Genetic Diversity of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) From 1996 to 2017 in China

Abstract

Porcine reproductive and respiratory syndrome (PRRS) is one of the most devastating diseases of the global swine industry. The causative agent porcine reproductive and respiratory syndrome virus (PRRSV) was first isolated in China in 1996 and has evolved quickly during the last two decades. To fully understand virus diversity, epidemic situation in the field, and make future predictions, a total of 365 PRRSV strains were used for evolution and genome analysis in which 353 strains were isolated from mainland China. The results showed that high diversity was found among PRRSV isolates. Total PRRSV isolates could be divided into eight subgroups. Among these subgroups strains, Original HP-PRRSV, NADC30-like, and Intermediate PRRSV were the major epidemic PRRSV strains circling in the field and would play a major role in PRRS epidemic in the future. Deletions, insertions, and recombinations have occurred frequently in the PRRSV genome. Deletions were the main driving force of viral evolution before 2006 and may also contribute further to the virus' evolution in a relatively closed or low strain diversity circumstance. The recombinant strains could be divided into three groups: the Inner group, Extensional group, and Propagating group. The evolutionary directions of the isolates in the Extensional and Propagating groups have changed, and the routes of recombination in the Propagating group were analyzed and sorted into three types. The increases in recombinant strains and high rates of recombination in recent years indicate that recombination has played a very important role in the virus' evolution. Isolates, which incorporate the advantages of their parental strains, will influence PRRSV evolution and make adverse effects on PRRS control in the future.

Keywords: evolution; genetic diversity; phylogenetic trees; porcine reproductive and respiratory syndrome virus (PRRSV); recombination.

Figure 1

Phylogenetic tree based on the analysis of the complete genome sequences of PRRSV isolates. The total PRRSV isolates were divided into eight subgroups: EU-type strain, MN184-like strain, NADC30-like strain, Classic NA strain, Intermediate PRRSV strain, Original HP-PRRSV strain, JXA1-P80-like strain, and PRRSV2010 strain, which are marked in green, orange, purple, blue, gray, black, red, and yellow, respectively. The date of isolation of each individual strain is marked as a black solid square, and recombinant strains are shown with red dots in the inner cycle.

Figure 2

Tendency of PRRSV and trends in recombinant isolates in different periods. PRRSV isolates belonging to EU-type strain, MN184-like strain, NADC30-like strain, Classical PRRSV strain, Intermediate PRRSV strain, Original HP-PRRSV strain, JXA1-P80-like strain, and PRRSV2010 strain are showed in green, orange, purple, blue, gray, black, red, and yellow, respectively. Trends in recombinant isolates in different periods were shown. The representative field strains were shown in red, killed vaccine strains were shown in blue, and live vaccine strains were shown in blue with underline.

Figure 3

Amino acid deletions and insertions in PRRSV strains. The distinct deletions of HP-PRRSV and NADC30 are shown with black rectangles and purple rectangles, respectively. Deletions that are not consistent with HP-PRRSV or NADC30 are marked with gray rectangles. Insertions are shown with red rectangles. The rough positions of deletions and insertions are shown, and the precise positions are marked beside the rectangle. All sites of amino acid deletion or insertion are based on the sequence of strain VR2332. Strains with unique deletions relative to HP-PRRSV or NADC30 in the NSP2 region are marked with black or purple labels, respectively. Deletions and insertions of GX1001 are not shown in the figure.

Figure 4

Recombination route and isolate ratio of PRRSV strains. EU-type strain, MN184-like strain, NADC30-like strain, Classic NA strain, Intermediate PRRSV strain, Original HP-PRRSV strain, JXA1-P80-like strain, and PRRSV2010 strain are marked with a background of green, orange, purple, blue, gray, black, red, and yellow, respectively. Recombinant strains are shown with red dots in the outer cycle. Recombinant strains belonging to the Inner group and Extensional group are shown with single thin green line and a thin red line, respectively. The major parent strains and minor parent strains of isolates belonging to the Propagating group are marked with the same color; major parent strains are shown with thick lines, and minor parent strains are shown with thin lines; lines 1 to 10 were marked with blue, red, light blue, black, yellow, orange, gray, light green, dark green and purple, respectively. The pie chart in the outer cycle represents the numbers of strains in the different recombinant and non-recombinant groups; the Inner group is shown in green, Extensional group is shown in red, Propagating group is shown in blue, and non-recombinant strains are shown in light gray. The number of strains in each group are labeled.

Figure 5

Recombinant region in each isolate. EU-type strain, MN184-like strain, NADC30-like strain, Classic NA strain, Intermediate PRRSV strain, Original HP-PRRSV strain, JXA1-P80-like strain, and PRRSV2010 strain are marked with green, orange, purple, blue, gray, black, red, and yellow rectangles, respectively. Major parental strains are shown with solid lines and minor parental strains with dotted lines. The rough sites of recombination are based on strain VR2332.