Epidemiological investigation on the prevalence of PEDV and PoRVA in Guizhou during 2017-2023 and genetic evolution analysis of VP7 and VP4 genes of PoRVA strains
To understand the prevalence of porcine epidemic diarrhea virus(PEDV)and porcine group A rotavirus(PoRVA)in Guizhou Province,165 piglet diarrhea samples from 139 pig farms in 9 regions of Guizhou Province from 2017 to 2023 were detected by TaqMan RT-qPCR,and RT-PCR amplification,sequencing,and genetic evolution analysis of VP7 and VP4 genes of PoRVA-positive samples were performed.The results showed that the infection rates of PEDV,PoRVA and PEDV+PoRVA were 67.88％(112/165),38.79％(64/165)and 21.21％(35/165),respectively,and the infections of the above three were detected in different years,regions and seasons.Genetic evolution analysis showed that 27 strains of PoRVA VP7 gene and 22 strains of VP4 gene were amplified and identified as 6 G-genotype and 3 P-genotype,among which G9(29.63％)and P[13](68.18％)were the dominant genotypes,and G3,G4,G5,G11,G26,P[6]and P[13]accounted for 7.41％,22.22％,22.22％,3.70％,14.81％,13.64％and 18.18％,respectively.Ten genotypes of G/P combinations were successfully identified in 21 PoRVA samples,among which G9P[13](19.05％)was the dominant combination genotype and G4P[13],G5P[13],G3P[13],G4P[6],G5P[23],G9P[23],G11P[13],G26P[6],G26P[13]accounting for 14.29％,14.29％,9.52％,9.52％,9.52％,9.52％,4.76％,4.76％,4.76％,respectively.The results of homology analysis showed that the homology between 27 strains of the VP7 gene and 22 strains of the VP4 gene with the NX vaccine strain,were 75.5％-94.0％and 68.5％-75.6％,and the homology of amino acids were 78.3％-96.6％and 72.0％-82.5％,respectively.Some PoRVA sequences had the highest homology with foreign and human-derived group A rotaviruses.The results of amino acid site variation analysis showed that compared to the NX vaccine strain,the amino acid sequences of PoRVA VP7 and VP4 all showed characteristic amino acid site mutations.There were no deletions or insertions of amino acid sites in G-genotype PoRVA VP7,3 mutations(I208T,K212AN/T,V271I)in G9 genotype PoRVA VP7,and 17 mutations(S28R/K,A29I/T/MN,L40I/V,V44L,S71T,Q73G/N/S/E,S90A/Q/K/R,G94N/S/A/K,N100D/E,T122A/S,T147A/G/N/D,Q189S/T,I208L/Q/T,K212T/I/P/N,A213N/T/D,E267D/N,V271I)in G3,G4,G5,Gi1 and G26 genotype PoRVA VP7.Three strains of P[6]genotype PoRVA VP4 lacked T in aa136,and 13 strains of P[13]genotype PoRVA VP4 inserted E/D-Y/F in aa188-aa189,and 26 mutations(I92V,Q94E,Q113T/P/N,T114N/Q/S/R,T115Q/E,N116S/L/T,P148A/QN/S/I,T180E/N/D,P162T,I174V/L,C269Y,R281N,A286L/S,T302N,A340S/V,T379S,T403A,S438P,R553K,A569A,M570L,A608S,E660D,I726F,K733N,S739T)in P[6],P[13]and P[23]genotype PoRVA VP4.The above results indicate that the infection rates of PEDV and PoRVA in Guizhou from 2017 to 2023 was high,and the genotypes were complex.Among them,PoRVA was mainly prevalent with G9 and P[13]genotypes,and the dominant combined genotype was G9P[13].This study enriched the epidemiological data of PEDV and PoRVA in Guizhou Province,providing reference data for the prevention and control the infection of PoRVA and the screening of candidate vaccine strains.
PEDVPoRVAmolecular epidemiologyVP7 and VP4 genesgene evolutionary analysis
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