’t closely related genetically to SARS-CoV-2 or to the two other coronaviruses that cause severe infections in humans — severe acute respiratory syndrome (SARS), which caused the 2002-2003 pandemic, and Middle East respiratory syndrome (MERS).

The researchers discovered the viruses while surveying bats in Myanmar as part of a government-funded program called PREDICT to identify infectious diseases that have the potential to hop from animals to humans. And bats are prime suspects, as the mammals are thought to host thousands of yet-to-be-discovered coronaviruses. SARS-CoV-2, which causes the disease COVID-19, is also thought to have originated in bats before taking up residence in humans, possibly taking a detour through some intermediary host first.

Between 2016 and 2018, they collected hundreds of samples of saliva and guano (or bat poop) from 464 bats from at least 11 different species; they sampled at three locations in Myanmar where humans come into close contact with wildlife due to land use changes and recreational and cultural activities — such as guano harvesting for fertilizer.

“Two of these sites also featured popular cave systems where people were routinely exposed to bats through guano harvesting, religious practices and ecotourism,” the researchers wrote in their study published online April 9 in the journal PLOS ONE.

The researchers analyzed genetic sequences from these samples and compared them with genomes of known coronaviruses. The new viruses were found in three bat species: the Greater Asiatic yellow house bat (Scotophilus heathii), where PREDICT-CoV-90 was found; the wrinkle-lipped free-tailed bat (Chaerephon plicatus), which was host to PREDICT-CoV-47 and -82; and Horsfield’s leaf-nosed bat (Hipposideros larvatus), which carried PREDICT-CoV-92, -93 and -96.

Further research is needed to understand the potential for these six newfound viruses to move to other species and how they might impact human health, the researchers said.

“Many coronaviruses may not pose a risk to people, but when we identify these diseases early on in animals, at the source, we have a valuable opportunity to investigate the potential threat,” study co-author Suzan Murray, director of the Smithsonian’s Global Health Program, said in a statement. “Vigilant surveillance, research and education are the best tools we have to prevent pandemics before they occur.”

Contact between humans and wildlife is only becoming more prevalent, they noted, adding that the current devastation caused by COVID-19 is just one reminder of how closely human health is linked to such interactions.

“Worldwide, humans are interacting with wildlife with increasing frequency, so the more we understand about these viruses in animals — what allows them to mutate and how they spread to other species –– the better we can reduce their pandemic potential,” lead study author Marc Valitutto, former wildlife veterinarian with the Smithsonian’s Global Health Program, said in the statement.

Indian pangolin, Manis crassicaudata. (Vicky_Chauhan/Getty Images)

More Evidence Suggests Pangolins May Have Passed Coronavirus From Bats to Humans

YANG ZHANG, CHENGXIN ZHANG & WEI ZHENG, THE CONVERSATION
11 APRIL 2020

Pangolins, not snakes, may be the missing link for transmission of the new coronavirus from bats to humans.

Since its initial outbreak at Huanan Seafood Wholesale Market in Wuhan, China, in late 2019, COVID-19 has since infected more than a million people across the globe. To understand and control the transmission of COVID-19, scientists are racing to study the coronavirus causing the disease: SARS-CoV-2, previously named 2019-nCoV.

SARS-CoV-2 is zoonotic, which means that the virus originated in animals and jumped to humans. A critical challenge is to determine which animal transmitted the virus to humans.

We are a team of bioinformaticians and we feel it is our responsibility to the global community to investigate the origin of this virus.

Based on the research in our lab, we believe that pangolins, as opposed to snakes, may have served as the hosts that transmitted the coronavirus to people and caused the ongoing COVID-19 pandemic. The pangolin, also known as a scaly anteater, is the only known mammal with scales and is found in Asia and Africa.

Mystery of zoonotic transmission

Since January 2020, the current consensus among the scientific community is that SARS-CoV-2 originated in horseshoe bats; however, it’s unlikely that bats directly gave the virus to humans based on what’s known about transmission of earlier zoonotic coronaviruses.

Instead, scientists suspected that the bat coronavirus infected another animal, an “intermediate host,” which subsequently transmitted the virus to humans.

