2019-nCoV related to SARS-like coronaviruses of bat origin

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A study on the novel coronavirus recently discovered in Wuhan, China has carried out genetic analysis of 10 viral genome sequences, obtained from nine patients, discovering that the virus (2019-nCoV) is most closely related to two bat-derived SARS-like coronaviruses.

The study, published in The Lancet, assessed eight complete genomes and two partial genomes taken from nine patients – eight of which had visited the Huanan seafood market implicated in the outbreak.

The researchers discovered that the samples shared more than 99.98% of the same genetic sequence, indicating a very recent emergence of the virus in humans. In addition, the authors compared the 2019-nCoV sequence to a library of viruses, discovering the most closely related were two SARS-like viruses of bat origin (bat-SL-CoVZC45 and bat-SL-CoVZXC21). They also demonstrated that 2019-nCoV was genetically distinct from SARS and MERS, although the spike protein of the virus did appear similar in structure to SARS.

Despite being most genetically similar to two SARS-like coronaviruses of bat origin, the authors suggest there may be another animal host acting as an intermediate host between bats and humans.

 Keep up to date with the latest case numbers and updates for 2019-nCoV >

Guizhen Wu, from the Chinese Center for Disease Control and Prevention, commented: “These data are consistent with a bat reservoir for coronaviruses in general and 2019-nCoV in particular. However, despite the importance of bats, it seems likely that another animal host is acting as an intermediate host between bats and humans,”

“First, the outbreak was first reported in late December 2019, when most bat species in Wuhan are hibernating. Second, no bats were sold or found at the Huanan seafood market, whereas many non-aquatic animals (including mammals) were. Third, the similarities in the genetic sequences between 2019-nCoV and its close relatives bat-SL-CoVZC45 and bat-SL-CoVZXC21 were less than 90%, meaning these two bat-derived coronaviruses are not direct ancestors of 2019-nCoV. Fourth, in both SARS and MERS, bats acted as the natural reservoir, with another animal acting as an intermediate host, and with humans as terminal hosts. This again highlights the hidden virus reservoir in wild animals and their potential to spill over into human populations.”

A second study was also published in The Lancet today, assessing 99 patients with laboratory-confirmed infections of the virus. This idenfitified some common clinical symptoms including fever (82 patients), cough (81 patients) and infection in both lungs (74 patients).

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Source: Lu R, Zhao X, Li J et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet doi:10.1016/S0140-6736(20)30251-8 (2020); Huang C, Wang Y, Li X et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet doi:10.1016/S0140-6736(20)30183-5 (2020); www.eurekalert.org/pub_releases/2020-01/tl-pss012920.php

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  1. Two Coronavirus genomes with greater similarity to nCoV have now been identified: One from a Yunnan bat sampled in 2013 and sequenced recently (GISAID accession number EPI_ISL_402131) and one from a Malaysian pangolin viromics short read archive data set (SRR10168377) not yet published, but discussed here: http://virological.org/t/ncov-2019-spike-protein-receptor-binding-domain-shares-high-amino-acid-identity-with-a-coronavirus-recovered-from-a-pangolin-viral-metagenomic-dataset/362

    The two bat Coronavirus genomes discussed above (CoVZC45.2017.MG772933 and CoVZXC21.2015.MG772934) have regions of very high similarity to the nCoV but other regions with less similarity, which was inditially thought to indicate that the nCoV was recombinant. But the GISAID bat Coronavirus sequence and the pangolin Coronavirus sequence, now make it evident that recombination is common in these Coronaviruses and it is not correct to consider the nCoV as the recombinant virus.
    More discussion can be found at the virological.org site.

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