Duck hepatitis a virus: Full-length genome-based phylogenetic and phylogeographic view during 1986-2020

Duck hepatitis A virus (DHAV) is one of key pathogens for duck viral hepatitis, especially in Asian duck industry. Currently, two main genotypes (DHAV-1 and -3) exist. To explore insightfully the evolutionary character, we assessed the available 141 full-length genome sequences of DHAV isolated in 1986-2020 globally and divided DHAV-1 and DHAV-3 into further seven (DHAV-1 a-g) and five (DHAV-3 a-e) sub-clades, respectively. Phylogenetic and phylogeographic network analyses indicated great genetic diversity of DHAV identified in China, where the DHAV-1 cluster and DHAV-3 cluster were linked by virus strain HDHV1-BJ (GenBank ID: FJ157172.1) and Du_CH_LSD_090612 (GenBank ID: JF828995.1) via a long mutational branch and intermediate strains. Several strains previously identified as DHAV-1 according to the partial gene sequences were actually clustered within DHAV-3 in full-length genome-based analysis. Furthermore, we identified 32 recombination events across virus genome with the recombination hotspot at the 5' end and upstream of the capsid coding region. The highest variability of DHAV polyprotein was shown at the upstream region of the N terminus P-loop region, e.g., amino acids 672-716, followed by the aa 334-359 in the Capsid encoding region. The results presented here provides a robust insight into the genetic exchange patterns of DHAV genomes during the past decades, which may be used to map the evolutionary history and facilitate preventive measures of DHAVs.

First complete genome characterization of duck plague virus from India

In this study, we report the complete genome sequencing of the Duck plague virus from India for the first time. The sequencing was done on the MinION nanopore sequencer from Oxford Nanopore Technologies. The closest relative is the European strain 2085v, with 99.98 and 99.8% identity at the amino acid and nucleotide level respectively. Moreover, 72 out of 77 ORFs are completely conserved between the 2 strains. The high similarity with the European strain over the only three other pathogenic strains reported from China points to the circulation of European strain in India. The fly pathways of migratory birds and co-habitation with native species being a probable reason. More complete genome data from diverse sampling locations are needed to characterize the genomic features, develop diagnostics, vaccines, and understand the evolution of the virus.

Molecular analysis of goose parvovirus field strains from a Derzsy's disease outbreak reveals local European-associated variants

Since its first recognition in the early 1960s, Derzsy's disease has caused significant economic losses in the goose meat industry through the world. Today, Derzsy's disease still maintains its importance for small-scale waterfowl farming, despite not having a significant impact on public health. In the present study, we investigated the distribution of goose parvovirus (GPV) and its potential variants from a 2019 outbreak in Turkey. Tissue samples were obtained from infected eggs and goslings that were raised in distinct farming areas of the various provinces. For this purpose, a novel primer set for amplification of a 630-bp region of VP3 was designed to confirm GPV infection by conventional PCR method. A 4709-base nucleotide sequence including the structural, non-structural, and 5' inverted terminal repeat regions was obtained from three samples from the Central Anatolian region. Multiple sequence comparisons and phylogenetic analysis demonstrated that the field strains clustered with European group 2 and contained a series of unique amino acid substitutions that might affect the virulence of the virus. These results confirmed that European-related field strains caused the outbreak in Asia Minor, and this might assist in understanding the circulation of GPV in Asia and Europe.

Duck hepatitis A virus 1 has lymphoid tissue tropism altering the organic immune responses of mature ducks

Duck hepatitis A virus 1 (DHAV-1) is a highly prevalent pathogen within adult ducks causing acute as well as chronic hepatitis which closely emulates the progression of human hepatitis. However, the underlying mechanisms of DHAV-1 persistence and the pathogenesis of chronic liver disease are not well defined. The association between hematopoietic reservoirs of virus and persistent infection is increasingly concerning. Here, we explored the ability of lymphoid replication of DHAV-1 and the effect on immunity. We found that DHAV-1 was able to infect and replicate productively in the lymphoid organs of model ducks, persisting over 6 months. Moreover, a significant correlation of viral loads between these organs and blood was found, documenting a major contribution of lymphoid replication to DHAV-1 viraemia. Along with viral replication, the mRNA of PRRs and immune-related cytokines was up-regulated in these organs during the early phase of infection, showing tissue-dependent expression patterns but all inclining towards Th2 responses due to the consistently higher level of IL-4 than IL-2 and IFN-γ. Additionally, the expression of CCL19, CCL21, MHC-I and MHC-II, which are involved in T cell homing to the periphery and priming, was dysmodulated. Our data indicate that DHAV-1 possesses lymphoid tissue tropism, contributing to persistent infection and chronic hepatitis via altering the early endogenous transcription of immune-related genes and thereby perturbing organic immunity. These results may be useful to develop novel strategies to treat chronic viral hepatitis based on stimulation of the early innate system and regulation of T-cell trafficking.