SARS-like Coronaviruses in Horseshoe Bats (<i>Rhinolophus</i> spp.) in Russia, 2020
Sergey Alkhovsky,
Sergey Lenshin,
Alexey Romashin,
Tatyana Vishnevskaya,
Oleg Vyshemirsky,
Yulia Bulycheva,
Dmitry Lvov,
Asya Gitelman
Affiliations
Sergey Alkhovsky
D.I. Ivanovsky Institute of Virology of N.F. Gamleya National Center for Epidemiology and Microbiology of Ministry of Health of Russian Federation, 18 Gamaleya Street, 123098 Moscow, Russia
Sergey Lenshin
Scientific Research Institute of Medical Primatology of Russian Academy of Science, 177 Mira Street, Veseoloe Village, 354376 Sochi, Russia
Alexey Romashin
Federal State Budgetary Institution Sochi National Park of Ministry of Natural Resources and Environment of Russian Federation, 74 Kurortniy Avenue, 354002 Sochi, Russia
Tatyana Vishnevskaya
D.I. Ivanovsky Institute of Virology of N.F. Gamleya National Center for Epidemiology and Microbiology of Ministry of Health of Russian Federation, 18 Gamaleya Street, 123098 Moscow, Russia
Oleg Vyshemirsky
Scientific Research Institute of Medical Primatology of Russian Academy of Science, 177 Mira Street, Veseoloe Village, 354376 Sochi, Russia
Yulia Bulycheva
D.I. Ivanovsky Institute of Virology of N.F. Gamleya National Center for Epidemiology and Microbiology of Ministry of Health of Russian Federation, 18 Gamaleya Street, 123098 Moscow, Russia
Dmitry Lvov
D.I. Ivanovsky Institute of Virology of N.F. Gamleya National Center for Epidemiology and Microbiology of Ministry of Health of Russian Federation, 18 Gamaleya Street, 123098 Moscow, Russia
Asya Gitelman
D.I. Ivanovsky Institute of Virology of N.F. Gamleya National Center for Epidemiology and Microbiology of Ministry of Health of Russian Federation, 18 Gamaleya Street, 123098 Moscow, Russia
We found and genetically described two novel SARS-like coronaviruses in feces and oral swabs of the greater (R. ferrumequinum) and the lesser (R. hipposideros) horseshoe bats in southern regions of Russia. The viruses, named Khosta-1 and Khosta-2, together with related viruses from Bulgaria and Kenya, form a separate phylogenetic lineage. We found evidence of recombination events in the evolutionary history of Khosta-1, which involved the acquisition of the structural proteins S, E, and M, as well as the nonstructural genes ORF3, ORF6, ORF7a, and ORF7b, from a virus that is related to the Kenyan isolate BtKY72. The examination of bats by RT-PCR revealed that 62.5% of the greater horseshoe bats in one of the caves were positive for Khosta-1 virus, while its overall prevalence was 14%. The prevalence of Khosta-2 was 1.75%. Our results show that SARS-like coronaviruses circulate in horseshoe bats in the region, and we provide new data on their genetic diversity.
