Identification of a Novel Recombinant Type 2 Porcine Reproductive and Respiratory Syndrome Virus in China
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection and Virus Isolation
2.2. RT-PCR Amplification and Genome Sequencing
2.3. Sequence Comparison and Phylogenetic Analysis
2.4. Putative Recombination Analysis
3. Results
3.1. Genome Characterization and Homology Analysis
3.2. Phylogenetic Analysis
3.3. Amino Acid Analysis of Nsp2 and GP5
3.4. Recombination Analysis
4. Discussion
5. Conclusions
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Reference Strains | Country/Year | Accession No. | Reference Strains | Country/Year | Accession No. |
---|---|---|---|---|---|
VR-2332 abc | USA/1995 | AY150564 | WUH4 a | CHN/2012 | JQ326271 |
CH-1a abc | CHN/1996 | AY032626 | HENAN-XINX a | CHN/2013 | KF611905 |
BJ-4 a | CHN/2000 | AF331831 | JL580 ab | CHN/2013 | KR706343 |
RespPRRS MLV ab | USA/2005 | AF066183 | XW015 a | USA/2013 | KF724409 |
JXA1 abc | CHN/2006 | EF112445 | FJ1402 a | CHN/2014 | KX169191 |
TJ ab | CHN/2006 | EU860248 | CHsx1401 ab | CHN/2014 | KP861625 |
MN184A a | USA/2006 | DQ176019 | HNjz15 ab | CHN/2015 | KT945017 |
jiangxi-3 a | CHN/2007 | EU200961 | FJZ03 a | CHN/2015 | KP860909 |
07BJ a | CHN/2007 | FJ393459 | HNyc15 a | CHN/2015 | KT945018 |
CH-1R a | CHN/2008 | EU807840 | FJY04 a | CHN/2015 | KP860910 |
NADC30 abc | USA/2008 | JN654459 | WUH5 a | CHN/2015 | KU523366 |
JXwn06 ab | CHN/2008 | EF641008 | HENZMD-9 a | CHN/2015 | KU950374 |
JXA1 P80 a | CHN/2008 | FJ548853 | HNhx a | CHN/2016 | KX766379 |
HENAN-HEB ab | CHN/2012 | KJ143621 |
JXA1 | JXwn06 | TJ | VR-2332 | RespPRRSV MLV | CH-1a | NADC30 | JL580 | CHsx1401 | HENAN-HEB | HNjz15 | LV | |
---|---|---|---|---|---|---|---|---|---|---|---|---|
JXA1-Like | VR-2332-Like | CH-1a-Like | NADC30-Like | Type 1 | ||||||||
Pairwise % Identity to SCcd17 (nt/aa) | ||||||||||||
Complete genome | 85.2 | 85.3 | 92.7 | 84.0 | 83.9 | 84.9 | 90.2 | 88.3 | 88.1 | 87.6 | 88.3 | 43.4 |
5′UTR | 97.8 | 97.8 | 94.9 | 92.7 | 92.7 | 96.7 | 92.2 | 91.5 | 90.3 | 92.2 | 90.9 | 49.2 |
ORF1a | 82.1 | 82.4 | 82.1 | 79.9 | 79.8 | 81.0 | 88.5 | 86.6 | 86.1 | 84.1 | 86.1 | 32.5 |
ORF1b | 94.3 | 94.4 | 94.1 | 89.1 | 89.0 | 92.3 | 85.6 | 84.5 | 84.7 | 84.7 | 83.6 | 50.0 |
nsp1α | 97.3/97.7 | 98.1/97.7 | 98.1/97.7 | 89.7/96.0 | 89.7/96.0 | 94.8/96.0 | 86.2/94.8 | 86.5/96.0 | 83.5/94.8 | 85.3/94.3 | 85.5/94.8 | 49.4/43.3 |
