Genetic diversity and phylogenetic analysis of newly discovered bat astroviruses in Korea

Abstract

Bats have been identified as a natural reservoir for several potentially zoonotic viruses. Recently, astroviruses have been reported in bats in many countries, but not Korea. We collected 363 bat samples from thirteen species at twenty-nine sites in Korea across 2016 and tested them for astrovirus. The detection of the RNA-dependent RNA polymerase (RdRp) gene in bat astroviruses was confirmed in thirty-four bats across four bat species in Korea: twenty-five from Miniopterus fuliginosusi, one from Myotis macrodactylus, four from M. petax, and four from Rhinolophus ferrumequinum. The highest detection rates for astrovirus were found in Sunchang (61.5%, 8/13 bats), and in the samples collected in April (63.2%, 12/19 bats). The amino acid identity of astroviral sequences identified from bat samples was ≥ 46.6%. More specifically, the amino acid identity within multiple clones from individual bats was ≥ 50.8%. Additionally, the phylogenetic topology between astroviruses from different bat families showed a close relationship. Furthermore, phylogenetic analysis of the partial ORF2 sequence of bat astroviruses was found to have a maximum similarity of 73.3-74.8% with available bat astrovirus sequences. These results indicate potential multiple-infection by several bat astrovirus species in individual bats, or hyperpolymorphism in the astrovirus strains, as well as the transmission of astroviruses across bat families; furthermore, our phylogenetic analysis of the partial ORF2 implied that a novel astrovirus may exist. However, the wide diversity of astroviral sequences appeared to have no significant correlation with bat species or the spatiotemporal distribution of Korean bat astroviruses.

Novel viruses detected in bats in the Republic of Korea

“…The coexistence of at least two distinct CoV genomes in one bat was reported in Lau et al 8 and Chu et al 28 . In addition, a genetic hyperpolymorphism between astrovirus haplotypes detected from one bat was reported in Lee et al 7 . In this study, we first identified the multiple infection of viruses of different genera in an individual bat.…”

“…In 2015, the first bat-derived viruses in the Republic of Korea (ROK) were discovered from bat fecal samples: coronaviruses, group H rotavirus, bunyavirus, and Banna virus 14 . Following this, alphacoronavirus, betacoronavirus, astrovirus, and paramyxovirus have also recently been reported 7,19,20 . Considering that the viruses detected in bats globally belong to more than 29 families 17 , it is estimated that only a small number of bat viruses have Detection of bat picornaviruses within various genera from 16BF77.…”

“…In addition, the shredded viral sequences from NGS were concatenated by a primer designed based on the metagenomic sequencing results obtained in this study ( Supplementary Table S7). Extraction and amplification of the total RNA from each individual sample was performed as previously described by Lee et al 7 . Amplification conditions were as follows: initial incubation at 94 ℃ for 1 min, followed by 35 cycles of denaturation 94 ℃ for 30 s, annealing at 50-58 ℃ for 30 s, and extension at 72 ℃ for 30 s, with a final extension at 72 ℃ for 5 min in a Mastercycler (Eppendorf, Hamburg, Germany).…”

“…In particular, infections of multiple viruses with various genotypes and haplotypes have been reported in an individual bat. Hyperpolymorphic astrovirus haplotypes, which have amino acid differences of approximately 50%, were identified in an individual bat, and the co-infection of coronaviruses with at least two distinct genotypes were also reported in the same bat 7,8 . The wide genetic diversity of bat viruses is known to be due to their unique ecological characteristics, such as frequently high population densities and crowded roosting behaviour 1,9 .…”

First Detection of Bat Astroviruses (BtAstVs) among Bats in Poland: The Genetic BtAstVs Diversity Reveals Multiple Co-Infection of Bats with Different Strains

“…They may carry both host-restricted astroviruses as well as more diverse strains closely related to other members of the mamastrovirus genus, such as fox, murine, ovine, mink and human AstVs and even avian astroviruses of the avastrovirus genus. Phylogenetic analyses of the partial genome revealed a significant strain diversity of bat astroviruses forming numerous recognized and proposed species [ 6 , 14 , 15 , 16 , 17 ], supposedly generated both by intraspecies and interspecies recombination as well as interspecies transmission [ 18 ]. The high prevalence of diverse astrovirus strains from multiple hosts suggests that bats play a key role in astrovirus diversity and interspecies transmission [ 18 ].…”