A new paper by four Chinese researchers says the acute pneumonia that has killed almost 20,000 people worldwide (so far) almost undoubtedly recombined in pangolins before eventually jumping to humans.
Suggesting firm transmission links from bats to humans via pangolins, the research was released last week on bioRxiv (pronounced “bio archive”), a web discussion forum for unpublished preprints in the life sciences. This service is a widely used industry gold standard that allows the scientific community to immediately see and comment on findings before these are submitted for the rigorous and often lengthy peer-review process.
SARS-CoV-2, the single-strand RNA virus that causes Covid-19, is a likely recombinant between bat and pangolin coronaviruses, and pangolins are “the most possible intermediate reservoir”, the joint research team has found. Together they represent Hainan University, Fujian Normal University, Central South University and Pilot National Laboratory for Marine Science and Technology.
Coronaviruses can infect a wide range of animals, including humans, and have caused major epidemics in the past.
Severe Acute Respiratory Syndrome via civets caused a global outbreak in 2003, followed by Middle East Respiratory Syndrome via camels in 2012. Each is a coronavirus transmitted through intermediate mammal hosts with original links to bats.
Likely entering people through meat consumption, these coronaviruses transformed their hosts into brand-new vectors and were then spread by human contact.
Ha! Bats! Or is it?
To determine the mammal linkages to SARS-CoV-2 — the seventh species of coronavirus to infect humans — researchers Jiao-Mei Huang, Syed Sajid Jan, Xiaobin Wei, Yi Wan and Songying Ouyang analysed genomes from various potential hosts.
The team’s initial results are consistent with an escalating body of recent evidence exposing bats as the original “reservoir” source of the virus, but stress that pangolins appear to reflect a slightly higher resonance in some key aspects.
Coming out on top for whole-genome similarity, a bat coronavirus genome is 96% similar to SARS-CoV-2, while pangolin coronavirus shows a 90% similarity, the team points out.
In genetic terms, this difference is not insignificant. So let’s, for a second, pretend these data points are our only genetic clues to what sort of animals the pandemic strain may have hijacked before infecting humans.
At such a crime scene, we would be forgiven for punching the air and exclaiming, “Ha! It’s bats!”
But the Chinese virology detectives wanted just that extra bit of certainty, and knew the value of taking a high-resolution look at the “S-protein” cauliflower stalks peppered across the coronavirus’s ball-like surface.
This is where we might get really suspicious of bats, because the S-protein is crucial for viral infection and, in bats, it is up to 97.43% similar to the S-protein observed in SARS-CoV-2, the paper found. (We’re not saying ‘S’ means suspicious at all — Ed.)
That is right. A bat’s whole coronavirus genome is a 96% match to the latest human coronavirus genome. Plus, bat coronavirus has a seriously suspicious S-protein that seems to be an even higher match to its human equivalent. This suggests the SARS-CoV-2 spillover event to humans happened via bats.
However, our virology sleuths were not content to leave it there and rush into the court of academia, waving nothing but a body of batty evidence. They would be crummy RNA investigators if they did.
For it is in a terminus of the S-protein cauliflower stalks that the Chinese team probed deeper — that’s because most coronaviruses hide some of their most lethal arsenal right here, in the “receptor-binding domain”, or “RBD”, and its associated amino acid residues.
Think of the RBD and its amino acid accomplices as Trojan soldiers whose most desirous existential mission is to infiltrate what they might, in the cross-examination dock, describe as a “Troy” cell*. For argument’s sake, that Troy cell is, potentially, your cells, or another mammal’s cells. But different RBDs like to hijack different cells — meaning they don’t have a universal entry code to unlock every safe.
To unlock the safe, they need to have evolved the correct amino acid entry code.
How, according to the Chinese paper, does the RBD entry code in bat coronavirus compare with the SARS-CoV-2 variety found in humans?
“Um, it’s only about 89.57% similar, advocate,” SARS-CoV-2 might quiver in its little viral boots if questioned about how it broke into Patient Zero’s Troy cell.
And how about a pangolin coronavirus? “At least 96%.”