nsp1β | 88.4/77.9 | 88.4/77.9 | 88.4/77.9 | 89.1/77.9 | 88.9/77.3 | 87.5/74.8 | 94.4/85.7 | 93.3/83.9 | 93.7/84.5 | 92.6/83.3 | 92.2/85.7 | 31.9/25.6 |
nsp2 | 67.1/66.3 | 67.0/66.4 | 66.5/66.4 | 71.7/67.4 | 71.6/67.3 | 68.1/64.9 | 92.3/89.9 | 82.7/80.2 | 89.0/85.5 | 85.0/82.0 | 89.6/87.4 | 23.6/20.9 |
nsp3 | 89.1/92.3 | 88.9/92.8 | 88.8/92.3 | 87.8/92.3 | 87.7/92.3 | 88.1/91.8 | 90.4/94.2 | 93.4/94.2 | 90.0/93.7 | 90.8/93.7 | 90.4/94.2 | 32.8/22.7 |
nsp4 | 97.8/98.0 | 97.9/98.0 | 97.9/98.0 | 92.4/92.9 | 92.4/92.9 | 95.8/94.4 | 88.1/91.8 | 97.0/97.0 | 87.6/92.3 | 86.9/90.2 | 87.8/91.3 | 44.8/54.9 |
nsp5 | 96.4/95.8 | 97.0/95.8 | 96.8/95.8 | 89.9/88.1 | 89.9/88.1 | 95.0/92.6 | 91.5/92.6 | 93.3/92.0 | 89.1/88.1 | 89.5/90.7 | 88.0/86.1 | 50.9/38.9 |
nsp6 | 97.9/100 | 97.9/100 | 95.6/100 | 93.3/93.1 | 93.3/93.1 | 95.5/100 | 95.6/93.1 | 97.9/100 | 82.7/85.7 | 90.6/93.1 | 92.1/93.1 | 58.1/69.0 |
nsp7α | 96.3/87.3 | 96.8/87.3 | 96.8/87.3 | 87.4/84.4 | 87.4/84.4 | 94.6/95.9 | 80.1/90.8 | 92.3/97.3 | 79.7/89.3 | 77.7/88.6 | 79.2/90.8 | 29.6/42.7 |
nsp7β | 95.3/96.3 | 96.0/97.2 | 95.6/96.3 | 81.7/76.3 | 81.7/76.3 | 90.9/91.4 | 73.2/67.8 | 73.9/72.7 | 71.9/65.2 | 72.1/66.5 | 68.8/63.9 | 22.8/20.9 |
nsp8 | 96.2/97.7 | 97.0/97.7 | 97.0/97.7 | 92.8/97.7 | 92.8/97.7 | 97.0/97.7 | 86.9/97.7 | 85.9/97.7 | 86.8/95.3 | 82.0/92.9 | 83.0/92.9 | 48.8/65.0 |
nsp9 | 96.0/98.7 | 96.1/99.0 | 95.8/99.0 | 89.4/97.4 | 89.4/97.4 | 93.6/98.1 | 84.3/97.2 | 83.2/96.3 | 83.9/96.3 | 83.5/96.3 | 82.5/96.6 | 54.0/69.8 |
nsp10 | 82.9/94.4 | 83.0/95.1 | 82.8/94.6 | 85.8/95.6 | 85.5/95.6 | 84.1/94.4 | 94.6/95.1 | 93.3/97.9 | 92.2/98.2 | 93.5/97.5 | 92.6/97.7 | 46.4/57.8 |
nsp11 | 88.2/94.4 | 88.6/94.9 | 88.2/94.4 | 86.9/92.5 | 87.6/94.0 | 91.1/94.4 | 94.5/94.9 | 92.2/94.4 | 88.4/93.5 | 94.6/95.4 | 92.3/94.4 | 53.5/74.5 |
nsp12 | 86.3/95.3 | 86.3/95.3 | 86.3/95.3 | 85.0/93.2 | 85.3/93.2 | 87.2/93.9 | 95.7/97.3 | 94.3/98.7 | 95.0/96.7 | 95.2/98.0 | 95.2/97.3 | 24.3/15.5 |
ORF2a | 84.3/85.2 | 84.6/85.2 | 84.6/85.2 | 88.3/89.7 | 88.0/89.2 | 86.1/87.9 | 92.8/92.3 | 91.8/91.4 | 90.9/91.0 | 91.6/90.1 | 92.3/93.1 | 52.4/62.0 |
ORF2b | 86.9/85.3 | 86.9/85.3 | 86.985.3 | 90.7/86.8 | 90.2/86.8 | 86.5/83.7 | 93.9/91.4 | 94.9/94.4 | 92.9/91.4 | 93.4/92.9 | 96.3/94.4 | 65.2/67.1 |
