Phylogenetic analysis and genetic evolution of porcine respiratory coronavirus in Guangxi province, Southern China from 2022 to 2024
Porcine respiratory coronavirus (PRCV) is an important coronavirus to cause respiratory syndrome in pigs. To analyze the genetic and evolutional characteristics of PRCV in Guangxi province, southern China, a total of 6,267 clinical samples were collected from different pig farms, harmless treatment...
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Frontiers Media S.A.
2025-07-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1625343/full |
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| author | Yuwen Shi Yuwen Shi Kaichuang Shi Kaichuang Shi Yanwen Yin Shuping Feng Feng Long Wenjun Lu Sujie Qu Yan Ma Jiakang He |
| author_facet | Yuwen Shi Yuwen Shi Kaichuang Shi Kaichuang Shi Yanwen Yin Shuping Feng Feng Long Wenjun Lu Sujie Qu Yan Ma Jiakang He |
| author_sort | Yuwen Shi |
| collection | DOAJ |
| description | Porcine respiratory coronavirus (PRCV) is an important coronavirus to cause respiratory syndrome in pigs. To analyze the genetic and evolutional characteristics of PRCV in Guangxi province, southern China, a total of 6,267 clinical samples were collected from different pig farms, harmless treatment plants and abattoirs in Guangxi province during 2022–2024. Seventeen positive samples of PRCV were selected to amplify and analyze the S, M, and N gene sequences. The results showed that the positivity rate of PRCV was 1.13% (71/6,267) using RT-qPCR. The homology analysis revealed that the nucleotide (amino acid) identity were 98.2–100% (96.6–100%) among the obtained 17 S, M, and N gene sequences, and 91.3–98.1% (88.8–98.0%) among the obtained strains and the reference strains from different countries. The phylogenetic analysis indicated that all PRCV strains could be divided into two groups, tentatively designated group I and group II, and each group was further divided into different clades. The strains obtained from Guangxi province distributed in group I, and formed an independent clade. They were most closely related to PRCV 137 isolate 86/135308 strain from the United Kingdom basing on the S, M, and N gene sequences. The sequence analysis revealed that all PRCV strains from Guangxi province obtained in this study showed 672 nt/224 aa deletion in the 5′ region of S gene, and there existed 37 amino acid mutations in different regions in S gene of different PCRV strains. Recombination analysis of S gene sequences did not find any recombination event. The Bayesian analysis indicated that all PRCV strains could be divided into Group I and II, and the obtained Guangxi strains belonged to group I. The population size of circulating PRCV strains kept slightly upward trend since its discovery in 1984 until 2010, showed a steady downward trend until 2020, and then a slight increase. The results suggested that the PRCV strains circulating in Guangxi province originated from Europe, and have evolved independently with genetic diversity. These findings enriched the epidemiological data of PRCV, and provided new information on the prevalence and genetic evolution of PRCV in Guangxi province of China. |
| format | Article |
| id | doaj-art-c8a45d088c134f53bfce0a8a54f65269 |
| institution | Kabale University |
| issn | 1664-302X |
| language | English |
| publishDate | 2025-07-01 |
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| series | Frontiers in Microbiology |
| spelling | doaj-art-c8a45d088c134f53bfce0a8a54f652692025-08-20T03:50:26ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2025-07-011610.3389/fmicb.2025.16253431625343Phylogenetic analysis and genetic evolution of porcine respiratory coronavirus in Guangxi province, Southern China from 2022 to 2024Yuwen Shi0Yuwen Shi1Kaichuang Shi2Kaichuang Shi3Yanwen Yin4Shuping Feng5Feng Long6Wenjun Lu7Sujie Qu8Yan Ma9Jiakang He10Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, ChinaNanning Kedi Biotechnology Co., Ltd, Nanning, ChinaGuangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, ChinaGuangxi Center for Animal Disease Control and Prevention, Nanning, ChinaGuangxi Center for Animal Disease Control and Prevention, Nanning, ChinaGuangxi Center for Animal Disease Control and Prevention, Nanning, ChinaGuangxi