That’s the humdinger. The RBD and its amino acids in pangolin coronavirus is more than 96% similar to its SARS-CoV-2 counterparts.
Pangolins as a ‘missing link’
This does not mean pangolins, also known as scaly anteaters, are the final link in the chain that mutated into SARS-CoV-2 and has upended the entire human world — especially since the pangolin coronavirus’s whole genome comparison does not seem to exceed 90%.
Instead, the Chinese paper said the complex dance between whole genome, S-protein, RBD and amino acids suggests bat and pangolin viruses at some point shared genetic material within the RBD and recombined to form the virus that became SARS-CoV-2.
Due to the high RBD/amino-acid correlation, the paper also suggested that the pangolin is the “most possible intermediate SARS-CoV-2 reservoir, which may have given rise to cross-species transmission to humans”.
Following “mutations in coding regions of 125 SARS-CoV-2 genomes”, the researchers also attempted to track the virus’s evolution.
“Another important outcome of our analysis is the genetic mutations and evolution of SARS-CoV-2 as it spread globally. These findings are very significant for controlling the SARS-CoV-2 pandemic,” they proposed.
‘Identical to that of a pangolin coronavirus’
The Chinese researchers’ work strongly supports earlier preliminary findings by a US team at Baylor College of Medicine in Texas.
In February, Daily Maverick was the first publication globally to report that the US team had homed in on the critically endangered Malayan pangolin (Manis javanica) as a likely intermediate reservoir of SARS-CoV-2.
Bioinformatics researcher Matthew Wong had found that the distinctive RBD docking mechanism in SARS-CoV-2 was “identical to that of a pangolin coronavirus”, his Baylor College lab supervisor, Professor Joseph Petrosino, told Daily Maverick.
A pangolin virus and bat virus may have found themselves in the same animal, he said, leading to what he described as a “devastating recombination event, creating the pandemic strain. This may have happened in the wild, or where these animals were brought together in unnaturally close proximity.”
Now being prepared for peer review, their analysis is based on a 2019 study of 21 Malayan pangolins — an especially popular species among traffickers — at a wildlife rescue centre in China’s Guangdong province.
The original research on the Guangdong pangolins was the first report on pangolins’ viral diversity.
Nonetheless, Petrosino was scientifically cautious — pangolins aren’t necessarily the closest link to humans.
“We do not know the order, or even where, the recombination events took place — whether it was in a bat, or a pangolin, or even whether there were other animals involved in the process that have yet to be discovered,” he said.
In January authorities had isolated SARS-CoV-2 in environmental samples from an unsanitary wildlife market in the Chinese city of Wuhan, but these results did not mean there were pangolins at the market.
For their part, there was only one thing Petrosino and his colleagues could say for certain.
“A virus known to exist in bats and a virus found in a pangolin-virus sample appeared to have recombined to form [SARS-CoV-2]. But, some viruses can be transmitted between mammals relatively easily, so there’s no way to tell whether there is another animal where these two viruses perhaps co-existed. More surveillance is necessary.”
Research gathers global momentum
Announced on the same day that Daily Maverick reported on the Baylor College findings, additional preliminary findings by a team of 26 researchers from South China Agricultural University had also found correlations between pangolin and SARS-CoV-2 RBDs.
This university’s detailed findings, posted on the bioRxiv forum on 20 February, made global headlines but have been challenged by some scientists.
However, since Baylor College emerged as the first academic team to share their seminal comparison study on bioRxiv on 13 February, at least 11 additional independent Australian, Chinese and US studies exploring pangolins as possible intermediate carriers have been made public on this very forum.
At the time of writing, the Baylor College and South China Agricultural University preprints had soared to the 99th percentile of some 15 million research outputs ever monitored by the forum’s global “attention tracker”.
And the other preprints — none of which were peer-reviewed when posted to the forum — generally agree:
In their conclusions, all preprints urged further research.
“Indeed, the discovery of viruses in pangolins suggests there is a wide diversity of coronaviruses still to be sampled in wildlife, some of which may be directly involved in the emergence of [SARS-CoV-2],” said researchers in yet another bioRxiv study, this time by Chinese and Australian institutions.