ORF3 | 83.2/80.0 | 83.0/80.5 | 83.2/80.5 | 88.2/83.8 | 88.6/84.7 | 85.2/81.9 | 84.5/84.3 | 82.7/80.0 | 84.5/85.2 | 93.7/83.8 | 83.2/84.3 | 52.7/47.1 |
ORF4 | 80.5/82.9 | 81.9/84.9 | 81.7/85.5 | 82.5/82.2 | 82.5/82.2 | 82.7/84.9 | 94.3/92.4 | 84.8/84.9 | 92.9/91.8 | 92.7/90.0 | 92.2/90.6 | 58.5/61.4 |
ORF5 | 88.8/83.0 | 89.0/83.6 | 89.0/83.6 | 89.1/81.2 | 89.2/81.8 | 90.2/84.2 | 96.4/92.7 | 94.9/88.8 | 95.4/91.6 | 95.3/91.6 | 95.7/93.2 | 46.2/42.2 |
ORF6 | 87.0/93.5 | 86.8/93.5 | 86.8/93.5 | 88.1/94.1 | 88.4/94.1 | 85.9/92.2 | 96.9/98.3 | 95.6/97.1 | 95.4/98.3 | 96.1/98.3 | 95.6/98.3 | 60.4/78.8 |
ORF7 | 87.7/87.9 | 85.6/83.2 | 87.7/87.9 | 90.4/91.5 | 90.4/91.5 | 89.0/89.7 | 97.2/96.7 | 95.5/94.1 | 94.3/92.4 | 94.9/94.1 | 95.8/95.9 | 55.0/51.7 |
3′UTR | 89.2 | 82.3 | 89.2 | 93.0 | 93.0 | 88.5 | 97.3 | 97.3 | 96.6 | 96.6 | 96.6 | 56.0 |
Strains | Amino Acid Sites | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
29 | 35 | 76 | 120 | 152 | 193 | 267 | 300 | 314 | 470 | 485 | 534 | 553 | 608 | 610 | 636 | 785 | 846 | 886 | 924 | 958 | 1093 | |
VR-2332 | A | A | P | E | L | S | E | Q | V | L | S | P | Q | E | S | K | Q | S | F | G | D | R |
RespPRRSMLV | A | A | P | E | L | S | E | Q | V | M | S | P | Q | E | S | K | Q | S | F | G | D | R |
CH-1a | A | A | P | E | L | S | E | Q | V | M | G | P | Q | G | S | K | Q | S | F | G | D | R |
JXA1 | A | A | P | E | L | S | E | Q | V | M | G | DL | DL | E | S | K | Q | S | F | G | D | R |
JXwn06 | A | A | P | E | L | S | E | Q | V | M | G | DL | DL | E | S | K | Q | S | F | G | D | R |
TJ | A | A | P | E | L | S | E | Q | V | L | G | DL | DL | E | S | K | Q | S | F | G | D | R |
NADC30 | A | A | P | E | L | F | E | Q | V | L | G | L | Q | E | S | K | Q | S | F | G | D | R |
CHsx1401 | A | A | P | E | L | S | E | Q | V | L | G | L | Q | E | S | K | Q | S | F | G | D | R |
JL580 | A | A | P | E | L | F | E | Q | V | L | G | L | Q | E | S | K | Q | S | F | G | D | R |
HENAN-HEB | A | A | P | E | L | S | E | Q | V | L | G | L | Q | E | S | K | P | S | F | G | D | R |
HNjz15 | A | A | P | E | L | S | E | Q | V | L | G | L | Q | E | S | K | Q | N | F | G | D | R |
SCcd17 | T | V | S | R | S | I | D | R | A | S | A | S | R | K | A | R | R | I | L | S | E | K |
Strains | Potential N-glycosylation Sites | |||||||
---|---|---|---|---|---|---|---|---|
30 | 32 | 33 | 34 | 35 | 44 | 51 | 58 | |
