Preliminary Evidence Suggests Coronavirus Jumped From Animals to Humans Multiple Times

The origin of the SARS-CoV-2 virus, which has caused the COVID-19 pandemic, has been hotly debated.

This debate has caused substantial difficulties in the Australia-China relationship, with a call by Foreign Minister Marise Payne for another inquiry into its origin being considered by China as a hostile act.

What’s not in doubt is the closest relatives of the virus are found in bats. How, where and when the virus spilled over into humans is the contentious issue.

One widely supported hypothesis is the spillover occurred in the “wet markets” of Wuhan, where many species of wildlife from across China are held in crowded conditions.

However, there’s no evidence the species of bats in which the closest relatives of SARS-CoV-2 are found were sold through the Wuhan wet markets at any time in the two years before the pandemic. This hypothesis requires the existence of a “bridge host,” another species that becomes infected via spillover from the original bat hosts, and then passes the virus onto humans.

Bridge hosts are well-known in many emerging human diseases. For example, Hendra virus, which my group studies, has flying foxes as its reservoir. Hendra spills over to horses with some frequency. Horses then amplify the virus as a bridge host and can infect humans.

Fortunately, this is extremely rare, with only seven known cases. Tragically, four of those people died. Hendra has never been known to spread directly from flying foxes to humans.

More evidence a lab leak is very unlikely

A second, much more contentious hypothesis is the origin of the pandemic was the result of a “lab leak.”

Wuhan has one of the most sophisticated virological laboratories in China, and the laboratory does work on bat viruses. The suggestion is the virus may have inadvertently been released into the general community via one of the workers. No direct evidence supports this hypothesis.

A new pre-print study, released online, provides strong evidence to support the “natural spillover” hypothesis, with results that are hard to reconcile with the “lab leak” hypothesis.

The study is yet to be peer reviewed. But it’s based on a detailed examination of the genetic sequences of two early lineages obtained from people infected in late 2019 and early 2020.

For convenience, these two lineages are called A and B. The two lineages differ by just two nucleotides (letters in the genetic code) at two different key sites in the genetic sequence.

Genetic sequencing isn’t perfect. Close examination of the 38 intermediates strongly suggested they were more likely to be sequencing errors of pure lineage A or lineage B than to be true intermediates.

The genetic evidence, therefore, suggests very strongly there have been at least two separate spillover events into human populations, one being from lineage A and another being from lineage B.

Did a human bring SARS-CoV-2 to the wet markets?

The data don’t tell us there have been only two spillover events — there may have been more. Nor do they tell us whether these spillovers happened directly from bats, or whether some or all happened via an intermediate bridge host.

A Nature news article suggests this evidence points to the spillover having happened via the wildlife trade, but I think this is taking it a step too far.

While some of the wildlife species sold through the Wuhan wet market can indeed become infected with SARS-CoV-2 (for example raccoon dogs and mink), there’s no evidence any sold through the market were infected.

Many of the earliest human viral sequences (all lineage B) were recovered from the Wuhan seafood market, but wet markets and abattoirs are well-known to be places where the SARS-CoV-2 virus spreads very well from human to human.

So, it may have been a human who brought the virus to the Wuhan seafood market, rather than a species of wildlife.

One thing we do know is this pandemic originated through a human coming in contact with another species infected with the virus.

It’s unknown whether this was a bat or a bridge host, and whether this contact occurred in a wildlife market, or in a bat cave, or somewhere else entirely different.

Nevertheless, as humans encroach more and more on the habitats of wild animals and as wild animals are brought more frequently into close contact with humans, we can expect further spillovers and pandemics to occur.

If there was a single lab escape event, the separation into lineages A and B must have happened after the lab escape. We would therefore expect to see a substantial number of intermediate lineages, with the lineage A nucleotide at one site, and the lineage B nucleotide at the other site.

However, if almost all of the genetic sequences obtained from humans are “pure” lineage A or pure lineage B, this suggests there were at least two different spillover events, either directly from bats or via bridge hosts.

And the evolution of the two lineages occurred before humans were infected.

The researchers downloaded all complete genetic sequences for SARS-CoV-2 that had been lodged in a widely used genomic database. Of these sequences, 369 were lineage A, 1,297 were lineage B and just 38 were intermediates.

Written by Hamish McCallum, Director, Centre for Planetary Health and Food Security, Griffith University.

This article was first published in The Conversation.

