Table 1.
Flavivirus isolates used in this study and results obtained by the dRRT-PCR and the RT-PCR methods used as reference.
| Flavivirus sero complex | Virus | Isolate (lineage) | Geographical origin | Species of origin | Year of isolation | Source | Duplex RRT-PCR | Reference PCR | |
|---|---|---|---|---|---|---|---|---|---|
| Fam (JE) | Joe (Ntaya) | ||||||||
| Japanese encephalitis (JE) | WNV | E-101 (1a) | Egypt | Human | 1951 | Institut Pasteur Lyon (France) | 21.33 | No Ct | 22.8a |
| IS-98 STD (1a) | Israel | White stork | 1998 | ANSES (France) | 29.55 | No Ct | 31.2a | ||
| NY99 034EDV (1a) | New York | American crow | 1999 | Diagnostic Virology Laboratory USDA Ames (USA) | 17.34 | No Ct | 17.02a | ||
| 04.05 (1a) | Morocco | Horse | 2003 | Biopharma Rabat (Morocco) | 18.26 | No Ct | 19.57a | ||
| GE-1b/B (1a) | Spain | Golden eagle | 2007 | INIA-CISA Madrid (Spain) | 18 | No Ct | 19.73a | ||
| 15803 (1a) | Italy | Magpie | 2008 | IZSLER Brescia (Italy) | 23.48 | No Ct | 26.61a | ||
| 225677/2009 (1a) | Italy | Jay | 2009 | IZSLER Brescia (Italy) | 24.55 | No Ct | 25.46a | ||
| 233184/4/2009 (1a) | Italy | Black headed gull | 2009 | IZSLER Brescia (Italy) | 24.19 | No Ct | 26.87a | ||
| Spain/2010/H-1b (1a) | Spain | Horse | 2010 | INIA-CISA Madrid (Spain) | 20.74 | No Ct | 20.98a | ||
| Spain/2012 (1a) | Spain | Horse | 2012 | LCV Algete (Spain) | 19.35 | No Ct | 20.57a | ||
| Kunjin KJ359-11 (1b) | Australia | Horse | 1984 | ISCIII Madrid (Spain) | 29.4 | No Ct | 33.67a | ||
| B956 (2) | Uganda | Human | 1937 | ATCC (USA) | 16.53 | No Ct | 17.07a | ||
| Austria/2008 (2) | Austria | Goshawk | 2008 | VetMedUni Vienna (Austria) | 26.48 | No Ct | 31.8a | ||
| WN/Horse/RSA/1/08 (2) | South Africa | Horse | 2008 | Onderstepoort Veterinary Institute Pretoria (South Africa) | 31.48 | No Ct | 35.22a | ||
| 178907/2013 (2) | Italy | Culex pipiens | 2013 | IZSLER Brescia (Italy) | 16.72 | No Ct | 19.32a | ||
| Rabensburg 97-103 (3) | Czech Republic | Culex pipiens | 1997 | ISCIII Madrid (Spain) | 18.78 | No Ct | Posc | ||
| MP502-66 (putative 6) | Malaysia | Culex pseudovishnui | 1966 | ISCIII Madrid (Spain) | 25.86 | No Ct | Posc | ||
| Koutango ArD96655 (putative 7) | Senegal | Rhipicephalus guihoni | 1993 | Institute Pasteur Dakar (Senegal) | 16.42 | No Ct | Posc | ||
| USUV | SAAR 1776/1958 | South Africa | Culex neavei | 1958 | ANSES (France) | 24.77 | No Ct | 28.31a | |
| 939 | Austria | Blackbird | 2001 | ISCIII Madrid (Spain) | 19.9 | No Ct | 22.25a | ||
| 231247/2011 | Italy | Blackbird | 2011 | IZSLER Brescia (Italy) | 22.19 | No Ct | 25.37a | ||
| 206795-3/2012 | Italy | Culex pipiens | 2012 | IZSLER Brescia (Italy) | 24.77 | No Ct | 28.31a | ||
| 229615-1/2013 | Italy | Culex pipiens | 2013 | IZSLER Brescia (Italy) | 23.3 | No Ct | 28.11a | ||
| HautRhin7315/France/2015 | France | Blackbird | 2015 | ANSES (France) | 25.39 | No Ct | 28.27a | ||
| JEV | Nakayama | Japan | – | 1935 | ISCIII Madrid (Spain) | 23.9 | No Ct | Posc | |
| MVEV | MV/1/1951 | – | – | 1951 | ISCIII Madrid (Spain) | 26.91 | No Ct | Posc | |
| SLEV | FL52 | – | – | – | ISCIII Madrid (Spain) | 38 | No Ct | Negc | |
| Ntaya | BAGV | Spain H/2010 | Spain | Red-legged partridge | 2010 | INIA-CISA Madrid (Spain) | No Ct | 25.46 | 24.71b |
| ITV | Vaccine strain | Israel | Domestic turkey | 1985 | Kimron Veterinary Institute (Israel) | No Ct | 27.73 | 26.74b | |
| 618 | Israel | Domestic turkey | 1995 | Kimron Veterinary Institute (Israel) | No Ct | 26.34 | 24.53b | ||
| 107458 | Israel | Domestic turkey | 2010 | Kimron Veterinary Institute (Israel) | No Ct | 19.19 | 17.61b | ||
| 106819 | Israel | Domestic turkey | 2010 | Kimron Veterinary Institute (Israel) | No Ct | 29.11 | 27.68b | ||
| 105520 | Israel | Domestic turkey | 2010 | Kimron Veterinary Institute (Israel) | No Ct | 30.69 | 27.96b | ||
| TMUV | UVE/TMUV/1955/MY/MM1775 | Malaysia | Culex tritaeniorhinchus | 1955 | European Virus Archive (EVAg) | No Ct | 19.85 | Posc | |
| Other flaviviruses | TBEV | Neudorfl | – | – | – | ISCIII Madrid (Spain) | No Ct | No Ct | Posc |
| Hypr | – | – | – | ANSES (France) | No Ct | No Ct | Posc | ||
| LIV | – | – | – | – | ISCIII Madrid (Spain) | No Ct | No Ct | Posc | |
| ZIKV | – | – | – | – | ISCIII Madrid (Spain) | No Ct | No Ct | Posc | |
| DENV | Hawaii | – | – | – | ISCIII Madrid (Spain) | No Ct | No Ct | Posc | |