SARS-like Coronaviruses in Horseshoe Bats (Rhinolophus spp.) in Russia, 2020

Abstract

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.

An ACE2-dependent Sarbecovirus in Russian bats is resistant to SARS-CoV-2 vaccines

“…Khosta-1 and −2 were identified by Alkhovsky and colleagues in bat samples collected between March-October 2020 near Sochi National Park( 5 ). Phylogenetic analysis of the conserved viral gene, Orf1ab, revealed these viruses were most closely related to another sarbecovirus found in Bulgaria in 2008 (known as BM48-31 or Bg08), and form a lineage sarbecoviruses distinct from human pathogens, SARS-CoV-1 and - 2( 5 ). A list of viruses and accession numbers used in this study can be found in table 1.…”

“…Khosta 1 and 2 viruses are most closely related to other clade 3 RBD viruses, which have been found across a much wider geographic range than the clade 1 viruses( 1 , 7 , 23 , 24 ). As the researchers who initially discovered the Khosta viruses note with their findings: the Khosta bat sarbecoviruses are genetically distinct from human SARS-CoVs in that they lack genetic information encoding for some of the genes thought to antagonize the immune system and contribute to pathogenicity, such as Orf8( 5 ). Unfortunately, because coronaviruses are known to recombine in co-infected hosts, the recent identification of SARS-CoV-2 spillover from humans back in wildlife populations opens the possibility of new human-compatible sarbecoviruses ( 13 – 15 , 20 – 22 ).…”

“…In late 2020, two clade 3 sarbecoviruses were identified in Rhinolophus bats in Russia: Khosta-1 was found in Rhinolophus ferrumequinum and Khosta-2 in R. hipposideros(5) . Similar to other European and African clade 3 viruses, the Khosta viruses are divergent from the RBD found in SARS-CoV-1 and −2.…”

Targeted genomic sequencing with probe capture for discovery and surveillance of coronaviruses in bats

“…The vastness of CoV diversity that remains to be characterized is evident by the continuing high rate of novel CoV discovery by research studies and surveillance programs, this current work included [ e.g. Tao 2017, Wang 2017, Markotter 2019, Wang 2019, Nziza 2020, Valitutto 2020, Kumakamba 2021, Shapiro 2021, Tan 2021, Wang 2021, Zhou 2021, Alkhovsky 2022, Ntumvi 2022].…”

Alphacoronavirus in a Daubenton’s Myotis Bat (Myotis daubentonii) in Sweden

“…Predicted virus sequences were then further annotated and confirmed using NCBI BLAST+ [ 23 ]. To analyze the similarity of the genomic organization of identified alpha-CoV with other alpha-CoV, we used Simplot analysis (see also [ 24 ] employing R packages ggmsa and gggenes.…”