COVID-19Griffith UniversityInfectious DiseasesThe ConversationVirology
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  • William Shissler

    This information is very helpful, thank you!

  • Clyde Spencer

    “Nevertheless, as humans encroach more and more on the habitats of wild animals and as wild animals are brought more frequently into close contact with humans, we can expect further spillovers and pandemics to occur.”

    Modern humans have been around for about 300,000 years. Most of that time humans lived in the habitat of wild animals and ate anything they could catch. Cities are a relatively new phenomena, being about 10,000 years old. However, even until recently, most humans were still living close to the wild habitat. What is really different over the last 300,000 years is that the human population is larger than it has ever been, and most people now live in cities. The Black Death demonstrated that cities are unhealthy places to live.

  • PROUDPurebloodpatriot

    They test for the flu since they’ve never isolated Covid-19. Which makes me wonder how they can tell there is a delta variant. They never isolated the virus but they use a test to show the damage of a solution does on monkey kidney cells then show the cellular debris as proof of the virus. So, they can use this method to claim an UNENDING! amount of variants. A lot of cancers and “viruses” are probably just different forms of parasites. Since the tests can’t differentiate between cold and flu and covid then doesn’t that mean ivermectin cures both the cold and the flu? Welcome to “they’ve been lying to us our entire lives about everything”.

  • pedro gutierrez

    Hammish McCallum references the article ‘Evidence Against the Veracity of SARS-CoV-2 Genomes Intermediate between Lineages A and B’, by Pekar to support the possible ‘natural spillover’ hypothesis.

    Pekar’s research group attempts to disprove the theory that there are intermediate lineages, such as C/C and T/T, between the Covid-19 A and B basic lineages. Simple A and B lineages for Covid-19, ‘natural spillover’, except for the following.

    “Of the 77 mutations seen in C/C intermediate genomes, 32 (41.6%) would need to be homoplasies if these C/C intermediates actually existed. Similarly, 7 (58.3%) of the 12 mutations seen in T/T genomes would need to be homoplasies if the T/T intermediates truly existed. These apparent homoplasies can arise from issues regarding sample preparation, contamination, sequencing technology, and/or consensus calling approaches (3). …..These findings cast substantial doubt on the veracity of C/C or T/T intermediate genomes in early 2020. We suggest that these early C/C and T/T genomes are erroneous and should be excluded from phylogenetic analyses. ”

    ‘Natural spillover’ except for the 77 eyewitnesses ‘intermediate’ genomes, that say, explain us! 77 intermediate genomes between the A and B lineages. The authors use the word ‘homoplasy’ at least three times?

    “A character state that evolved because of convergent evolution but was not acquired through common evolutionary lineage is called homoplasy” › medicine-and-dentistry

    ‘A homoplasy is a shared character between two or more animals that did not arise from a common ancestor. A homoplasy is the opposite of a homology, where a common ancestor provided the genes that gave rise to the trait in two or more animals.’

    Homoplasy, no common evolution, no common ancestor, another name for different outbreak sources? ‘Natural spillover’, except for these 77 intermediate genomes.
    Figure 2 of the Pekar article above shows many of the genomes in ‘error’ to be at the same phylogenic level of the first mutation T28144C . Multiple outbreak sources? No natural spillover?

    Pekar and his co-authors may have more difficult hurdles to leap, regarding a new lineage C for Covid-19. A lineage at the same levels of the A and B lineages. This new lineage pertains to D614G mutation.

    “Our analyses show support for three distinct lineages of SARS-CoV-2 actively spreading around the world . These lineages are highly unlikely to have been generated under the same coalescent process….Lineage C was predominantly European with no evidence that it circulated in China . This lineage was well supported as monophyletic (node posterior support (.99, 91% bootstrap support, Fig. 1) and diverged from Lineage B in late January (95% highest posterior density late January to early February). Linked non-synonymous mutations differentiated
    this lineage in the S gene (sites 23402-04 or D614G) and ORF1ab
    (14407-09) regions….. We were able to identify three lineages that were not only genetically distinctive but also had unique demographic signatures, revealing insights into the underlying epidemiology of this pandemic.’
    ‘Emerging phylogenetic structure of the SARS-CoV-2 pandemic’,
    Nicholas M. Fountain-Jones, Virus Evolution, 2020, Vol. 6, No. 1

    Let’s hope that no one is introducing new base lineages of Covid-19 into this world of ‘natural spillovers’. In Christ Jesus.