Identification of a new alphacoronavirus (Coronaviridae: <i>Alphacoronavirus</i>) associated with the greater horseshoe bat (<i>Rhinolophus ferrumequinum</i>) in the south of European part of Russia.
S V Lenshin1
T V Vishnevskaya2
A V Romashin3
Y I Bulycheva2
O I Vyshemirsky4
S A Solovyeva2
A K Gitelman2
A S Pazilin2
D K Lvov2
B Hu5
Z Shi5,6
S V Alkhovsky2
Affiliations6 institutions
Stavropol Plague Control Research Institute of Rospotrebnadzor.
D.I. Ivanovsky institute of virology of N.F Gamaleya national research center on epidemiology and microbiology of Ministry of health of Russian Federation.
Sochi National Park.
National Research Center «Kurchatov Institute».
Wuhan Institute of Virology, Chinese Academy of Sciences.
Bats are recognized as primary natural reservoirs for alpha- and betacoronaviruses. The interspecies transmission of bat coronaviruses to other mammalian hosts, including livestock and humans, can lead to epidemics, epizootics, and global pandemics. This study aims to describe coronaviruses associated with horseshoe bats (<i>Rhinolophus</i> spp.) in the southern regions of the European part of Russia. Fecal samples were collected from bats inhabiting caves on the southern macroslope of the Greater Caucasus (Sochi-Adler region) during 2020, 2021, and 2024. Viral genomes were detected and analyzed using high-throughput sequencing (NGS) and RT-PCR. A novel alphacoronavirus, designated Kudep virus (GenBank acc. # PQ649435), was identified in <i>R. ferrumequinum</i>. Presumably the Kudep virus represents a novel species within the subgenus <i>Decacovirus</i> of the genus <i>Alphacoronavirus. </i>The virus Showed 72% nucleotide identity to a Cardioderma bat coronavirus from Kenya and up to 67% nucleotide identity to the YN2012 virus group found in horseshoe bats in China. RT-PCR screening revealed active circulation of both Kudep virus and the previously described SARS-like betacoronavirus Khosta-1 in the study area. Infection rates in a single <i>R. ferrumequinum</i> colony during autumn 2021 reached 59.2% and 70.5% for Kudep and Khosta-1, respectively. Frequent co-infections with both viruses were observed in individual bats. Our findings expand the understanding of the distribution of bat alphacoronaviruses and their genetic diversity. We demonstrate the presence of a persistent natural foci of two potentially zoonotic bat coronaviruses, ecologically associated with <i>R. ferrumequinum</i> in the southern European part of Russia.
Rhinolophus ferrumequinum bats in southern European Russia act as natural reservoirs with persistent infection foci for Kudep virus, a novel alphacoronavirus.
A novel alphacoronavirus, designated Kudep virus, was identified in R. ferrumequinum. RT-PCR screening revealed active circulation of both Kudep virus and the previously described SARS-like betacoronavirus Khosta-1 in the study area. Infection rates in a single R. ferrumequinum colony during autumn 2021 reached 59.2% and 70.5% for Kudep and Khosta-1, respectively. We demonstrate the presence of a persistent natural foci of two potentially zoonotic bat coronaviruses, ecologically associated with R. ferrumequinum in the southern European part of Russia.
Method
RT-PCR; high-throughput sequencing
Sample type
fecal samples
Geographic raw
southern European part of Russia
Country inferred
Russia
Reservoir EcologyExtraction confidence 0.85
Key finding
Rhinolophus ferrumequinum bats in southern European Russia maintain a persistent natural focus of Khosta-1, a SARS-like betacoronavirus, indicating ongoing reservoir activity.
RT-PCR screening revealed active circulation of both Kudep virus and the previously described SARS-like betacoronavirus Khosta-1 in the study area. Infection rates in a single R. ferrumequinum colony during autumn 2021 reached 70.5% for Khosta-1. We demonstrate the presence of a persistent natural foci of two potentially zoonotic bat coronaviruses, ecologically associated with R. ferrumequinum in the southern European part of Russia.
Method
RT-PCR
Sample type
fecal samples
Geographic raw
southern European part of Russia
Country inferred
Russia
Zoonotic Surveillance2 records
Zoonotic SurveillanceExtraction confidence 0.95
Key finding
Zoonotic surveillance of Rhinolophus ferrumequinum bats in southern Russia detected the novel Kudep alphacoronavirus and Khosta-1 betacoronavirus using fecal samples screened by RT-PCR and NGS.
Fecal samples were collected from bats inhabiting caves on the southern macroslope of the Greater Caucasus (Sochi-Adler region) during 2020, 2021, and 2024. Viral genomes were detected and analyzed using high-throughput sequencing (NGS) and RT-PCR. A novel alphacoronavirus, designated Kudep virus, was identified in R. ferrumequinum. RT-PCR screening revealed active circulation of both Kudep virus and the previously described SARS-like betacoronavirus Khosta-1 in the study area.
Method
RT-PCR; high-throughput sequencing
Sample type
feces
Geographic raw
Sochi-Adler region
Country inferred
Russia
Zoonotic SurveillanceExtraction confidence 0.95
Key finding
Surveillance of Rhinolophus ferrumequinum bats revealed active circulation of the SARS-like betacoronavirus Khosta-1 with high infection rates and co-infection with Kudep virus in southern Russia.
RT-PCR screening revealed active circulation of both Kudep virus and the previously described SARS-like betacoronavirus Khosta-1 in the study area. Infection rates in a single R. ferrumequinum colony during autumn 2021 reached 59.2% and 70.5% for Kudep and Khosta-1, respectively. Frequent co-infections with both viruses were observed in individual bats.
Method
RT-PCR; high-throughput sequencing
Sample type
feces
Geographic raw
Sochi-Adler region
Country inferred
Russia
Genomic Evolution1 records
Genomic EvolutionExtraction confidence 0.90
Key finding
Genome sequencing and phylogenetic comparison revealed a new alphacoronavirus, Kudep virus, in Rhinolophus ferrumequinum bats, with 67–72% similarity to bat coronaviruses from Africa and Asia, indicating a distinct evolutionary lineage within the Decacovirus subgenus.
A novel alphacoronavirus, designated Kudep virus (GenBank acc. # PQ649435), was identified in <i>R. ferrumequinum</i>. Presumably the Kudep virus represents a novel species within the subgenus <i>Decacovirus</i> of the genus <i>Alphacoronavirus.</i> The virus showed 72% nucleotide identity to a Cardioderma bat coronavirus from Kenya and up to 67% nucleotide identity to the YN2012 virus group found in horseshoe bats in China. Viral genomes were detected and analyzed using high-throughput sequencing (NGS) and RT-PCR.
