No Evidence of Influenza A Virus RNA in South African Backyard Swine in the uMgungundlovu District of the KwaZulu-Natal Province

Abstract

Background: Influenza A virus (IAV) is the most widely reported influenza type in swine populations worldwide. Since no information was available on IAV prevalence in backyard swine populations in South Africa, we, for the first time, performed a molecular surveillance for detecting IAV prevalence in backyard swine in the uMgungundlovu District of the KwaZulu-Natal province of South Africa. Methods: Swine oral secretion (saliva) samples (n=102) were collected from three backyard farms distantly located in the uMgungundlovu District in March 2021. Total RNA was used to detect IAV using a one-step real-time RT-PCR assay with matrix gene-specific oligonucleotide primers and a TaqMan probe. Result: None of the samples amplified the IAV matrix gene suggesting that the swine under investigation were free from IAV active infection; however, the quantified viral RNA of swine saliva samples needs further investigation to determine the presence of other RNA viruses. The present study was conducted during COVID-19 related lockdown restrictions in South Africa, during which a significantly decreased influenza activity was reported in the Southern Hemisphere. Increased alertness and behavioural changes in people, such as maintaining hygiene and using a face mask for day-to-day operations, might have limited the transmission of IAV between humans and swine.