Global transmission dynamics of avian influenza viruses in swine and prevalence of influenza A and other RNA viruses in saliva samples of backyard swine in KwaZulu-Natal province of South Africa.

Abstract

Background: The presence of α-2,3 and α-2,6 sialic acid receptors in the upper respiratory tract of swine makes them an ideal host for efficiently acquiring and disseminating avian and human origin influenza A virus (IAV) subtypes. Numerous reports have documented spillover of various avian IAV subtypes to swine in several countries. The prevalence of swine and avian IAVs in swine populations and their interactions with circulating human IAV strains may facilitate reassortment and the emergence of novel IAV strain(s) with pandemic potential, representing a severe threat to public safety. Four IAV disease pandemics have occurred and claimed millions of human lives in the past. Apart from IAV, numerous other RNA viruses such as classical swine fever virus, foot and mouth disease virus, porcine epidemic diarrhoea virus, porcine reproductive and respiratory syndrome virus, rotaviruses, transmissible gastroenteritis virus etc. may inflict severe diseases in swine and may result in significant economic losses to swine farmers, have been reported in swine populations in various countries. Of note, backyard swine farming faces a considerable challenge in viral RNA was extracted using the NucleoMag Pathogen kit, and library preparation was performed using the Illumina Stranded Total RNA Prep. Deep sequencing was performed on an Illumina HiSeq X instrument. The fastq files containing paired-end reads were analyzed using Genome Detective v 1.135. The assembled nucleotide sequences were analyzed using nucleotide BLAST and PhyML phylogenetic tree. Results and Discussion: From the downloaded sequences, we identified that various wild and domestic avian species had transmitted eleven of the IAV subtypes to the swine populations in several countries globally. Some of these avian IAVs had already been adapted in swine because they had acquired specific mammalian adaptation markers. Intriguingly, multiple spillover events of highly pathogenic H5N1 and low pathogenic H9N2 viruses from various avian species to swine were determined, while the spillover events of other nine avian influenza viruses were limited. While we did not detect IAV RNA in swine saliva samples obtained from the three backyard farms in the KwaZulu-Natal province of South Africa, we were able to quantify viral RNA in the saliva samples under investigation which prompted us to perform deep sequencing analysis of selected saliva samples (n=3) to explore the diversity of RNA viruses in backyard swine saliva. As a result, we identified a high diversity of swine enteric viruses in two of these saliva samples, which originated from backyard swine farm 2 (BSF2) and BSF3. In contrast, only a few RNA viruses were present in the saliva sample obtained from BSF1. These viruses belonged to 13 families of animal viruses, two families of plant viruses, two species of fungal viruses, five unclassified virus species, and a few viruses classified in the Order Picornavirales. Intriguingly, Porcine astroviruses were prevalent in these swine saliva samples; however, either partial or complete genome segments of Porcine rotavirus A, Human rotavirus B, and Rotavirus C were also identified in the saliva, which originated from BSF2, while Rotavirus C genome sequences were obtained from the saliva originated from BSF3. In addition, a near full-length Hepatitis E virus (HEV) genome was detected in the saliva sample obtained from BSF3. Conclusion: Interactions between avian species (domestic or wild) and swine poses a significant threat to the interspecies transmission of IAV. While this study determined the events of avian to swine transmission of various avian IAV subtypes globally, the absence of active IAV infection in the present study, which comprised a limited backyard swine population of the KwaZulu-Natal province, does not exclude the presence of IAV infection in other backyard swine holdings in South Africa. While low biosecurity standards at the backyard swine farms would facilitate interspecies transmission of IAV from domestic or wild avian species and humans to the swine, it requires continued IAV surveillance at the backyard swine farms to monitor the disease status. Of concern was the high diversity of swine enteric viruses at BSF2 and BSF3, which suggests an increased risk of diarrhoeic diseases at the backyard farms. In addition, the occurrence of rotaviruses and HEV in backyard swine makes it imperative to implement adequate biosecurity to prevent the zoonotic transmission of these viruses from swine to humans in the households to ensure public safety. Therefore, we recommend nationwide molecular surveillance to detect and track the circulation and evolution of IAV and other RNA viruses in backyard swine populations in South Africa which is critical to sustainable backyard swine farming and ensuring public health.