The preprints made other pointed recommendations, such as introducing urgent mechanisms to end wildlife trade; removing pangolins from wet markets to halt zoonotic transfer; and extensively monitoring pangolin virology.
“Large surveillance of coronaviruses in pangolins,” recommended another study by Chinese and US institutions, “could improve our understanding of the spectrum of coronaviruses in pangolins.”
Big academia weigh in: it is NOT biological warfare
Wild and unsubstantiated conspiracy rumours have been floated about the genesis of the virus, including that it escaped from a Wuhan laboratory — but a paper published in Nature Medicine last week thoroughly debunked this.
As a peer-reviewed paper in one of the world’s most respected journals, it also added authority to the hypothesis of pangolins as a likely intermediate vector.
The paper, by Australian, UK and US institutions, attributed the virus origins to zoonotic transfer from an animal, possibly arising in the Rhinolophus affinis bat and then spilling over into a pangolin.
“It is possible that a progenitor of SARS-CoV-2 jumped into humans,” they report, “acquiring the genomic features described above through adaptation during undetected human-to-human transmission. Once acquired, these adaptations would enable the pandemic to take off.”
Will pangolins come and save us?
“In the midst of the global Covid-19 public-health emergency,” the Nature study offered, “it is reasonable to wonder why the origins of the pandemic matter.”
But they do matter.
“The trade in and consumption of wild animals is not only an animal welfare issue, it’s a human rights travesty as attested by a pandemic that has brought the world to its knees,” said Audrey Delsink, wildlife director at Humane Society International in Africa.
“Detailed understanding of how an animal virus jumped species boundaries to infect humans so productively will help in the prevention of future zoonotic events,” the Nature study concluded. “If SARS-CoV-2 pre-adapted in another animal species, then there is the risk of future re-emergence events.”
Peter Knights of international conservation organisation WildAid warned that pangolins, among the world’s most endangered and trafficked mammals, are highly pathogenic.
“Whether or not Covid-19 is found to have been transmitted through pangolins, it certainly could have been — and, if current levels of illegal trade continue, they could be a vector for another new disease. Pangolins have high pathogen loads and carry parasites, like ticks. They are also massively stressed, malnourished and dehydrated when in trade,” said Knights, who in recent years has had success working with the Chinese government to reduce the consumption of shark-fin soup by a reported 80%.
Scientists may have mapped only a fraction of wildlife viruses, which have co-evolved in a staggering variety of insects and animals — not just pangolins and bats.
The majority of known emerging infectious diseases — especially viruses — are of animal origin, said a Royal Society paper by scientists from Cambridge University, London’s Zoological Society and EcoHealth Alliance. The proportion of those emerging from wildlife hosts, they noted, increased substantially over the 20th century’s last four decades.
This underlined the urgency of redrawing the architecture of medical science to join holistic dots between public health, non-human life, the hidden costs of economic development and degraded ecosystems, which biodiversity scientists warn are a hotbed for emerging infectious diseases. Our relatively poor understanding of the extent of disease in wildlife shows that the virology-research vessel may have hit only the tip of the iceberg and, to conservationists like Knights, this makes the trajectory of emergency response obvious, not just in China, but in other key regions of the human planet.
“All governments with bushmeat and wildlife consumption primarily in South East Asia and West and Central Africa should review their legislation, penalties, enforcement efforts and public awareness of the risks at this time. All live wildlife markets should be closed around the world,” he urged.
It seems African governments may be following suit. Last week the Nyasa Times reported that Malawi would ban the sale and consumption of bushmeat. A mass Covid-19 “sensitisation” campaign would follow.
Knights cautioned: “It’s obvious that some species should not be allowed to be consumed at all, while there may be some ‘safe’ species: like rabbits, quail, some deer and antelope and grasscutters.
“As we add species of conservation concern or health risk, the banned list gets longer and longer. Instead, we should be looking at a short ‘clean’ list of animals that can be legally consumed and enforced, and the public [will] know that everything else is off limits.” DM
* “Troy cell” is used metaphorically to illustrate an example. It’s not meant to be used or interpreted as a scientific term.
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