Ecology, evolution and classification of bat coronaviruses in the aftermath of SARS

Abstract

In 2002/2003, a novel coronavirus (CoV) caused a pandemic, infecting more than 8000 people, of whom nearly 10% died. This virus, termed severe acute respiratory syndrome-CoV was linked to a zoonotic origin from rhinolophid bats in 2005. Since then, numerous studies have described novel bat CoVs, including close relatives of the newly emerging Middle East respiratory syndrome (MERS)-CoV. In this paper we discuss CoV genomic properties and compare different taxonomic approaches in light of the technical difficulties of obtaining full genomic sequences directly from bat specimens. We first present an overview of the available studies on bat CoVs, with details on their chiropteran hosts, then comparatively analyze the increase in bat CoV studies and novel genomic sequences obtained since the SARS pandemic. We then conduct a comprehensive phylogenetic analysis of the genera Alpha- and Betacoronavirus, to show that bats harbour more CoV diversity than other mammalian hosts and are widely represented in most, but not all parts of the tree of mammalian CoVs. We next discuss preliminary evidence for phylogenetic co-segregation of CoVs and bat hosts encompassing the Betacoronavirus clades b and d, with an emphasis on the sampling bias that exists among bat species and other mammals, then present examples of CoVs infecting different hosts on the one hand and viruses apparently confined to host genera on the other. We also demonstrate a geographic bias within available studies on bat CoVs, and identify a critical lack of information from biodiversity hotspots in Africa, Asia and Latin America. We then present evidence for a zoonotic origin of four of the six known human CoVs (HCoV), three of which likely involved bats, namely SARS-CoV, MERS-CoV and HCoV-229E; compare the available data on CoV pathogenesis in bats to that in other mammalian hosts; and discuss hypotheses on the putative insect origins of CoV ancestors. Finally, we suggest caution with conclusions on the zoonotic potential of bat viruses, based only on genomic sequence data, and emphasize the need to preserve these ecologically highly relevant animals. This paper forms part of a symposium in Antiviral Research on "from SARS to MERS: 10years of research on highly pathogenic human coronaviruses".

Coronavirus Host Range Expansion and Middle East Respiratory Syndrome Coronavirus Emergence: Biochemical Mechanisms and Evolutionary Perspectives

“…As of June 2015, there were 1,227 laboratory-confirmed cases of MERS-CoV infection, with at least 449 related deaths, resulting in a 37% mortality rate (43). MERS-CoV is grouped phylogenetically into the C betacoronavirus clade along with the bat coronaviruses BtCoV-HKU4 and BtCoV-HKU5 (Figure 1) (29,44). Unlike SARS-CoV, MERS-CoV utilizes dipeptidyl peptidase 4 (DPP4) as an entry receptor (45).…”

“…Other coronaviruses have been detected in only a single mammalian order, such as the many SARS-like coronaviruses that have been found only in bats (24,25). With a focus centered on bats as reservoirs, metagenomics analyses have found varying levels of coronavirus diversity in bat populations in North America (26) and China (27,28), as well as detecting individual strains in bat populations worldwide (reviewed in 29). Novel coronaviruses continue to be discovered in bat populations globally; recent examples include samples from Mexico (30), Brazil (31), and South Africa (32).…”

Network analysis of host–virus communities in bats and rodents reveals determinants of cross‐species transmission

“…; Drexler et al . ), and bats appear to be major and ancient natural reservoirs of several viral families, including hepaciviruses, pegiviruses, paramyxoviruses, coronaviruses and influenza A viruses ( Drexler, et al . , ; Quan et al .…”

Middle East respiratory syndrome coronavirus (MERS-CoV) RNA and neutralising antibodies in milk collected according to local customs from dromedary camels, Qatar, April 2014

“…MERS-CoV belongs to lineage C within the Betacoronavirus genus (Coronavirinae subfamily), along with several viruses detected in bats in Europe, Africa and China [39].…”