MOLECULAR BARRIERS TO THE EMERGENCE OF CORONAVIRUSES IN HUMANS

Context. The emergence of new viruses threatens human health and prosperity. The main source of these 'new' viruses is the 'spillover' of existing animal viruses into human populations. This is the case with the COVID-19 pandemic, where a 'new' coronavirus (SARS-CoV-2) was transmitted from horseshoe bats to humans (possibly via an intermediate animal species). Other coronavirus (CoV) spillover events include SARS and MERS, and evidence suggests CoVs may be particularly adept at jumping between species. If future CoV pandemics are to be prevented, there is an urgent need to better predict which animal CoVs are poised to emerge in human populations, and to identify the factors that permit or prevent such transmission.

There are multiple barriers to the transmission of viruses from animals to humans. Humans must have contact with the animal reservoir, and the virus must also be able to interact with 'human versions' of the molecules needed to complete the viral lifecycle. For example, the viral spike protein of SARS-CoV-2 interacts with the host receptor protein ACE2 (in order to invade human cells). However, the SARS-CoV-2 spike protein cannot use the mouse version of ACE2, and this effectively forms a barrier that protects mice from SARS-CoV-2 infection.

As a further barrier, human and animal cells contain an arsenal of defences that can block viruses. Viruses must evolve to overcome these antiviral defences in their normal host species, but these strategies may not be effective in a new host species. Thus, the antiviral defences within our cells can form an important barrier that must be overcome in order for viruses to emerge in human populations. Through the study of diverse viruses, many such antiviral defences have been identified, and these defences are often stimulated by interferons, which are proteins released by cells in response to viral infection. Thus, by examining interferon-stimulated genes (ISGs), unidentified antiviral defences can be found. Our proposed work will identify antiviral ISG defences that might constrain CoV emergence. Moreover, as interferon responses can heavily influence the severity of coronavirus-induced disease, improving our understanding of the effect of interferons and ISGs on CoVs could shed light on COVID-19 pathogenesis.

Aims. We will identify CoVs most likely to emerge in humans by using artificial intelligence/machine learning to search for patterns in the genome sequences of CoVs currently circulating in bats. As most existing human CoVs have origins in bats, and bats harbour other viruses like SARS-CoV-2, this will help us pinpoint specific CoVs with human pandemic potential.

To identify the antiviral ISG defences impacting CoVs, we will carry out screens to systematically measure the ability of >1000 individual ISGs to inhibit either the specific 'high risk' bat CoVs (deemed using machine learning), the human SARS CoVs, or human seasonal CoVs. This approach will reveal the ISG defences that target coronaviruses. To uncover which of these factors might prevent/permit the emergence of specific bat CoVs, we will compare the abilities of the equivalent antiviral ISG defences from horseshoe bats (the reservoir species), humans and a panel of possible intermediate species, to act as a barrier to coronavirus emergence in humans.

Applications and benefits. During this project we will illuminate an important area of coronavirus biology, communicate effectively about the risks of virus emergence, train the next generation of virologists and stimulate further research in this field. In the longer term, our research defining the molecular details of coronavirus emergence will help identify coronaviruses with increased pandemic potential, improving global surveillance efforts. In addition, the pivotal role that interferons play in coronavirus pathogenesis means this research could potentially shed light on SARS-CoV-2 disease outcomes.

We hypothesise that certain circulating bat coronaviruses (CoVs) could emerge in human populations with devastating consequences (similar to SARS-CoV-2). However, the existing human CoVs all appear to have emerged via transmission from possible intermediate species, rather than directly from bats, suggesting that specific molecular barriers may hinder direct zoonotic transmission from bats to humans. We therefore aim to identify both the bat CoVs with increased risk of emerging in humans, as well as genome-encoded defences that could constrain CoV cross-species transmission.
By combining supervised machine learning with evolutionary and bioinformatic analyses, we will identify bat CoVs with an increased risk of emergence in humans. Six of these 'poised' bat CoVs will then be synthesised, and combined with highly pathogenic human CoVs, and seasonal human CoVs, to create a cross-species CoV test panel, on which we will focus further molecular experimentation.

Previous studies have shown that genome-encoded antiviral defences can form powerful barriers to cross-species transmission of viruses, and are often encoded by interferon-stimulated genes (ISGs). We will therefore define the interferome of horseshoe bats (the reservoir of SARS-CoVs) and construct a library of ~150 horseshoe bat ISGs. These bat ISGs, along with our existing ISG libraries (human, macaque, bovine) will then be used to identify ISGs that inhibit any coronaviruses in our cross-species test panel (described above).

Subsequent analyses will examine patterns of restriction of the anti-CoV ISGs in potential intermediate species, in order to identify blocks to cross-species transmission. Together, this knowledge should improve our capacity to make predictions about which CoVs are likely to make successful cross-species 'jumps', aiding surveillance of CoVs with pandemic potential. In addition, understanding how ISGs inhibit CoVs could potentially improve our understanding of SARS-CoV-2 pathogenesis.