tetano
Editor, Senior Moderator
Viruses
. 2022 Dec 17;14(12):2820.
doi: 10.3390/v14122820.
A Novel Coronavirus and a Broad Range of Viruses in Kenyan Cave Bats
Joseph Kamau[SUP] 1 [/SUP], Koray Ergunay[SUP] 2 3 4 5 [/SUP], Paul W Webala[SUP] 6 [/SUP], Silvia A Justi[SUP] 2 3 5 [/SUP], Brian P Bourke[SUP] 2 3 5 [/SUP], Maureen W Kamau[SUP] 7 8 [/SUP], James Hassell[SUP] 7 9 10 [/SUP], Mary N Chege[SUP] 1 [/SUP], David K Mwaura[SUP] 1 [/SUP], Cynthia Simiyu[SUP] 6 [/SUP], Sospeter Kibiwot[SUP] 6 [/SUP], Samson Onyuok[SUP] 11 [/SUP], Laura Caicedo-Quiroga[SUP] 2 3 5 [/SUP], Tao Li[SUP] 12 [/SUP], Dawn M Zimmerman[SUP] 2 5 11 [/SUP], Yvonne-Marie Linton[SUP] 2 3 5 [/SUP]
Affiliations
Abstract
Background and methods: To investigate virus diversity in hot zones of probable pathogen spillover, 54 oral-fecal swabs were processed from five bat species collected from three cave systems in Kenya, using metagenome sequencing.
Results: Viruses belonging to the Astroviridae, Circoviridae, Coronaviridae, Dicistroviridae, Herpesviridae and Retroviridae were detected, with unclassified viruses. Retroviral sequences were prevalent; 74.1% of all samples were positive, with distinct correlations between virus, site and host bat species. Detected retroviruses comprised Myotis myotis, Myotis ricketti, Myotis daubentonii and Galidia endogenous retroviruses, murine leukemia virus-related virus and Rhinolophus ferrumequinum retrovirus (RFRV). A near-complete genome of a local RFRV strain with identical genome organization and 2.8% nucleotide divergence from the prototype isolate was characterized. Bat coronavirus sequences were detected with a prevalence of 24.1%, where analyses on the ORF1ab region revealed a novel alphacoronavirus lineage. Astrovirus sequences were detected in 25.9%of all samples, with considerable diversity. In 9.2% of the samples, other viruses including Actinidia yellowing virus 2, bat betaherpesvirus, Bole tick virus 4, Cyclovirus and Rhopalosiphum padi virus were identified.
Conclusions: Further monitoring of bats across Kenya is essential to facilitate early recognition of possibly emergent zoonotic viruses.
Keywords: Africa; Kenya; astrovirus; bat; coronavirus; metagenome; retrovirus.
. 2022 Dec 17;14(12):2820.
doi: 10.3390/v14122820.
A Novel Coronavirus and a Broad Range of Viruses in Kenyan Cave Bats
Joseph Kamau[SUP] 1 [/SUP], Koray Ergunay[SUP] 2 3 4 5 [/SUP], Paul W Webala[SUP] 6 [/SUP], Silvia A Justi[SUP] 2 3 5 [/SUP], Brian P Bourke[SUP] 2 3 5 [/SUP], Maureen W Kamau[SUP] 7 8 [/SUP], James Hassell[SUP] 7 9 10 [/SUP], Mary N Chege[SUP] 1 [/SUP], David K Mwaura[SUP] 1 [/SUP], Cynthia Simiyu[SUP] 6 [/SUP], Sospeter Kibiwot[SUP] 6 [/SUP], Samson Onyuok[SUP] 11 [/SUP], Laura Caicedo-Quiroga[SUP] 2 3 5 [/SUP], Tao Li[SUP] 12 [/SUP], Dawn M Zimmerman[SUP] 2 5 11 [/SUP], Yvonne-Marie Linton[SUP] 2 3 5 [/SUP]
Affiliations
- PMID: 36560824
- DOI: 10.3390/v14122820
Abstract
Background and methods: To investigate virus diversity in hot zones of probable pathogen spillover, 54 oral-fecal swabs were processed from five bat species collected from three cave systems in Kenya, using metagenome sequencing.
Results: Viruses belonging to the Astroviridae, Circoviridae, Coronaviridae, Dicistroviridae, Herpesviridae and Retroviridae were detected, with unclassified viruses. Retroviral sequences were prevalent; 74.1% of all samples were positive, with distinct correlations between virus, site and host bat species. Detected retroviruses comprised Myotis myotis, Myotis ricketti, Myotis daubentonii and Galidia endogenous retroviruses, murine leukemia virus-related virus and Rhinolophus ferrumequinum retrovirus (RFRV). A near-complete genome of a local RFRV strain with identical genome organization and 2.8% nucleotide divergence from the prototype isolate was characterized. Bat coronavirus sequences were detected with a prevalence of 24.1%, where analyses on the ORF1ab region revealed a novel alphacoronavirus lineage. Astrovirus sequences were detected in 25.9%of all samples, with considerable diversity. In 9.2% of the samples, other viruses including Actinidia yellowing virus 2, bat betaherpesvirus, Bole tick virus 4, Cyclovirus and Rhopalosiphum padi virus were identified.
Conclusions: Further monitoring of bats across Kenya is essential to facilitate early recognition of possibly emergent zoonotic viruses.
Keywords: Africa; Kenya; astrovirus; bat; coronavirus; metagenome; retrovirus.