Viral infection detection using metagenomics technology in six poultry farms of eastern China

Abstract

With rapidly increasing animal pathogen surveillance requirements, new technologies are needed for a comprehensive understanding of the roles of pathogens in the occurrence and development of animal diseases. We applied metagenomic technology to avian virus surveillance to study the main viruses infecting six poultry farms in two provinces in eastern China. Cloacal/throat double swabs were collected from 60 birds at each farm according to a random sampling method. The results showed that the method could simultaneously detect major viruses infecting farms, including avian influenza virus, infectious bronchitis virus, Newcastle disease virus, rotavirus G, duck hepatitis B virus, and avian leukemia virus subgroup J in several farms. The test results were consistent with the results from traditional polymerase chain reaction (PCR) or reverse transcription-PCR analyses. Five H9N2 and one H3N8 avian influenza viruses were detected at the farms and were identified as low pathogenic avian influenza viruses according to HA cleavage sites analysis. One detected Newcastle disease virus was classified as Class II genotype I and avirulent type according to F0 cleavage sites analysis. Three avian infectious bronchitis viruses were identified as 4/91, CK/CH/LSC/99I and TC07-2 genotypes by phylogenetic analysis of S1 genes. The viral infection surveillance method using metagenomics technology enables the monitoring of multiple viral infections, which allows the detection of main infectious viruses.

Simple and visible detection of duck hepatitis B virus in ducks and geese using loop-mediated isothermal amplification

“…However, DHBV has been reported to not only infect ducks but also to cause some diseases in geese (Funk et al, 2007 ). The infection rate of DHBV is very high in eastern China based on avian virus surveillance (Qiu et al, 2019 ). The characteristics of DHBV call for increased attention to related diseases.…”

Metagenomics and its relevance to animal diseases and gut health

“…From 2009 to 2017 almost 20 animal and zoonotic viral disease agents were diagnosed using metagenomic technique (Hoeper et al, 2017). A limited scale metagenomics-based pathogen surveillance study on 6 poultry farms detected the main infectious viruses of poultry, and it analyzed Indian Journal of Animal Health, Special Issue, December, 2020 the subtypes, genotypes and pathogenicity of some detected viruses (Qiu et al, 2019). Subsequent to the metagenomic investigation of astroviruses in enteric disorders in humans (Finkbeiner et al, 2009), a divergent strain was demonstrated to be associated with the brain tissue of shaking mink syndrome affected minks (Blomström et al, 2010).…”

Metagenomic characterization reveals virus coinfections associated with Newcastle disease virus among poultry in Kenya

“…Several approaches have been employed to study the epidemiology of viral infections affecting poultry, including pathogen surveillance and tracking the molecular epidemiology of pathogens [12]. Previous methods employed polymerase chain reaction (PCR)-based methods, especially reverse transcription PCR [12]. Using this strategy, several viruses have been implicated in poultry diseases, including astroviruses [13], parvoviruses [14], reoviruses [15], rotaviruses [16], paramyxoviruses [17], and coronaviruses [18,19].…”

“…Currently, metagenomics-based detection methods are being applied successfully to characterize viral populations in different hosts and environments [20]. This has facilitated the discovery of many novel viral agents from different types of tissues, including the gastrointestinal tract and the oral-pharyngeal regions in poultry and other livestock [12,[20][21][22][23][24][25]. The popularity of these techniques is largely due to their high sensitivity and wide coverage as they target the entire genome [12,25].…”