Genetic Diversity Characterization of Porcine Reproductive and Respiratory Syndrome Virus Isolates in Romania, Based on Phylogenetic Analysis
Abstract
:1. Introduction
2. Results and Discussion
3. Experimental Section
3.1. Sampling and RNA Extraction
3.2. PCR Analysis
3.3. Sequencing and Phylogenetic Analysis
4. Conclusions
References
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Location (City) | Sample identification number | ORF5 | ORF7 | ||
---|---|---|---|---|---|
Isolate | GenBank accession No. | Isolate | GenBank accesion No. | ||
Braila | 1069 | Rom6 | JX075097 | Rom4 | JX075095 |
Braila | 1070 | Rom3 | JX075094 | Rom4 | JX075095 |
Braila | 1071 | Rom3 | JX075094 | Rom4 | JX075095 |
Braila | 1076 | Rom3 | JX075094 | Rom4 | JX075095 |
Braila | 1077 | Rom3 | JX075094 | Rom4 | JX075095 |
Braila | 1078 | Rom3 | JX075094 | Rom4 | JX075095 |
Braila | 1079 | Rom5 | JX075096 | Rom4 | JX075095 |
Braila | 1104 | Rom5 | JX075096 | Rom4 | JX075095 |
Braila | 1105 | Rom3 | JX075094 | Rom4 | JX075095 |
Braila | 1106 | Rom3 | JX075094 | Rom4 | JX075095 |
Braila | 776 | Rom12 | JX099577 | Rom22 | JX134062 |
Braila | 865 | Rom3 | JX075094 | Rom23 | JX134063 |
Braila | 849 | Rom3 | JX075094 | Rom4 | JX075095 |
Braila | 836 | Rom3 | JX075094 | Rom4 | JX075095 |
Braila | 835 | Rom13 | JX099578 | Rom23 | JX134063 |
Iasi | 1 | Rom3 | JX075094 | - | - |
Iasi | 4 | Rom7 | JX090163 | - | - |
Iasi | 6 | Rom8 | JX090167 | - | - |
Iasi | 7 | Rom3 | JX075094 | - | - |
Iasi | 8 | Rom3 | JX075094 | - | - |
Iasi | 9 | Rom9 | JX090164 | - | - |
Cluj-Napoca | 70 | Rom21 | JX105431 | Rom 30 | JX134070 |
Cluj-Napoca | 73 | Rom14 | JX099572 | Rom24 | JX134064 |
Cluj-Napoca | 74 | Rom18 | JX099576 | Rom28 | JX134068 |
Cluj-Napoca | 75 | Rom17 | JX099575 | Rom27 | JX134067 |
Cluj-Napoca | 77 | Rom20 | JX105430 | Rom 30 | JX134070 |
Cluj-Napoca | 79 | Rom15 | JX099573 | Rom25 | JX134065 |
Cluj-Napoca | 82 | Rom19 | JX099579 | Rom29 | JX134069 |
Cluj-Napoca | 87 | Rom16 | JX099574 | Rom26 | JX134066 |
Arad | 13 | Rom5 | JX075096 | - | - |
Arad | 14 | Rom10 | JX090165 | - | - |
Arad | 18 | Rom3 | JX075094 | - | - |
Arad | 19 | Rom11 | JX090166 | - | - |
Geographical Area | Total number of swine | Total number of swine in county | Number of samples analyzed |
---|---|---|---|
N-E | 257,071 | 22,337/Iasi | 85 |
S-E | 516,930 | 160,870/Braila | 260 |
S-W | 690,657 | 116,099/Arad | 200 |
N-W | 182,550 | 4,665/Cluj | 60 |
Sequence number | Farm and sequence name | Country | Year | Gene Bank ACC No. | |
---|---|---|---|---|---|
ORF5 | ORF7 | ||||
1 | 2888 | Austria | - | AY875855 | - |
2 | 2906/2 | Austria | - | AY875862 | - |
3 | 2234 | Austria | - | AY875858 | - |
4 | AN | Belarus | 2001 | - | EU071252 |
5 | Bel | Belarus | 2004 | DQ324669 | DQ324699 |
6 | MN | Belarus | 1999 | - | EU071253 |
7 | Bor | Belarus | 2004 | - | DQ324701 |
8 | BR | Belarus | 2001 | - | EU071254 |
9 | Obu | Belarus | 2005 | DQ324676 | DQ324707 |
10 | Okt | Belarus | 2004 | - | DQ324708 |
11 | PK | Belarus | 2002 | - | - |
12 | Sno | Belarus | 2004 | - | DQ324713 |
13 | Soz | Belarus | 2004 | DQ324686 | DQ324719 |
14 | Soz (2) | Belarus | 2006 | EU071227 | EU071222 |
15 | Soz (3) | Belarus | 2006 | EU071228 | EU071223 |
