Metagenomic analysis of endemic viruses in oral secretions from Chinese pigs

Abstract

Background: Pigs are unique reservoirs for virus ecology. Despite the increased use of improved biosecurity measures, pig viruses readily circulate in Chinese swine farms. Objectives:The main objective of this study was to examine archived swine oral secretion samples with a panel of pan-species viral assays such that we might better describe the viral ecology of swine endemic viruses in Chinese farms. Methodology: Two hundred (n = 200) swine oral secretion samples, collected during 2015 and 2016 from healthy pigs on six swine farms in two provinces in China, were screened with molecular pan-species assays for coronaviruses (CoVs), adenoviruses (AdVs), enteroviruses (EVs), and paramyxoviruses (PMV). Samples were also screened for porcine circovirus (PCV) 3, porcine reproductive and respiratory syndrome virus (PRRSV) and influenza A virus (IAV).Results: Among 200 swine oral secretion samples, 152 (76.0%) were found to have at least one viral detection. Thirty-four samples (17%) were positive for more than one virus, including 24 (70.5%) with dual detection and 10 (29.5%) with triple detection.Seventy-eight (39.0%) samples were positive for porcine AdVs, 22 (11.0%) were positive for porcine CoVs, 21 (10.5%) were positive for IAVs, 13 (6.5%) were positive for PCV, 7 (3.5%) were positive for PMV, six (3.0%) were positive for PRRSV and five (2.5%) were positive for porcine EV. Conclusion:Our findings underscore the high prevalence of numerous viruses among production pigs in China and highlight the need for routine, periodic surveillance for novel virus emergence with the goal of protecting pigs.

Successful Whole Genome Nanopore Sequencing of Swine Influenza A Virus (swIAV) Directly from Oral Fluids Collected in Polish Pig Herds

“…Whenever a broader screening is needed, metagenomics could also be applied. However, one should bear in mind that oral fluid composition is highly impacted by environmental contaminants [ 14 , 40 , 41 , 42 , 43 ].…”

Influenza D virus was not detected among prospectively studied swine farm in multiple provinces of China

“…[19][20][21][22] These farms were visited on a monthly basis to collect four types of samples (pig oral secretion samples, aerosol samples, environmental swab samples, and swine wastewater samples) at different stages of pig production (growers, finishers, sows, and boars) as described in our previous publications. [19][20][21][22] A total of 396 each of environmental swab, wastewater, bioaerosol, and 3300 pig oral secretion specimens were collected. From a database of original samples, a total of 400 pig oral secretion samples, 200 environmental swab samples, 200 wastewater samples, and 150 bioaerosol samples were selected using random number generating software (https://www.random.org/).…”

“…In this work we studied archived specimens which were collected study to assess influenza virus ecology at six Chinese swine farms in Jiangsu and Shandong Provinces (Figure 1). [19][20][21][22] These farms were visited on a monthly basis to collect four types of samples (pig oral secretion samples, aerosol samples, environmental swab samples, and swine wastewater samples) at different stages of pig production (growers, finishers, sows, and boars) as described in our previous publications. [19][20][21][22] A total of 396 each of environmental swab, wastewater, bioaerosol, and 3300 pig oral secretion specimens were collected.…”