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.

Keywords: Poland; SARS-related CoV; bats; coronaviruses; phylogenetics; prevalence.

Figure 1

Map showing the voivodeships of Poland and the origin of bat samples included in the study with their RT-PCR results (black: negative; red: positive (alphaCoV); green: positive (SARS-related CoV)). The number of positive vs. total samples per region is indicated. AlphaCoVs were detected in bat feces collected in June 2020 at Warmian-Masurian (WM, accession number ON873766) and in September 2021 at Mazovian (MA, accession number ON873768). SARS-related CoVs were detected in bat samples collected in May 2021 and May 2022 at Lower Silesia (LS), accession numbers: ON873767, ON873769, and ON873770. Abbreviations: MA: Mazovian; LS: Lower Silesia; WP: Greater Poland; SL: Silesia; PM: Pomerania; LD: Łódź; MP: Lesser Poland; ZP: West Pomerania; LB: Lubusz; KP: Kuyavian-Pomeranian; OP: Opole; PD: Podlaskie; SW: Świętokrzyskie; WM: Warmian-Masurian; PK: Subcarpathian; LU: Lublin.

Figure 2

Phylogenetic tree based on the 379 bp-long nucleotide fragment of the RNA-dependent RNA polymerase gene of BtCoVs selected as the most homologous (A) and BtCoVs detected in Poland and the other distinct CoVs (B), generated using the neighbor-joining method with the Kimura2-parameter model and MEGA 5 software. Green circles indicate SARS-related CoVs detected in horseshoe bats in Poland, whereas red circles refer to alphacoronaviruses detected in Myotis bats in Poland. Bootstrap values (1000 replicates) over 70% indicating significant support for the tree topology are shown next to the branches. Sequences of delta- and gamma CoVs isolated from poultry in Poland were used as the outgroup in Figure 2A.

Figure 2

Phylogenetic tree based on the 379 bp-long nucleotide fragment of the RNA-dependent RNA polymerase gene of BtCoVs selected as the most homologous (A) and BtCoVs detected in Poland and the other distinct CoVs (B), generated using the neighbor-joining method with the Kimura2-parameter model and MEGA 5 software. Green circles indicate SARS-related CoVs detected in horseshoe bats in Poland, whereas red circles refer to alphacoronaviruses detected in Myotis bats in Poland. Bootstrap values (1000 replicates) over 70% indicating significant support for the tree topology are shown next to the branches. Sequences of delta- and gamma CoVs isolated from poultry in Poland were used as the outgroup in Figure 2A.