Emerging strains of porcine epidemic diarrhoea virus (PEDv) in Mexico

Reveles‐Félix, Saúl; Carreón‐Nápoles, Rosalba; Mendoza‐Elvira, Susana; Quintero‐Ramírez, Víctor; García‐Sánchez, Juvencio; Martínez‐Bautista, Rebeca; Saavedra‐Montañez, Manuel; Mosqueda Gualito, Juan Joel; Sánchez‐Betancourt, José Ivan

As an emerging disease, the porcine epidemic diarrhoea virus has caused substantial economic losses to the pork industry in Mexico, leading to piglet mortality rates of up to 100%. For detection, sequencing and genetic characterization of the virus, 68 samples of one‐week‐old piglets from pork farms in 17 states of Mexico were analysed. In total, 53 samples were positive by real‐time RT‐PCR, confirming the presence of the virus in 15 states. Twenty‐eight samples from 10 states were amplified by endpoint RT‐PCR, and 20 sequences of the spike gene were obtained. A phylogenetic analysis based on the spike gene demonstrated that all Mexican strains are in Group II and are classified as non‐Indel‐S emerging variants. Three strains showed amino acid insertions: PEDv/MEX/GTO/LI‐DMZC15/2015 and PEDv/MEX/QRO/LI‐DMZC45/2016 showed one amino acid insertion ((424)Y(425) and (447)D(448), respectively), and PEDv/MEX/QRO/LI‐DMZC49/2019 showed one and two amino acid insertions ((422)C(423) and (537)SQ(538)), with the second insertion in the COE region. These results provide evidence of the prevalence of emerging, non‐Indel‐S strains of the virus are currently circulating in Mexico during 2016–2018, when three of which have amino acid insertions: PEDv/MEX/GTO/IN‐DMZC15/2015 and PEDv/MEX/QRO/IN‐DMZC45/2016 have one amino acid insertion each ((424)Y(425) and (447)D(448), respectively), and PEDv/MEX/QRO/IN‐DMZC49/2019 has one ((422)C(423)) and two amino acid insertions ((537)SQ(538)), the latter being in the COE region, which could generate new antigenic variants.