16 | Vas | Belarus | 2005 | - | DQ324722 |
17 | MG | Belarus | 1999 | - | EU071255 |
18 | Vos | Belarus | 2004 | DQ324690 | DQ324725 |
19 | Yus | Belarus | 2004 | - | DQ324727 |
20 | ZD | Belarus | 2000 | - | EU071256 |
21 | Zad | Belarus | 2004 | DQ324694 | DQ324729 |
22 | Zap | Belarus | 2004 | - | DQ324734 |
23 | V-501 | Czech Republic | 1996 | AF253531 | - |
24 | KT | Czech Republic | 2006 | - | EU071224 |
25 | 361–4 | Denmark | 1994 | AY035915 | AY035960 |
26 | 28639/98 | Denmark | 1998 | AY035912 | AY035957 |
27 | 2567/96 | Italy | 1996 | AY035932 | AY035976 |
28 | 2029/97 | Italy | 1997 | AY035930 | AY035973 |
29 | IT7 | Italy | 2004 | AY739963 | - |
30 | IT8 | Italy | 2004 | AY739964 | - |
31 | IT15 | Italy | 2004 | AY739971 | - |
32 | IT19 | Italy | 2002 | AY739975 | - |
33 | IT42 | Italy | 2003 | - | - |
34 | IT62 | Italy | 2003 | AY743932 | - |
35 | Aus | Lithuania | 2000 | - | AF438362 |
36 | Sid | Lithuania | 2000 | - | AF438363 |
37 | Che | Poland | 2005 | - | DQ324703 |
38 | Dob | Poland | 2007 | - | EU071225 |
39 | Dzi | Poland | 2005 | - | DQ324705 |
40 | Prz | Poland | 2005 | - | DQ324711 |
41 | Sok | Poland | 2004 | - | DQ324715 |
42 | RS | Russia | 2005 | EU071230 | EU071257 |
43 | BK | Russia | 2006 | EU071231 | EU071258 |
44 | BLG | Russia | 2006 | EU071232 | EU071259 |
45 | FR | Russia | 2000 | - | EU071260 |
46 | GB-1 | Russia | 1997 | - | EU071261 |
47 | GB-2 | Russia | 2000 | - | EU071262 |
48 | RV | Russia | 2003 | - | EU071263 |
49 | VR | Russia | 2005 | EU071233 | EU071264 |
50 | KM | Russia | 1999 | - | EU071265 |
51 | KH-1 | Russia | 2004 | - | EU071266 |
52 | KH-2 | Russia | 2005 | EU071234 | EU071267 |
53 | KH-3 | Russia | 2005 | EU071235 | EU071268 |
54 | SHV | Russia | 2006 | EU071236 | EU071269 |
55 | IN | Russia | 2005 | EU071237 | EU071270 |
56 | KR | Russia | 2000 | - | EU071271 |
57 | MB-1 | Russia | 2004 | - | EU071272 |
58 | MB-2 | Russia | 2005 | EU071238 | EU071273 |
59 | KZ-1 | Russia | 1999 | - | EU071274 |
60 | KZ-2 | Russia | 2004 | EU071239 | EU071275 |
61 | DZ | Russia | 2000 | - | EU071276 |
62 | IL-1 | Russia | 1997 | EU071240 | EU071277 |
63 | IL-2 | Russia | 1999 | - | EU071278 |
64 | VD | Russia | 1997 | - | EU071279 |
65 | NB | Russia | 2006 | EU071241 | EU071280 |
66 | NV-1 | Russia | 1996 | - | EU071281 |
67 | NV-2 | Russia | 2004 | - | EU071282 |
68 | NV-3 | Russia | 2006 | EU071242 | EU071283 |
69 | OR | Russia | 2000 | - | EU071284 |
70 | PMP | Russia | 2006 | EU071243 | EU071285 |
71 | PN | Russia | 2000 | - | EU071286 |
72 | PR | Russia | 1998 | - | EU071287 |
73 | SM | Russia | 1998 | - | EU071288 |
74 | SP | Russia | 1999 | - | EU071289 |
75 | NE | Russia | 1999 | - | EU071290 |
76 | SNK-1 | Russia | 1999 | - | EU071291 |
77 | SNK-2 | Russia | 2004 | - | EU071292 |
78 | TM-1 | Russia | 2000 | - | EU071293 |
79 | TM-2 | Russia | 2005 | EU071244 | EU071294 |
80 | TT | Russia | 1998 | - | EU071295 |
81 | TL | Russia | 1999 | - | EU071296 |
82 | ZV | Russia | 2004 | EU071245 | EU071297 |
83 | UD | Russia | 2001 | - | EU071298 |
84 | VL-1 | Russia | 2001 | - | EU071299 |
85 | VL-2 | Russia | 2004 | - | EU071300 |
86 | VL-3 | Russia | 2006 | EU071246 | EU071301 |
87 | BT-1 | Russia | 2000 | - | EU071302 |
88 | BT-2 | Russia | 2006 | EU071247 | EU071303 |