Center for Animal Disease Control and Prevention, Nanning, ChinaGuangxi Center for Animal Disease Control and Prevention, Nanning, ChinaGuangxi Center for Animal Disease Control and Prevention, Nanning, ChinaGuangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, ChinaGuangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, ChinaPorcine respiratory coronavirus (PRCV) is an important coronavirus to cause respiratory syndrome in pigs. To analyze the genetic and evolutional characteristics of PRCV in Guangxi province, southern China, a total of 6,267 clinical samples were collected from different pig farms, harmless treatment plants and abattoirs in Guangxi province during 2022–2024. Seventeen positive samples of PRCV were selected to amplify and analyze the S, M, and N gene sequences. The results showed that the positivity rate of PRCV was 1.13% (71/6,267) using RT-qPCR. The homology analysis revealed that the nucleotide (amino acid) identity were 98.2–100% (96.6–100%) among the obtained 17 S, M, and N gene sequences, and 91.3–98.1% (88.8–98.0%) among the obtained strains and the reference strains from different countries. The phylogenetic analysis indicated that all PRCV strains could be divided into two groups, tentatively designated group I and group II, and each group was further divided into different clades. The strains obtained from Guangxi province distributed in group I, and formed an independent clade. They were most closely related to PRCV 137 isolate 86/135308 strain from the United Kingdom basing on the S, M, and N gene sequences. The sequence analysis revealed that all PRCV strains from Guangxi province obtained in this study showed 672 nt/224 aa deletion in the 5′ region of S gene, and there existed 37 amino acid mutations in different regions in S gene of different PCRV strains. Recombination analysis of S gene sequences did not find any recombination event. The Bayesian analysis indicated that all PRCV strains could be divided into Group I and II, and the obtained Guangxi strains belonged to group I. The population size of circulating PRCV strains kept slightly upward trend since its discovery in 1984 until 2010, showed a steady downward trend until 2020, and then a slight increase. The results suggested that the PRCV strains circulating in Guangxi province originated from Europe, and have evolved independently with genetic diversity. These findings enriched the epidemiological data of PRCV, and provided new information on the prevalence and genetic evolution of PRCV in Guangxi province of China.https://www.frontiersin.org/articles/10.3389/fmicb.2025.1625343/fullporcine respiratory coronavirusphylogenetic analysisgenetic evolutionrecombinationgene sequence |
| spellingShingle | Yuwen Shi Yuwen Shi Kaichuang Shi Kaichuang Shi Yanwen Yin Shuping Feng Feng Long Wenjun Lu Sujie Qu Yan Ma Jiakang He Phylogenetic analysis and genetic evolution of porcine respiratory coronavirus in Guangxi province, Southern China from 2022 to 2024 Frontiers in Microbiology porcine respiratory coronavirus phylogenetic analysis genetic evolution recombination gene sequence |
| title | Phylogenetic analysis and genetic evolution of porcine respiratory coronavirus in Guangxi province, Southern China from 2022 to 2024 |
| title_full | Phylogenetic analysis and genetic evolution of porcine respiratory coronavirus in Guangxi province, Southern China from 2022 to 2024 |
| title_fullStr | Phylogenetic analysis and genetic evolution of porcine respiratory coronavirus in Guangxi province, Southern China from 2022 to 2024 |
| title_full_unstemmed | Phylogenetic analysis and genetic evolution of porcine respiratory coronavirus in Guangxi province, Southern China from 2022 to 2024 |
| title_short | Phylogenetic analysis and genetic evolution of porcine respiratory coronavirus in Guangxi province, Southern China from 2022 to 2024 |
| title_sort | phylogenetic analysis and genetic evolution of porcine respiratory coronavirus in guangxi province southern china from 2022 to 2024 |
| topic | porcine respiratory coronavirus phylogenetic analysis genetic evolution recombination gene sequence |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1625343/full |
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