A Novel Pan-Flavivirus Detection and Identification Assay Based on RT-qPCR and Microarray

Table 2

Screening of mosquito pools collected in Greece. Review of the screening of the 340 mosquito pools (50 mosquitoes each) collected in Greece. All RT-qPCR positive and 6 RT-qPCR negative pools were tested further by microarray and direct sequencing. All other pools tested showed a Cq > 38 and Tm < 78°C.

Mosquito pool	Cq	Tm (°C)	Microarray	DNA sequencing result
MPGr.01	37.3	81.4	WNV.2 Austria	Nea Santa-Greece-2010 HQ537483
MPGr.02	31.6	81.6	WNV.2 Austria	Nea Santa-Greece-2010 HQ537483
MPGr.03	21.5	81.7	WNV.2 Austria	Nea Santa-Greece-2010 HQ537483
MPGr.04	32.5	81.9	WNV.2 Austria	Nea Santa-Greece-2010 (with 1 mutation)
MPGr.05	38.5	81.6	WNV.2 Austria	Negative
MPGr.06	35.6	80,4	?	Marisma mosquito virus (93% identity)
MPGr.07	39.6	81.0	Culex Flav	New Mosq Culex Flavivirus (78% identity)
MPGr.08	39.8	79.4	Negative	Negative
MPGr.09	41.4	83.0	Negative	Negative
MPGr.10	38.6	81.2	Negative	Negative (residual sequence: Salmonella sp.)
MPGr.11	40.1	82.4	Negative	Negative
MPGr.12	40.6	79.2	Negative	Negative
MPGr.13	39.6	80.7	Negative	Negative (residual sequence: Pseudomonas sp.)