Bat-borne virus diversity, spillover and emergence

Letko, Michael; Seifert, Stephanie N.; Olival, Kevin J.; Plowright, Raina K.; Munster, Vincent J.

doi:10.1038/s41579-020-0394-z

Cited by 365 publications

(395 citation statements)

References 176 publications

(206 reference statements)

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“…Reverse genetics and synthetic nucleic acids offer a path to biological validation when virions are unavailable, such as those predicted from sequence alone [37,38]. Innovative fields such as high-throughput functional viromics [39] leverage these broad and rapidly growing collections of viral sequences, and can inform evidence-based policies responding to emerging pandemics [40,41].…”

Section: Discussionmentioning

confidence: 99%

Petabase-scale sequence alignment catalyses viral discovery

Edgar¹,

Taylor²,

Lin³

et al. 2020

Preprint

117

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Public sequence data represents a major opportunity for viral discovery, but its exploration has been inhibited by a lack of efficient methods for searching this corpus, which is currently at the petabase scale and growing exponentially. To address the ongoing pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 and expand the known sequence diversity of viruses, we aligned pangenomes for coronaviruses (CoV) and other viral families to 5.6 petabases of public sequencing data from 3.8 million biologically diverse samples. To implement this strategy, we developed a cloud computing architecture, `Serratus`, tailored for ultra-high throughput sequence alignment at the petabase scale. From this search, we identified and assembled thousands of CoV and CoV-like genomes and genome fragments ranging from known strains to putatively novel genera. We generalise this strategy to other viral families, identifying several novel deltaviruses and huge bacteriophages. To catalyse a new era of viral discovery we made millions of viral alignments and family identifications freely available to the research community (https://serratus.io). Expanding the known diversity and zoonotic reservoirs of CoV and other emerging pathogens can accelerate vaccine and therapeutic developments for the current pandemic, and help us anticipate and mitigate future ones.

show abstract

Section: Discussionmentioning

confidence: 99%

Petabase-scale sequence alignment catalyses viral discovery

Edgar¹,

Taylor²,

Lin³

et al. 2020

Preprint

117

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show abstract

“…The COVID-19 epidemic is a life-size experiment in virus evolution. Remarkably, we neither know the real origin of the virus [46], nor where it will lead us. This explains why the vast majority of studies of the SARS-CoV-2 virus and its evolution are essentially descriptive.…”

Section: Discussionmentioning

confidence: 99%

Biochemical and mathematical lessons from the evolution of the SARS-CoV-2 virus: paths for novel antiviral warfare

Cluzel¹,

Lambert

Maday³

et al. 2020

Preprint

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In the fight against the spread of COVID-19 the emphasis is on vaccination or on reactivating existing drugs used for other purposes. The tight links that necessarily exist between the virus as it multiplies and the metabolism of its host are systematically ignored. Here we show that the metabolism of all cells is coordinated by the availability of a core building block of the cell’s genome, cytidine triphosphate (CTP). This metabolite is also the key to the synthesis of the viral envelope and to the translation of its genome into proteins. This unique role explains why evolution has led to the early emergence in animals of an antiviral immunity enzyme, viperin, that synthesizes a toxic analogue of CTP. The constraints arising from this dependency guide the evolution of the virus. With this in mind, we explored the real-time experiment taking place before our eyes using probabilistic modelling approaches to the molecular evolution of the virus. We have thus followed, almost on a daily basis, the evolution of the composition of the viral genome to link it to the progeny produced over time, particularly in the form of blooms that sparked a firework of viral mutations. Some of those certainly increase the propagation of the virus. This led us to make out the critical role in this evolution of several proteins of the virus, such as its nucleocapsid N, and more generally to begin to understand how the virus ties up the host metabolism to its own benefit. A way for the virus to escape CTP-dependent control in cells would be to infect cells that are not expected to grow, such as neurons. This may account for unexpected body sites of viral development in the present epidemic.

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“…As in previous zoonotic coronavirus spillover events of global concern, a bat species is most likely the evolutionary host to the on-going SARS-CoV-2 pandemic ( 4 ). Initially, in December 2019, human cases, were epidemiologically linked to a seafood market in Wuhan, China, where live wild animals were sold and slaughtered for consumption ( 5 ).…”

Section: What Do We Know?mentioning

confidence: 93%

COVID-19 and the Curse of Piecemeal Perspectives

Walzer

2020

Front. Vet. Sci.

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The world is in turmoil. A novel coronavirus (SARS-CoV-2) has catapulted across the ever-evolving interface between humans and wild places relentlessly spreading coronavirus disease (COVID-19) amongst humans and bringing immense suffering and death to the farthest reaches of our planet. What was immediately apparent was that the virus responsible for this outbreak originated in wild animals. A wildlife source does not come as a surprise as the majority of emerging infectious diseases are zoonotic and two-thirds have their origin in wildlife. The commercial use of wildlife for consumption encompassing both legal and illegal trade is poorly regulated with porous boundaries between the two entities. This trade, particularly in live animals, creates super-interfaces along the food value chain co-mingling species from many different geographies and habitats while creating perfect conditions for the exchange and recombination of viruses. Since the SARS outbreak in 2002/2003, broad scientific consensus exists that long term, structural changes, and wildlife trade and market closures will be required to prevent future epidemics. The pragmatic, most cost-effective action governments can take with immediate effect is to ban the commercial trade of wild birds and mammals for consumption. Most importantly, this reduces the risk of future zoonotic transmission while also safeguarding resources for those Indigenous Peoples and local communities who rely on wild meat to meet their nutritional requirements.

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Bat-borne virus diversity, spillover and emergence

Cited by 365 publications

References 176 publications

Petabase-scale sequence alignment catalyses viral discovery

Petabase-scale sequence alignment catalyses viral discovery

Biochemical and mathematical lessons from the evolution of the SARS-CoV-2 virus: paths for novel antiviral warfare

COVID-19 and the Curse of Piecemeal Perspectives

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