The Genetic Characterization of the First Detected Bat Coronaviruses in Poland Revealed SARS-Related Types and Alphacoronaviruses

Abstract

Bats are a major global reservoir of alphacoronaviruses (alphaCoVs) and betaCoVs. Attempts to discover the causative agents of COVID-19 and SARS have revealed horseshoe bats (Rhinolophidae) to be the most probable source of the virus. We report the first detection of bat coronaviruses (BtCoVs) in insectivorous bats in Poland and highlight SARS-related coronaviruses found in Rhinolophidae bats. The study included 503 (397 oral swabs and 106 fecal) samples collected from 20 bat species. Genetically diverse BtCoVs (n = 20) of the Alpha- and Betacoronavirus genera were found in fecal samples of two bat species. SARS-related CoVs were in 18 out of 58 lesser horseshoe bat (Rhinolophus hipposideros) samples (31%, 95% CI 20.6–43.8), and alphaCoVs were in 2 out of 55 Daubenton’s bat (Myotis daubentonii) samples (3.6%, 95% CI 0.6–12.3). The overall BtCoV prevalence was 4.0% (95% CI 2.6–6.1). High identity was determined for BtCoVs isolated from European M. daubentonii and R. hipposideros bats. The detection of SARS-related and alphaCoVs in Polish bats with high phylogenetic relatedness to reference BtCoVs isolated in different European countries but from the same species confirms their high host restriction. Our data elucidate the molecular epidemiology, prevalence, and geographic distribution of coronaviruses and particularly SARS-related types in the bat population.

Sarbecoviruses of British Horseshoe Bats; Sequence Variation and Epidemiology

“…This study found no detectable SARS-CoV-2 in British bats, in particular none in horseshoe bats which might be expected to be most at risk of infection. This is similar to the findings of other studies of European bats during the COVID-19 pandemic, none of which demonstrated SARS-CoV-2 infection including from, three common pipistrelles in the UK (Jones, Bell et al 2022), 503 samples from 20 bat species including 58 lesser horseshoe bats in Poland (Orłowska, Smreczak et al 2022), 197 samples from five bat species including 82 samples from lesser horseshoe bats, 104 from greater horseshoe bats and five from Mediterranean horseshoe bats ( Rhinolophus euyale) from Sochi in Russia (Alkhovsky, Lenshin et al 2022) and 76 lesser horseshoe bats in the UK (Crook, Murphy et al 2021).…”

“…British lesser horseshoe bats were, however, found to be frequently infected with a Sarbecovirus similar to that described previously in this species (Rihtaric, Hostnik et al 2010, Crook, Murphy et al 2021, Alkhovsky, Lenshin et al 2022, Orłowska, Smreczak et al 2022, Sander, Moreira-Soto et al 2022) and distinct from sarbecoviruses previously described in greater horseshoe bats in Bulgaria (Muth, Corman et al 2018) and Russia (Alkhovsky, Lenshin et al 2022). Although the sampling strategy in this study, based on opportunistic sampling linked to bat survey and conservation studies, did not allow a prevalence to be calculated, the frequency at which the virus was detected within and between populations suggests a prevalence not dissimilar to that found in Poland of around 30% (Orłowska, Smreczak et al 2022). That study, unlike this, detected virus in oronasal swabs as well as faeces, and this may reflect the smaller amount of material collected on swabs in this study (rectal swabs were also less frequently positive in the qPCR assay than faecal samples).…”

Sarbecoviruses of British horseshoe bats; sequence variation and epidemiology

“…This study found no detectable SARS-CoV-2 in British bats, in particular none in horseshoe bats, which might be expected to be most at risk of infection. This is similar to the findings of other studies of European bats during the COVID-19 pandemic, none of which demonstrated SARS-CoV-2 infection including from, three common pipistrelles in the UK [65], 503 samples from 20 bat species including 58 lesser horseshoe bats in Poland [66], 197 samples from five bat species including 82 samples from lesser horseshoe bats, 104 from greater horseshoe bats and five from Mediterranean horseshoe bats (Rhinolophus euyale) from Sochi in Russia [36] and 53 lesser horseshoe bats in the UK [41].…”

Circulation of SARS-CoV–Related Coronaviruses and Alphacoronaviruses in Bats from Croatia

“…Horseshoe bats, populating Asia, Europe, and Africa, are considered to be natural reservoirs of sarbecoviruses that belong to the Betacoronavirus (betaCoV) genus. Most epidemiological studies of sarbecoviruses originate from China [2,4,[6][7][8][9][10]; however, there is a growing number of reports from other countries [5,[11][12][13][14][15][16][17], including Europe [18][19][20][21][22][23].…”

“…Until 30 November 2022, World Organisation for Animal Health (WOAH) recorded 695 cases of SARS-CoV-2 infections in 26 animal species [24]. In the Netherlands and Denmark, SARS-CoV-2 was transmitted to farm-kept minks, then spread to other domestic mink populations, and then transmitted back to farm workers [23,25,26]. More recent cases include hamster-to-hamster-to-human transmission [27], deer-to-deer [28], and humanto-cat-to-human transmission [29].…”