A newly developed tetraplex real‐time RT‐PCR for simultaneous screening of influenza virus types A, B, C and D

Abstract

BackgroundHuman‐ or avian‐to‐swine transmissions have founded several autonomously circulating influenza A virus (IAV) lineages in swine populations that cause economically important respiratory disease. Little is known on other human influenza virus types, like B (IBV) and C (ICV) in European swine, and of the recently detected novel animal influenza virus type D (IDV).ObjectivesDevelopment of a cost‐effective diagnostic tool for large‐scale surveillance programmes targeting all four influenza virus types.MethodsAn influenza ABCD tetraplex real‐time RT‐PCR (RT‐qPCR) was developed in the frame of this study. A selection of reference virus strains and more than 4000 porcine samples from a passive IAV surveillance programme in European swine with acute respiratory disease were examined.ResultsTwo IBV, a single IDV but no ICV infections were identified by tetraplex RT‐qPCR. IBV and IDV results were confirmed by conventional RT‐PCR and partial sequence analysis.ConclusionsThe tetraplex RT‐qPCR proved fit for purpose as a sensitive, specific and high‐throughput tool to study influenza virus transmission at the human‐animal interface. Complementing close‐meshed active virological and serological surveillance is required to better understand the true incidence and prevalence of influenza virus type B, C and D infections in swine.

Assessment of Influenza D Virus in Domestic Pigs and Wild Boars in France: Apparent Limited Spread within Swine Populations Despite Serological Evidence of Breeding Sow Exposure

“…Thus, the very low seroprevalence of IDV in domestic pigs in France (this study) and the short shedding period reported after experimental infection [1] probably contributed to the absence of detection of IDV genome in nasal swab samples in this country. Nevertheless, our virological results are consistent with those obtained in a large-scale study conducted on 3753 nasal swabs taken from pigs with respiratory illness, in 682 farms located in twelve European countries, including France but excluding Italy and Luxembourg [22]. Among them, 1166 nasal swabs were sampled in 2015-2017 on pigs reared in France, and they all tested negative towards IDV in a tetraplex RT-qPCR.…”

“…Questions about IDV host range relate especially to the role pigs may play in IDV ecology. Indeed, the virus was first isolated from a pig exhibiting a respiratory syndrome [1]; pigs were demonstrated to be sensitive to IDV infection experimentally [1,21], and similarly to cattle, IDV was isolated or molecularly detected in pigs in different continents, i.e., America [1], Asia [11] and Europe [6][7][8]22]. Serological investigations also confirmed IDV infections in domestic pig and feral swine populations, although with very different positivity rates from one country and/or one study to another [1,7,8,13,17].…”

Interspecies Transmission of Reassortant Swine Influenza A Virus Containing Genes from Swine Influenza A(H1N1)pdm09 and A(H1N2) Viruses

“…Since the global dissemination of pH1N1 virus, this lineage has also undergone reassortment with swine IAV strains endemic to the corresponding geographic region (5). Within Europe, this diversification of pH1N1 virus in pigs has increased the circulating swine IAVs from 4 to >25 genotypes (6,7). Diversification has been rapid; pH1N1 reassortant viruses incorporating enzootic swine virus HA and NA, or NA alone, detected during 2010 in the United Kingdom (8) and Italy (9), have emerged.…”

Development of a multiplex isothermal amplification molecular diagnosis method for on-site diagnosis of influenza

“…The influenza viruses are classified into types A, B, C, and D on the basis of their core proteins [5]. Among the four influenza types, influenza A viruses cause most of the global flu epidemics, influenza B viruses cause smaller localized outbreaks, influenza C viruses generally cause mild illness, and influenza D viruses are not known to cause illness in people [6][7][8]. Thus, influenza A and B viruses comprise the major respiratory pathogens in humans that cause seasonal flu epidemics [9,10].…”