Dengue virus type 3 (DENV-3) genotype III circulated across East Africa between 1984 and 1993, but virulent strains is now considered essential public health activity. DENV serotype 3 (DENV-3) was first isolated during a DHF epidemic in Manila in 1956 [11] and is now circulating in Asia and South America [12,13,14]. This serotype is often associated with more severe diseases and dengue hemorrhagic fever than other serotypes [15,16,17]. Little is known about DENV-3 activity in Africa. Serotype 3 was first detected in Africa during a 1984 epidemic event in Pemba (Mozambique), where at least 45% of the local population was affected [18]. This high proportion could be explained at least in part by the naïve immune status of the population against this new serotype. Since then, sporadic occurrences of the serotype 3 were reported, such as in Kenya in 1991 and in Somalia in 1993 [19]. DENV-3 was responsible for 2 epidemics in Sudan in 2004-2005 and 2010 [20]. The latter affected over 3765 people [21]. In West Africa, DENV-3 circulation was first published in 2008 in Cote d'Ivoire, during a yellow fever alert [22,23].Moreover, subtle changes such as the ones at the lineage level could alter the potential of the dengue virus to cause severity, as it has already been observed in Sri Lankan DENV-3 strains [24,25]. The E protein is the major target gene for genetic variations with a possible impact on virulence [26,27] (Table 1).
Materials and Methods
Virus isolationSingle T25 C6/36 cells flask (2,6.106 cells) was inoculated with a mix made of 200 μl of serum with 2 ml of L-15 cell culture medium (Gibco), 2% FCS and 20 μl of heparin and filtered on a 22μm sterile filter. Culture flask was incubated at 28 °C. After 7 days, 2 ml of media was removed and added to a new T25 C6/36 cells flask. Culture flask was incubated at 28 °C, under 5% CO2 during 5 days. The supernatant was then removed and used for RT-PCR.
Reverse-Transcription and sequencingViral RNA was extracted from 140 μl of cell culture supernatant using QIAamp Viral RNA Mini Kits (Qiagen, Germany). RT-PCR and amplification was processed as previously described by Lanciotti et al. [17]: To generate two overlapping fragments covering the PrM/M and E genes region, primers pairs F1 (5'-GCTCCCCATGTCGGCATGGGACTGG-3')/ R1(5'-CATCCCTTTGAGTTTCAATTTGTCCAT-3') (1541bp) and F2 (5'-CTAGGATCTCAAGAAGGAGCAATGCA-3')/R2 (5'-CGCGGATCCATGGCTGTTGCCACTCTTTTGGGGGA-3') (865bp) were used in 2 separate reactions. These 2 overlapping fragments amplify a global region of 2272bp. RNA was first transcribed to cDNA using the Super Script III one-step RT-PCR kit (Invitrogen). The reaction mix was 25 µl of 2X reaction mix, 5 µl of template RNA, 1µl of sense primer 10µM (F1 or F2), 1µl of anti-sense primer 10 µM (R1 or R2), 2 µL of SuperScript III RT/Platinum Taq Mix and up to 50 µl of autoclaved distilled water according to manufacturer instruction. The cycle used was 56 °C during 30 min then 94 °C during 2 min followed by 40 cycles of 94 °C (15 s), 56 °C (30 s) and 68 °C (1 min 30). T...