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Exploring the cause of diarrhoea and poor growth in 8–11-week-old pigs from an australian pig herd using metagenomic sequencing
journal contribution
posted on 2021-08-01, 00:00 authored by Tarka Bhatta, Anthony Chamings, Soren AlexandersenSoren AlexandersenDiarrhoea and poor growth among growing pigs is responsible for significant economic losses in pig herds globally and can have a wide range of possible aetiologies. Next generation sequencing (NGS) technologies are useful for the detection and characterisation of diverse groups of viruses and bacteria and can thereby provide a better understanding of complex interactions among microorganisms potentially causing clinical disease. Here, we used a metagenomics approach to identify and characterise the possible pathogens in colon and lung samples from pigs with diarrhoea and poor growth in an Australian pig herd. We identified and characterized a wide diversity of porcine viruses including RNA viruses, in particular several picornaviruses—porcine sapelovirus (PSV), enterovirus G (EV-G), and porcine teschovirus (PTV), and a porcine astrovirus (PAstV). Single stranded DNA viruses were also detected and included parvoviruses like porcine bocavirus (PBoV) and porcine parvovirus 2 (PPV2), porcine parvovirus 7 (PPV7), porcine bufa virus (PBuV), and porcine adeno-associated virus (AAV). We also detected single stranded circular DNA viruses such as porcine circovirus type 2 (PCV2) at very low abundance and torque teno sus viruses (TTSuVk2a and TTSuVk2b). Some of the viruses detected here may have had an evolutionary past including recombination events, which may be of importance and potential involvement in clinical disease in the pigs. In addition, our metagenomics data found evidence of the presence of the bacteria Lawsonia intracellularis, Brachyspira spp., and Campylobacter spp. that may, together with these viruses, have contributed to the development of clinical disease and poor growth.
History
Journal
VirusesVolume
13Issue
8Article number
1608Pagination
1 - 21Publisher
MDPILocation
Basel, SwitzerlandPublisher DOI
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1999-4915eISSN
1999-4915Language
EnglishPublication classification
C1 Refereed article in a scholarly journalUsage metrics
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Keywords
abundancebacteriaBOCA-LIKE VIRUSCOMPLETE GENOME SEQUENCEdiseaseENTEROVIRUS-GGENETIC DIVERSITYHIGH PREVALENCEINFECTING PIGSLife Sciences & Biomedicinemetagenomic sequencingMOLECULAR CHARACTERIZATIONphylogenetic analysisPORCINE CIRCOVIRUS TYPE-2SAPELOVIRUS-AScience & TechnologyTENO SUS VIRUSVirologyvirusesMicrobiology
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