Viral communities associated with porcine respiratory disease complex in intensive commercial farms in Sichuan province, China

Abstract

Porcine respiratory disease complex (PRDC), a common piglet disease, causes substantive economic losses in pig farming. To investigate the viral diversity associated with PRDC, the viral communities in serum and nasal swabs from 26 PRDC-affected piglets were investigated using metagenomics. By deep sequencing and de novo assembly, 17 viruses were identified in two pooled libraries (16 viruses from serum, nine from nasal swabs). Porcine circovirus (PCV)-2, porcine reproductive and respiratory syndrome virus (PRRSV) and pseudorabies virus, all commonly associated with PRDC, were identified in the two pooled samples by metagenomics, but most viruses comprised small linear and circular DNAs (e.g. parvoviruses, bocaviruses and circoviruses). PCR was used to compare the detection rates of each virus in the serum samples from 36 PRDC-affected piglets versus 38 location-matched clinically healthy controls. The average virus category per sample was 6.81 for the PRDC-affected piglets and 4.09 for the controls. Single or co-infections with PCV-2 or PRRSV had very high detection rates in the PRDC-affected piglets. Interestingly, porcine parvovirus (PPV)-2, PPV-3, PPV-6 and torque teno sus virus 1a were significantly associated with PRDC. These results illustrate the complexity of viral communities in the PRDC-affected piglets and highlight the candidate viruses associated with it.

A Metagenomic Analysis of Mosquito Virome Collected From Different Animal Farms at Yunnan–Myanmar Border of China

“…Among PPVs, PPV1 causes major reproductive failure in sows ( Karniychuk and Nauwynck, 2013 ) and is an economically important viral pathogen for pig industry worldwide ( Zhou and Yang, 2010 ), whereas other PPVs are usually coinfected with other pathogens and may play associated role in disease development ( Saekhow et al, 2016 ; Ghosh et al, 2018 ). PPVs have spread widely in Chinese swine herds and are also frequently reported in single infections or coinfections with other porcine viruses, such as porcine circovirus 2, porcine reproductive and respiratory virus, and torque teno sus virus 1a ( Sun et al, 2015 ; Qin et al, 2018 ). In our previous investigation of mosquito virome from pig farms of Shanghai, we detected highly abundant reads of PPV2, PPV3, PPV4, PPV5, and PPV6 ( Hameed et al, 2020 ).…”

The porcine respiratory microbiome: recent insights and future challenges

“…Fungal and viral communities are known interact with members of the bacterial microbiome in humans [32]. To date, the porcine airway mycobiome has not been investigated, whereas the virome residing in the porcine airways has been evaluated by only two studies focused on the URT [47,48]. Results of both studies converge towards a complexity of viral communities in the pig upper airways [47,48].…”

“…Viral and fungal communities play a key role in the microbiome of the human and animal respiratory tract. Nevertheless, studies investigating the pig respiratory virome are scarce [47,48], whereas to the best of our knowledge, studies of mycobiome of the porcine respiratory tract are completely lacking. Expanding the community profiling to non-bacterial members of the pig respiratory microbiome (e.g.…”

PCR-based detection and genetic characterization of porcine parvoviruses in South Korea in 2018

“…Accordingly, the type of sample and age group of the pigs could affect to the detection rates for PPVs, which might be the main reason this study detected PPV7 at a very low rate of 1.32% compared to the previous study [13]. Genotypes 1-7 of PPV were detected in many countries, such as USA [16], Poland [14] and China [17], etc. However, to our best knowledge, only PPV1 [9,12], PPV2 [18] and PPV7 [13] have been reported in South Korea to date.…”