Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2015 Jan 1:474:19-27.
doi: 10.1016/j.virol.2014.10.017. Epub 2014 Nov 9.

Discovery, diversity and evolution of novel coronaviruses sampled from rodents in China

Wen Wang  1 , Xian-Dan Lin  2 , Wen-Ping Guo  1 , Run-Hong Zhou  3 , Miao-Ruo Wang  4 , Cai-Qiao Wang  3 , Shuang Ge  3 , Sheng-Hua Mei  4 , Ming-Hui Li  1 , Mang Shi  5 , Edward C Holmes  5 , Yong-Zhen Zhang  6
Affiliations

Discovery, diversity and evolution of novel coronaviruses sampled from rodents in China

Wen Wang et al. Virology. .

Abstract

Although rodents are important reservoirs for RNA viruses, to date only one species of rodent coronavirus (CoV) has been identified. Herein, we describe a new CoV, denoted Lucheng Rn rat coronavirus (LRNV), and novel variants of two Betacoronavirus species termed Longquan Aa mouse coronavirus (LAMV) and Longquan Rl rat coronavirus (LRLV), that were identified in a survey of 1465 rodents sampled in China during 2011-2013. Phylogenetic analysis revealed that LAMV and LRLV fell into lineage A of the genus Betacoronavirus, which included CoVs discovered in humans and domestic and wild animals. In contrast, LRNV harbored by Rattus norvegicus formed a distinct lineage within the genus Alphacoronavirus in the 3CL(pro), RdRp, and Hel gene trees, but formed a more divergent lineage in the N and S gene trees, indicative of a recombinant origin. Additional recombination events were identified in LRLV. Together, these data suggest that rodents may carry additional unrecognized CoVs.

Keywords: Coronavirus; Evolution; Phylogeny; Recombination; Rodents.

PubMed Disclaimer

Figures

Fig. 1
Fig. 1
A map of Zhejiang province, China showing the location of trap sites in which rodents were captured and surveyed for coronaviruses.
Fig. 2
Fig. 2
Genome organization of coronaviruses. The three CoVs discovered in this study are shown in bold. The star signifies the presence of a betacoronavirus-like NS2a gene in LRNV.
Fig. 3
Fig. 3
Phylogenetic analyses of the amino acid sequences of the 3CLpro, RdRp, Hel, and N genes of Lucheng Rn rat coronavirus (LRNV) Lucheng-19, Longquan Aa mouse coronavirus (LAMV) Longquan-343, and Longquan Rl rat coronaviruses (LRLV) Longquan-708, Longquan-189, and Longquan-370. Numbers (>70) above or below branches indicate percentage bootstrap values. The trees were mid-point rooted for clarity only. The scale bar represents the number of amino acid substitutions per site. The GenBank accession numbers of the viruses used in this analysis are shown in Table S1.
Fig. 4
Fig. 4
Phylogenetic analyses of the amino acid sequences of the S genes of LRNV, LAMV and LRLV. Numbers (>70) above or below branches indicate percentage bootstrap values. The trees were mid-point rooted for clarity only. The scale bar represents the number of amino acid substitutions per site. The GenBank accession numbers of other CoVs are given in Table S1.
Fig. 5
Fig. 5
Recombination within the genome of LRLV Longquan-708. A sequence similarity plot (A) reveals three recombination break-points shown by black dashed lines, with their locations indicated at the bottom. The plot shows genome scale similarity comparisons of the Longquan-708 (query) against Longquan Rl Rat Coronavirus (parental group 1, red) and Murine hepatitis virus (parental group 2, blue). The background color of parental region A is white, while that of parental region B is gray. Phylogenies of parental region A (B) and parental region B (C) are shown below the similarity plot. Numbers (>70) above or below branches indicate percentage bootstrap values. The GenBank accession numbers of the viruses used in this analysis are shown in Table S1.
See this image and copyright information in PMC

References

    1. Annan A., Baldwin H.J., Corman V.M., Klose S.M., Owusu M., Nkrumah E.E., Badu E.K., Anti P., Agbenyega O., Meyer B., Oppong S., Sarkodie Y.A., Kalko E.K., Lina P.H., Godlevska E.V., Reusken C., Seebens A., Gloza-Rausch F., Vallo P., Tschapka M., Drosten C., Drexler J.F. Human Betacoronavirus 2c EMC/2012-related viruses in bats. Ghana and Eur. Emerg. Infect. Dis. 2013;19:456–459. - PMC - PubMed
    1. Apweiler R., Attwood T.K., Bairoch A., Bateman A., Birney E., Biswas M., Bucher P., Cerutti L., Corpet F., Croning M.D., Durbin R., Falquet L., Fleischmann W., Gouzy J., Hermjakob H., Hulo N., Jonassen I., Kahn D., Kanapin A., Karavidopoulou Y., Lopez R., Marx B., Mulder N.J., Oinn T.M., Pagni M., Servant F., Sigrist C.J., Zdobnov E.M. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucl. Acids. Res. 2001;29:37–40. - PMC - PubMed
    1. Azhar E.I., El-Kafrawy S.A., Farraj S.A., Hassan A.M., Al-Saeed M.S., Hashem A.M., Madani T.A. Evidence for camel-to-human transmission of MERS coronavirus. N. Engl. J. Med. 2014;370:2499–2505. - PubMed
    1. Bateman A., Birney E., Cerruti L., Durbin R., Etwiller L., Eddy S.R., Griffiths-Jones S., Howe K.L., Marshall M., Sonnhammer E.L. The Pfam protein families database. Nucl. Acids. Res. 2002;30:276–280. - PMC - PubMed
    1. Beaudette F.R., Hudson C.B. Cultivation of the virus of infectious bronchitis. J. Am. Vet. Med. Assoc. 1937;90:51–58.

Publication types

MeSH terms

Substances

Associated data