VR-2332 | + | - | + | - | - | + | + | - |
RespPRRS MLV | + | - | + | - | - | + | + | - |
CH-1a | - | - | - | + | - | + | + | - |
JXA1 | + | - | - | + | + | + | + | - |
JXwn06 | + | - | - | + | + | + | + | - |
TJ | + | - | - | + | + | + | + | - |
NADC30 | - | - | - | + | - | + | + | - |
CHsx1401 | - | - | - | + | - | + | + | - |
JL580 | - | - | - | + | - | + | + | - |
HENAN-HEB | - | + | - | - | - | + | + | - |
HNzj15 | - | - | - | + | - | + | + | - |
SCcd17 | - | + | - | + | - | + | + | + |
Strains | Isolation Date | Recombination with | Recombination Regions | Accession No. | References |
---|---|---|---|---|---|
HENAN-HEB | 2013 | JXA1 | nsp2 | KJ143621 | [29] |
HENAN-XINX | 2013 | VR-2332 | nsp2–5 | KF611905 | [29] |
JL580 | 2014 | 09NEN1 (JXA1-like) | nsp2, nsp3, nsp7, ORF2a, ORF4 | KR706343 | [19] |
Chsx1401 | 2014 | VR-2332 | nsp11 | KP861625 | [29] |
FJ1402 | 2014 | GD (JXA1-like) | nsp2–3, nsp12, ORF3 | KX169191 | [27] |
HENZMD-9 | 2015 | JXA1 | 5′-UTR-nsp2, nsp4–9 | KU950374 | [30] |
HNyc15 | 2015 | VR-2332/CH-1a | ORF2–4 | KT945018 | [26] |
15HEN1 | 2015 | JXA1-R a | nsp3–9 | KX815413 | [38] |
15LN3 | 2015 | JXA1-R a | nsp3–9 | KX815425 | [38] |
15SC3 | 2015 | JXA1-R a | 5′-UTR-nsp2, nsp7–nsp9 | KX815428 | [38] |
TJnh1501 | 2015 | TJbd14-1(JXA1-like) | nsp2 | KX510269 | [28] |
SCnj16 | 2016 | JXA1 | 5′-UTR, nsp1–2, nsp3–9 | MF196906 | [32] |
HNhx | 2016 | JXA1 | nsp4–9 | KX766379 | [30] |
SCcd17 | 2017 | JXA1+VR-2332 | JXA1(5′-UTR-nsp1α, nsp3–9) VR-2332 (ORF3–4) | MG914067 | This study |
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Zhou, L.; Kang, R.; Xie, B.; Tian, Y.; Wu, X.; Lv, X.; Yang, X.; Wang, H. Identification of a Novel Recombinant Type 2 Porcine Reproductive and Respiratory Syndrome Virus in China. Viruses 2018, 10, 151. https://doi.org/10.3390/v10040151
Zhou L, Kang R, Xie B, Tian Y, Wu X, Lv X, Yang X, Wang H. Identification of a Novel Recombinant Type 2 Porcine Reproductive and Respiratory Syndrome Virus in China. Viruses. 2018; 10(4):151. https://doi.org/10.3390/v10040151
Chicago/Turabian StyleZhou, Long, Runmin Kang, Bo Xie, Yiming Tian, Xuan Wu, Xuebin Lv, Xin Yang, and Hongning Wang. 2018. "Identification of a Novel Recombinant Type 2 Porcine Reproductive and Respiratory Syndrome Virus in China" Viruses 10, no. 4: 151. https://doi.org/10.3390/v10040151