Genomic surveillance and evolutionary dynamics of type 2 porcine reproductive and respiratory syndrome virus in China spanning the African swine fever outbreak

Figures

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  Figure 1.. The lineage composition and spatiotemporal distribution of PRRSV-2 in China during 2012–21. (A) The PRRSV-2 lineage distribution of Chinese provinces during 2012–21. The number of strains and their relative proportions are illustrated by pie charts in each province. Information for 30 provinces of China: AH, Anhui (n = 3); BJ, Beijing (n = 12); CQ, Chongqing (n = 9); FJ, Fujian (n = 90); GS, Gansu (n = 2); GD, Guangdong (n = 289); GZ, Guizhou (n = 5); HA, Henan (n = 281); HB, Hubei (n = 11); HE, Hebei (n = 34); HI, Hainan (n = 1); HL, Heilongjiang (n = 108); HN, Hunan (n = 15); IM, Inner Mongolia (n = 2); JL, Jilin (n = 9); JS, Jiangsu (n = 26); JX, Jiangxi (n = 47); LN, Liaoning (n = 18); QH, Qinghai (n = 3); SC, Sichuan (n = 64); SD, Shandong (n = 86); SH, Shanghai (n = 5); SN, Shannxi (n = 3); SX, Shanxi (n = 13); TJ, Tianjin (n = 5); TW, Taiwan (n = 67); XJ, Xinjiang (n = 16); YN, Yunnan (n = 29); ZJ, Zhejiang (n = 33). (B) The ML tree of PRRSV-2 in China during 2012–21. (C) Changes in the number and lineage composition of PRRSV-2 isolated from China during 2012–21. (D) The linear correlation analysis of Chinese L1 and L8 with insolation time during 2012–21.

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  Figure 2.. Maps of parental lineages of genomes and inter-lineage recombination patterns in China from 2018.8 to 2021. Top, full-length genome structure. With reference to VR-2332, the positions and boundaries of NSPs within ORF1a and ORF1b are shown, as well as other ORFs. (A, C) A map of parental lineages of genomes during 2018.8–2019 (A) and 2020–21(C). The accession number and isolation time of each recombination strain are displayed on the left, and the corresponding full-length genome of the major parent (longer fragment) source lineage and the minor parent (shorter fragment) source lineage is displayed on the right. (B, D) Major and minor parental strain contributors in recombinants observed during various time periods during 2018.8–2019 (B) and 2020–21(D). The major parent is shown on the outer ring, and the corresponding minor parent is shown in the pie chart. (E) The frequency stacking plot of minor parental sequences in inter-lineage of each lineage during 2018.8–2021. The X-axis represents the PRRSV genome position, and the Y-axis represents the lineage and frequency of minor parent sequences at a specific site. ‘*’ refers to the recombinants potentially generated through…

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  Figure 3.. Maps of intra-lineage recombination patterns in China from 2018.8 to 2021. (A, B) A map of parental lineages of genomes during 2018.8–2019 (A) and 2020–21 (B). The accession number and isolation time of each recombination strain are displayed on the left, and the bars on the right represent the region where recombination occurred. (C) The frequency stacking plot of minor parental sequences in intra-lineage of each lineage during 2018.8–2021. The X-axis represents the PRRSV genome position, and the Y-axis represents the lineage and frequency of minor parent sequences at a specific site. ‘*’ refers to the recombinants potentially generated through genetic inheritance. ‘1’ and ‘2’ respectively represent the first class and second class of shared-origin recombinants in similar recombination breakpoints.

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  Figure 4.. The patterns and changes of NSP2 indel of PRRSV-2 in China during 2012–21. (A) The NSP2 indel occurring patterns of PRRSV-2 in China. On the left is the name of the patterns, and there are twenty-five types. In the middle, based on VR2332 as a reference, there are the specific indel forms for each pattern. The right side shows the number of strains isolated in China during 2012–21 for each pattern. (B) The Gantt chart showing the NSP2 indel patterns. (C) The bar graphs showing the proportion of each indel pattern during three different periods, along with Fisher’s test for difference significance analysis. The three periods are before the outbreak of ASF (2012–2018.7), the ASF spread period (2018.8–2019), and the ASF stable period (2020–21). The proportion is the number of a certain pattern strains isolated during a period divided by the total number of strains isolated during that period.

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  Figure 5.. The domestic transmission of L1 PRRSVs. (A, C) The cross-regional transmission map of NADC30-like (A) and NADC34-like (C) in China. (B, D) Bayesian trees of NADC30-like (B) and NADC34-like (D).

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  Figure 6.. The domestic prevalence of vaccine-associated recombinant strains of L1 PRRSV. (A, B) The MDS clustering between vaccine strains and their prototype strains and NADC30-like strain (A) and NADC34-like strain (B), respectively. (B, C) The recombinant sequences were verified by ML tree, where the vaccine strain (include “MLV”) and its prototype strain (include “VR2332”) are in blue, and the vaccine recombinant strain is in orange. (E, F) The recombinant sequences were further verified by Simplot. The NADC30 prototype strain isolated in the USA in 2008 is in red, and the vaccine strain MLV_RespPRRS is in blue.