A novel group of avian astroviruses in wild aquatic birds

Abstract

Using a pan-astrovirus reverse transcription-PCR assay, a great diversity of novel avastroviruses was detected from wild bird and poultry samples. Two groups of astroviruses detected from wild birds are genetically related or highly similar to previously known viruses in poultry. Most interestingly, a novel group of astroviruses was detected in wild aquatic birds. Our results also reveal that different groups of astroviruses might have difference host ranges. This study has expanded our understanding regarding avastrovirus ecology.

Fig 1

Phylogenetic analysis on RdRp genes of astroviruses using PhyML. Avastroviruses can be divided into 3 major groups. Astroviruses detected from this study (n = 92), excluding 14 viral sequences that yielded poor sequencing reads, were included in the analysis (highlighted in bold type). Viruses detected from northern pintail, northern shoveler, common teal, and Eurasian wigeon are highlighted in green, red, blue, and brown, respectively. The sampling site (for wild birds, KG = KFBG, Hong Kong, KH = Cambodia, and MPJ or MPK = Mai Po, Hong Kong; for poultry, HK = Hong Kong and SL = Sri Lanka), bird species (if available), and sampling time (indicated as last two digits of year, month, and day [YYMMDD]) of each sample is shown. Approximate likelihood ratio test (aLRT) values of major branches with values > 0.7 are indicated. GenBank accession numbers of retrieved genes are indicated in parentheses.

Fig 2

Mean amino acid sequence identities of representative viruses within and between the three major groups of avastroviruses were estimated. Standard deviations of the values are also indicated. The number of representative sequences used in each group is indicated in parentheses. An asterisk indicates that the intragroup sequence identity was found to be significantly higher than the relevant intergroup sequence identities (P < 0.0005, Student's t test). Viruses were selected for the analysis as follows. (A) Group 1, TAstV1, KH08-0856/lesser whistling duck, MPJ0597/northern shoveler, DuHV3, MPK601/Eurasian wigeon, TAstV2, DuAstV, MPJ0554/northern shoveler, MPK514/common teal, ChAstV2, and ChAstV1; group 2, MPJ0918/Tringa nebularia, KH08-1314/pond heron, KH08-1279/pond heron, MPJ0829/Platalea minor, KH08-1285/pond heron, wood pigeon astrovirus strain 06/15660-1, feral pigeon astrovirus strain 03/603-5, KG703/spotted dove, ANV1, and ANV2; group 3, MPJ0552/northern shoveler, MPJ1484/northern shoveler, MPJ1561/Eurasian wigeon, MPJ1332/northern pintail, MPJ0126/common teal, and MPJ1350/northern pintail. (B) Group 1, TAstV, chicken AstV GA2011, duck AstV DA08, TAstV3, and TAstV2; group 2, KH08-1279/pond heron, ANV China, ANV1, ANV2, KG119/rock dove, wood pigeon astrovirus 06/15660-1, and feral pigeon astrovirus 03/603-5; group 3, MPJ1332/northern pintail/capsid, MPJ1442/northern pintail/capsid, and MPJ1433/northern pintail.

Fig 3

Phylogenetic analysis of the 5′ region of capsid genes (1,458 bp) of avastroviruses using PhyML. The capsid gene of human astrovirus was used as an outgroup. aLRT values of major branches with values > 0.7 are indicated. Due to the lack of sequence homology of the 3′ region of capsid genes (∼1,000 bp), this was removed. The findings determined for the three major groups of avastroviruses shown in the analysis of RdRp genes were supported by this analysis of capsid genes. Novel viruses detected from wild birds in this study are indicated in bold type. GenBank accession numbers of retrieved genes are indicated in parentheses.