Simultaneous detection and genomic characterization of Zika virus Protein M, E and NS1 using optimized primers from Asian and African Lineage

Purpose Despite positive serological outcome, molecular confirmations have encountered little/no success either due to protocol accuracy, primer targets, or choice of sample amongst others. This study aims at providing an optimized protocol for the molecular detection of Zika virus amongst serologically positive respondent using samples from 2 selected hospitals in North Central Nigeria. Materials and methods About five (5) ml of blood samples was collected from a total of 400 participants for serological analysis, the IgM-positive samples were processed for molecular analysis using target primers from Asian and African lineage while a structured questionnaire was used to evaluate risk factors. Results Prevalence of 19% (38) and 45% (90) IgM and IgG positivity was recorded amongst respondent in Federal Medical Center (FMC), Keffi (R2=1) while 36% (72) and 42% (84) was recorded in General Hospital (GH), Minna (R2=1). The respective risk factors such as proximity of respondent to stagnant water or drainage channel, frequency of mosquito bite, prevention strategy, implementation of the prevention strategies for mosquito, and consumption of bushmeat were significant at set standard of P<0.05. Molecular quantification revealed cut-off values (Ct) from 21.73 to 25.75 for all the 3 targeted protein while sequence analysis showed relatedness to deposited sequences in GenBank. Conclusions The abundance of the viral proteins as well as the genetic relatedness is indicative of presence of multiple strains of the virus or conservation of region across different geolocations. In lieu of the outcome, primers from multiple lineages is thereby recommended to forestall/overcome the challenge of cross-reactivity/false-negativity with Zika virus detection.