Avian viral surveillance in Victoria, Australia, and detection of two novel avian herpesviruses

Abstract

Viruses in avian hosts can pose threats to avian health and some have zoonotic potential. Hospitals that provide veterinary care for avian patients may serve as a site of exposure of other birds and human staff in the facility to these viruses. They can also provide a useful location to collect samples from avian patients in order to examine the viruses present in wild birds. This study aimed to investigate viruses of biosecurity and/or zoonotic significance in Australian birds by screening samples collected from 409 birds presented to the Australian Wildlife Health Centre at Zoos Victoria's Healesville Sanctuary for veterinary care between December 2014 and December 2015. Samples were tested for avian influenza viruses, herpesviruses, paramyxoviruses and coronaviruses, using genus- or family-wide polymerase chain reaction methods coupled with sequencing and phylogenetic analyses for detection and identification of both known and novel viruses. A very low prevalence of viruses was detected. Columbid alphaherpesvirus 1 was detected from a powerful owl (Ninox strenua) with inclusion body hepatitis, and an avian paramyxovirus most similar to Avian avulavirus 5 was detected from a musk lorikeet (Glossopsitta concinna). Two distinct novel avian alphaherpesviruses were detected in samples from a sulphur-crested cockatoo (Cacatua galerita) and a tawny frogmouth (Podargus strigoides). Avian influenza viruses and avian coronaviruses were not detected. The clinical significance of the newly detected viruses remains undetermined. Further studies are needed to assess the host specificity, epidemiology, pathogenicity and host-pathogen relationships of these novel viruses. Further genome characterization is also indicated, and would be required before these viruses can be formally classified taxonomically. The detection of these viruses contributes to our knowledge on avian virodiversity. The low level of avian virus detection, and the absence of any viruses with zoonotic potential, suggests low risk to biosecurity and human health.

Fig 1. PhyML maximum likelihood phylogenetic tree of avian alphaherpesviruses.

Generated from a ClustalW2 alignment [59] of the partial DNA polymerase gene sequences of Podargid alphaherpesvirus 1 and Cacatuid alphaherpesvirus 1 with published avian alphaherpesvirus nucleotide sequences available in GenBank, with the two novel alphaherpesviruses detected in this study highlighted in bold [60]. The GenBank accession numbers for sequences used are included in the tip labels, and Macropodid alphaherpesvirus 1 (highlighted in italics) is included as an outgroup. Branching with greater than 50% support from 100 bootstrap replicates is indicated at major node points. The distances indicated by black horizontal lines correspond to genetic distances, with the scale bar representing nucleotide substitutions/site.

Fig 2. Unrooted maximum likelihood phylogenetic tree for the family Herpesviridae.

Generated from a ClustalW2 alignment of amino acid translations of partial DNA polymerase gene sequences from 40 representative herpesviruses retrieved from GenBank from the three subfamilies: Alphaherpesvirinae (α), Betaherpesvirinae (β) and Gammaherpesvirinae (γ) from a range of host species, and including the two novel alphaherpesviruses detected in this study (highlighted in bold) [60]. The GenBank accession numbers for sequences used are as follows: Accipitrid alphaherpesvirus 1 AY571851; Alcelaphine gammaherpesvirus 1 AF005370; Anatid alphaherpesvirus 1 EF643560; Bovine alphaherpesvirus 1 X94677; Bovine alphaherpesvirus 2 AF181249; Bovine gammaherpesvirus 4 AF031811; Bovine gammaherpesvirus 6 AF031808; Cacatuid alphaherpesvirus 1 MF576271; Columbid alphaherpesvirus 1 AF141890; Elephantid betaherpesvirus 1 AF322977; Elephantid gammaherpesvirus 3 DQ238845; Equid alphaherpesvirus 1 KF434378; Equid gammaherpesvirus 2 NC001650; Equid alphaherpesvirus 4 KT324743; Felid alphaherpesvirus 1 KR296657; Fregatid alphaherpesvirus 1 EU867220; Gallid alphaherpesvirus 1 NC006623; Gallid alphaherpesvirus 2 AF147806; Gallid alphaherpesvirus 3 HQ840738; Gaviid alphaherpesvirus 1 GU130289; Human alphaherpesvirus 1 HQ123098; Human alphaherpesvirus 3 X04370; Human betaherpesvirus 5 NC006273; Human betaherpesvirus 6 X83413; Macacine gammaherpesvirus 5 AF029302; Macropodid alphaherpesvirus 1 NC029132; Macropodid gammaherpesvirus 3 EF467663; Meleagrid alphaherpesvirus 1 AF291866; Murid betaherpesvirus 2 AY728086; Passerid alphaherpesvirus 1 AF520812; Phascolarctid gammaherpesvirus 2 JQ996387; Phocid alphaherpesvirus 1 PHU92269; Phoenicopterid alphaherpesvirus 1 KP244360; Podargid alphaherpesvirus 1 MF576272; Psittacid alphaherpesvirus 1 AY372243; Psittacid alphaherpesvirus 2 AY623124; Psittacid alphaherpesvirus 3 JX028240; Saimiriine gammaherpesvirus 2 AJ410493; Spheniscid alphaherpesvirus 1 KJ720217; Spheniscid alphaherpesvirus 2 LT608135; Suid alphaherpesvirus 1 BK001744; Suid betaherpesvirus 2 AF268042. Percentage support from 100 bootstrap replicates is indicated at major branch points. The scale bar represents amino acid substitutions/site.

Fig 3. Phylogenetic tree for the genus avulvirus of the family Paramyxoviridae based on partial RNA-dependent RNA polymerase gene sequences.

Maximum likelihood phylogenetic tree constructed using PhyML from a ClustalW2 alignment of the partial RNA-dependent RNA polymerase (large polymerase or L protein) gene sequences of the avian avulavirus detected from a musk lorikeet (Glossopsitta concinna) in this study (unclassified avian avulavirus strain musk lorikeet/Melbourne/ML22-141263/2014; highlighted in bold) and published paramyxovirus sequences retrieved from GenBank [60]. The GenBank accession numbers for sequences used are indicated in brackets in the tip labels. Human rubulavirus 2 (highlighted in italics) is included as an outgroup. Branching with greater than 50% support from 100 bootstrap replicates is indicated at major node points. The distances indicated by black horizontal lines correspond to genetic distances, with the scale bar representing nucleotide substitutions/site.