89 | ND-1 | Russia | 1998 | EU071248 | EU071304 |
90 | ND-2 | Russia | 1999 | - | EU071305 |
91 | ND-3 | Russia | 2006 | EU071249 | EU071306 |
92 | VSH | Russia | 2005 | EU071250 | EU071307 |
93 | GK | Russia | 2005 | EU071251 | EU071308 |
94 | IV3140 | South Korea | - | DQ355821 | DQ355822 |
95 | CP6874 | South Korea | - | EF031042 | - |
96 | 1751/93 | Spain | 1991 | AY035935 | AY035979 |
97 | CRESA9 | Spain | - | DQ009634 | - |
98 | CRESA11 | Spain | - | DQ009626 | - |
99 | CRESA13 | Spain | - | DQ009637 | - |
100 | CRESA14 | Spain | - | DQ009638 | - |
101 | CRESA22 | Spain | - | DQ009645 | - |
102 | 28/2003 | Spain | - | DQ345755 | - |
103 | 01RB1 | Thailand | 2001 | - | AY796316 |
104 | Amervac PRRS | Spain | vaccine | - | DQ324698 |
105 | Pyrsvac-183 | Spain | vaccine | - | DQ324712 |
106 | Porcilis PRRS | The Netherlands | vaccine | - | DQ324710 |
107 | Porcilis PRRS | Italy | 2004 | AY743931 | - |
108 | Rom3 | Romania | 2012 | JX075094 | - |
109 | Rom5 | Romania | 2012 | JX075096 | - |
110 | Rom6 | Romania | 2012 | JX075097 | - |
111 | Rom7 | Romania | 2012 | JX090163 | - |
112 | Rom8 | Romania | 2012 | JX090167 | - |
113 | Rom9 | Romania | 2012 | JX090164 | - |
114 | Rom10 | Romania | 2012 | JX090165 | - |
115 | Rom11 | Romania | 2012 | JX090166 | - |
116 | Rom12 | Romania | 2012 | JX099577 | - |
117 | Rom13 | Romania | 2012 | JX099578 | - |
118 | Rom14 | Romania | 2012 | JX099572 | - |
119 | Rom15 | Romania | 2012 | JX099573 | - |
120 | Rom16 | Romania | 2012 | JX099574 | - |
121 | Rom17 | Romania | 2012 | JX099575 | - |
122 | Rom18 | Romania | 2012 | JX099576 | - |
123 | Rom19 | Romania | 2012 | JX099579 | - |
124 | Rom20 | Romania | 2012 | JX105430 | - |
125 | Rom21 | Romania | 2012 | JX105431 | - |
126 | Rom4 | Romania | 2012 | - | JX075095 |
127 | Rom22 | Romania | 2012 | - | JX134062 |
128 | Rom23 | Romania | 2012 | - | JX134063 |
129 | Rom24 | Romania | 2012 | - | JX134064 |
130 | Rom25 | Romania | 2012 | - | JX134065 |
131 | Rom26 | Romania | 2012 | - | JX134066 |
132 | Rom27 | Romania | 2012 | - | JX134067 |
133 | Rom28 | Romania | 2012 | - | JX134068 |
134 | Rom29 | Romania | 2012 | - | JX134069 |
135 | Rom30 | Romania | 2012 | - | JX134070 |
136 | Lelystad | Netherlands | 1993 | M 96262 | M 96262 |
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Zaulet, M.; Gurau, M.R.; Petrovan, V.; Buburuzan, L. Genetic Diversity Characterization of Porcine Reproductive and Respiratory Syndrome Virus Isolates in Romania, Based on Phylogenetic Analysis. Int. J. Mol. Sci. 2012, 13, 12046-12061. https://doi.org/10.3390/ijms130912046
Zaulet M, Gurau MR, Petrovan V, Buburuzan L. Genetic Diversity Characterization of Porcine Reproductive and Respiratory Syndrome Virus Isolates in Romania, Based on Phylogenetic Analysis. International Journal of Molecular Sciences. 2012; 13(9):12046-12061. https://doi.org/10.3390/ijms130912046
Chicago/Turabian StyleZaulet, Mihaela, Maria Rodica Gurau, Vlad Petrovan, and Laura Buburuzan. 2012. "Genetic Diversity Characterization of Porcine Reproductive and Respiratory Syndrome Virus Isolates in Romania, Based on Phylogenetic Analysis" International Journal of Molecular Sciences 13, no. 9: 12046-12061. https://doi.org/10.3390/ijms130912046