For example, SARS-CoV, which is the coronavirus that caused the severe acute respiratory syndrome (SARS) pandemic in 2003, is a close relative of SARS-CoV-2. It was also found to have been transmitted from bats to an intermediate host – the masked palm civet – which subsequently infected humans.

Similarly, MERS-CoV, the coronavirus that caused Middle East respiratory syndrome (MERS) in 2012, jumped from bats to another intermediate host, the dromedary camel, before infecting humans.

The identity of the intermediate host of SARS-CoV-2 is therefore a mystery that many researchers hope to solve, as knowing the intermediate host is very helpful for prevention of further spread of epidemic.

An early study claimed that snakes such as the Chinese krait and the Chinese cobra were likely to be the intermediate hosts for SARS-CoV-2. Yet, this conclusion quickly drew skepticism, partly because there exists no previous evidence that coronaviruses can jump from a cold-blooded animal, such as snakes, to human beings.

Snakes make unlikely host

The early claim that snakes transmitted SARS-CoV-2 was based on an analysis of the virus’s genetic sequence. For both viruses and animal cells to function, genetic sequences (RNA or DNA) must be translated into proteins, which then carry out many tasks of the virus and the cell.

These proteins exist as linked chains of single amino acids; each amino acid in a protein is encoded by a group of three nucleotides, also known as a codon, in the genetic sequence.

Since there are 64 possible different codons but only 20 amino acids, several codons can correspond to the same amino acid; different organisms will have different preference for which codon is used for a given amino acid.

The early study hypothesized that for the coronavirus to effectively grow inside an animal cell, the codon usage preferences of the coronavirus should match that of the host cell.

The researchers compared the codon usage in the SARS-CoV-2 virus against that of the cells in eight animals at the Wuhan Huanan Seafood Wholesale Market. That study found that the snakes share the most similar codon usage pattern to SARS-CoV-2, thereby declaring that snakes were the most likely intermediate hosts.

However, their central hypothesis that coronaviruses and their animal hosts share similar codon usage was never verified. Our team at the University of Michigan scrutinized this hypothesis, and performed a more systematic analysis that we published in a recent follow-up study.

We compared the codon usages of three coronaviruses (SARS-CoV-2, SARS-CoV and MERS-CoV) to those of more than 10,000 different kinds of animals.

To our surprise, we found that the codon usage of a coronavirus is not determined by its hosts. For example, the codon usage of SARS-CoV and MERS-CoV is much closer to frogs and snakes than to their real animal hosts (civets and camels, respectively).

This shows that it is not possible to use only codon usage in animals’ cells to infer the hosts of coronaviruses, suggesting that the early claim of snake-borne transmission of SARS-CoV-2 is likely to be incorrect.

Discovering the pangolin as a likely missing link

Our follow-up study also found that the genetic sequence of a coronavirus, discovered in lung samples of Malayan pangolins, was highly similar to SARS-CoV-2. The two viruses shared 91 percent of their genetic sequence.

There is a particularly strong similarity between the spike proteins of these two viruses. The spike protein, which is on the surface of a coronavirus, is used by the virus to get into an animal cell.

The bat coronavirus, which was the ancestor of SARS-CoV-2, has 19 amino acids on the spike protein that are different from SARS-CoV-2; the pangolin coronavirus only has five amino acids that are different from SARS-CoV-2.

Meanwhile, several other research groups have found further experimental evidence of pangolins being infected by coronaviruses highly similar to SARS-CoV-2.

While pangolins are now our top suspect as the intermediate host, our study concludes that other potential intermediate hosts should still be considered.

A coronavirus can use more than one kind of animal to infect humans: for example, while civets are best known for transmitting SARS, other animals such as raccoon dogs and ferret badgers are also able to carry SARS.

Similarly, cats and ferrets can also be infected by SARS-CoV-2; it is still unknown whether humans can get infected by the coronavirus residing within these animals.

[You need to understand the coronavirus pandemic, and we can help. Read The Conversation’s newsletter.]

Yang Zhang, Professor of Computational Medicine & Bioinformatics, University of Michigan; Chengxin Zhang, PhD Candidate in Bioinformatics, University of Michigan, and Wei Zheng, Postdoctoral Fellow of Computational Medicine and Bioinformatics, University of Michigan.

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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