Diversity of bat astroviruses in Lao PDR and Cambodia

Abstract

Astroviruses are known to infect humans and a wide range of animal species, and can cause gastroenteritis in their hosts. Recent studies have reported astroviruses in bats in Europe and in several locations in China. We sampled 1876 bats from 17 genera at 45 sites from 14 and 13 provinces in Cambodia and Lao PDR respectively, and tested them for astroviruses. Our study revealed a high diversity of astroviruses among various Yangochiroptera and Yinpterochiroptera bats. Evidence for varying degrees of host restriction for astroviruses in bats was found. Furthermore, additional Pteropodid hosts were detected. The astroviruses formed distinct phylogenetic clusters within the genus Mamastrovirus, most closely related to other known bat astroviruses. The astrovirus sequences were found to be highly saturated indicating that phylogenetic relationships should be interpreted carefully. An astrovirus clustering in a group with other viruses from diverse hosts, including from ungulates and porcupines, was found in a Rousettus bat. These findings suggest that diverse astroviruses can be found in many species of mammals, including bats.

Keywords: Astroviruses; Bats; Cambodia; Genetic diversity; Lao PDR.

Graphical abstract

Fig. 1

Relationship of astroviruses constructed using a multiple alignment of 112 amino acids of the partial RdRp gene of detected astroviruses and selected members of Mamastrovirus. The tree was constructed using the Neighbor-Joining method. Bootstrap values were determined by 1000 replicates. PoAstV: Porcine astrovirus (astV); BovAstV: bovine astVs; HAstV: human astV; DromAstV: dromadery astV; PcpAstV: porcupine astV; AvAstV: avian astV. The genus of bat host is given for Bat astroviruses, i.e. Min: Miniopterus; Hip: Hipposideros; Tph: Taphozous; Pip: Pipistrellus; Tyl: Tylonycterys; Sco: Scotophilus; Rs: Rousettus; Myo: Myotis; Mgd: Megaderma; Eon: Eonycteris; Ia: Ia; Rhin: Rhinolophus. For each detected sequence, the strain, sample name and bat genus were included in the nomenclature. For clarity, strains named “PREDICT-MAstV-xx” are abbreviated as “MAstV-xx” in the tree. Accession numbers of the sequences are listed in the Supplementary Table 2. An avian astrovirus (AB033998) is used as outgroup. The tree was constructed using the Neighbor-Joining method. Bootstrap values were determined by 1000 replicates. PoAstV: Porcine astrovirus (astV); BovAstV: bovine astVs; HAstV: human astV; DromAstV: dromadery astV; PcpAstV: porcupine astV; AvAstV: avian astV. The genus of bat host is given for Bat astroviruses, i.e. Min: Miniopterus; Hip: Hipposideros; Tph: Taphozous; Pip: Pipistrellus; Tyl: Tylonycterys; Sco: Scotophilus; Rs: Rousettus; Myo: Myotis; Mgd: Megaderma; Eon: Eonycteris; Ia: Ia; Rhin: Rhinolophus. For each detected sequence, the strain, sample name and bat genus were included in the nomenclature. For clarity, strains named “PREDICT-MAstV-xx” are abbreviated as “MAstV-xx” in the tree. Accession numbers of the sequences are listed in the Supplementary Table 2. An avian astrovirus (AB033998) is used as outgroup.

Fig. 2

Relationship of the partial ORF1b and ORF2 sequences of the bat astrovirus PREDICT-MAstV-13_A91_Rs to other species of astroviruses. a) Relationship of the partial ORF1b (~ 230 aa) sequence of the bat astrovirus PREDICT-MAstV-13_A91_Rs to other species of astroviruses. b) Relationship of the partial ORF2 (~ 380 aa) sequence of the bat astrovirus PREDICT-MAstV-13_A91_Rs to other species of astroviruses. Alignments were based on the encoded amino acid sequences. Trees were constructed using the Neighbor-Joining method. Five other bat astrovirus sequences (BatAstV-LD38, BatAstV-LS11 and BatAstV-AFCD11, BatAstV-AFCD57, BatAstV-LD77) corresponding to groups 2, 5, and 6 in Fig. 1, are included. The strain PREDICT-MAstV-13_A91_Rs is marked with a bullet. Astroviruses are abbreviated as follows: PoAstV: Porcine astrovirus (astV); BatAstV: bat astV; BovAstV: bovine astVs; HAstV: human astV; DromAstV: dromadery astV; PcpAstV: porcupine astV; AvAstV: avian astV. The genus of bat host is given for Bat astroviruses, i.e. Min: Miniopterus; Hip: Hipposideros; Tph: Taphozous; Pip: Pipistrellus. An avian astrovirus (AB033998) was used as outgroup.