Metagenomic characterisation of avian parvoviruses and picornaviruses from Australian wild ducks

Abstract

Ducks can shed and disseminate viruses and thus play a role in cross-species transmission. In the current study, we detected and characterised various avian parvoviruses and picornaviruses from wild Pacific black ducks, Chestnut teals, Grey teals and Wood ducks sampled at multiple time points from a single location using metagenomics. We characterised 46 different avian parvoviruses belonging to three different genera Dependoparvovirus, Aveparvovirus and Chaphamaparvovirus, and 11 different avian picornaviruses tentatively belonging to four different genera Sicinivirus, Anativirus, Megrivirus and Aalivirus. Most of these viruses were genetically different from other currently known viruses from the NCBI dataset. The study showed that the abundance and number of avian picornaviruses and parvoviruses varied considerably throughout the year, with the high number of virus reads in some of the duck samples highly suggestive of an active infection at the time of sampling. The detection and characterisation of several parvoviruses and picornaviruses from the individual duck samples also suggests co-infection, which may lead to the emergence of novel viruses through possible recombination. Therefore, as new and emerging diseases evolve, it is relevant to explore and monitor potential animal reservoirs in their natural habitat.

Figure 1

Phylogenetic analysis of partial NS1 amino acid sequences of duck parvoviruses and representative viruses from subfamily Parvovirinae. Parvoviruses belonging to the genera Dependoparvirus and Aveparvovirus from the subfamily Parvovirinae were detected in the Australian ducks from the current study. The evolutionary history was inferred by using the Maximum Likelihood method based on the LG+G model. The analysis involved 34 amino acid sequences. All positions containing gaps and missing data were eliminated. There was a total of 235 amino acid positions in the final dataset. The robustness of different nodes was assessed by bootstrap analysis using 1,000 replicates for amino acid alignments. The numbers at the nodes represent bootstrap values and only bootstrap values at or above 60% are shown. The genera from subfamily Parvovirinae with viruses from the duck samples is shown in blue colour. Pacific black duck viruses are shown with black triangle.

Figure 2

Phylogenetic analysis of non-structural amino acid sequence of duck chaphamaparvoviruses (CPaV) encoding complete NS1 protein and representative viruses from subfamily Hamaparvovirinae. Parvoviruses belonging to the genus Chaphamaparvovirus from the subfamily Hamaparvovirinae were detected in the Australian ducks from the current study. The evolutionary history was inferred by using the Maximum Likelihood method based on the LG+G+F model. The analysis involved 31 amino acid sequences. All positions containing gaps and missing data were eliminated. There was a total of 442 amino acid positions in the final dataset. The robustness of different nodes was assessed by bootstrap analysis using 1,000 replicates for amino acid alignments. The numbers at the nodes represent bootstrap values and only bootstrap values at or above 60% are shown. The genus from subfamily Hamaparvovirinae with viruses from the duck samples is shown in blue colour. Pacific black duck viruses are shown with black triangle and Chestnut teal viruses are with brown square.

Figure 3

Phylogenetic analysis of the non-structural amino acid sequence of duck chaphamaparvoviruses (CPaV) encoding complete NS1 protein. The evolutionary history was inferred by using the Maximum Likelihood method based on the model LG+G+I+F. The analysis involved 25 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 525 positions in the final dataset. The robustness of different nodes was assessed by bootstrap analysis using 1,000 replicates for amino acid alignments. The numbers at the nodes represent bootstrap values and only bootstrap values at or above 60% are shown. The highlighted section shows duck CPaV lineages/clusters. Pacific black duck virus is shown with (black triangle) and Chestnut teal viruses are shown with (brown square).

Figure 4

Phylogenetic analysis of the partial RdRp region of the duck picornaviruses and of representative viruses from Picornaviridae family. The picornavirus sequences detected in the Australian ducks from the current study tentatively belong to four different genera: Sicinivirus, Anativirus, Megrivirus and Aalivirus. The evolutionary history was inferred by using the Maximum Likelihood method based on the LG+G+I model. The analysis involved 129 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 313 amino acid positions in the final dataset. The robustness of different nodes was assessed by bootstrap analysis using 1,000 replicates for amino acid alignments. The numbers at the nodes represent bootstrap values and only bootstrap values at or above 60% are shown. Each of the genus from Picornaviridae is shown with viruses from the duck samples in blue colour. Pacific black duck viruses are shown in black triangle, Chestnut teal viruses in brown square and Wood duck viruses in green circle. Supergroup 1 consists of viruses from genus Ailurivirus, Aphthovirus, Bopivirus, Cardiovirus, Cosavirus, Erbovirus, Hunnivirus, Malagasivirus, Mischivirus, Mosavirus, Mupivirus, Senecavirus, Teschovirus, Torchivirus and Tottorivirus. Supergroup 5 consists of viruses from genus Crahelivirus, Fipivirus, Gruhelivirus, Hepatovirus, Rohelivirus and Tremovirus. Supergroup 6 contains virus from the genus Harkavirus. Supergroup 7 consists of virus from the genus Ampivirus.

Figure 5

Phylogenetic analysis of the amino acid sequence of the RdRp, Helicase, Peptidase C3 of Aalivirus (AaV) sequences. Phylogenetic analysis shows three new species in the genus Aalivirus. The evolutionary history was inferred by using the Maximum Likelihood method based on the model LG+G. The analysis involved 10 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 794 amino acid positions in the final dataset. MH453803.1 Duck Avehepatovirus-like virus is an unassigned virus. The robustness of different nodes was assessed by bootstrap analysis using 1,000 replicates for amino acid alignments. The numbers at the nodes represent bootstrap values and only bootstrap values at or above 60% are shown. Pacific black duck viruses are shown in black triangle and Chestnut teal viruses in brown square.