Dynamics and genetic variation of dengue virus serotypes circulating during the 2022 outbreak in Karachi

Dengue virus (DENV) poses a critical health threat causing millions of cases every year. The absence of proof-reading activity of the RNA-dependent RNA polymerases (RdRp) leads to significant mutations in its genome. This may result in genetic diversity among the genotypes which contribute to severe complications during the infection. Targeting these mutations may help to understand the viral transmission and identify a potential treatment. An aggregate of 152 dengue positive serum samples were collected from different tertiary care hospitals in Karachi. RNA isolation, cDNA synthesis as well as amplification of the C-prM region was performed, followed by the Sanger sequencing. The resultant sequences of each serotype were aligned with their respective genome sequences and phylogenetic trees based on genotypes were constructed using Maximum Likelihood (ML) method with 1000 bootstraps replicates. The sequences were then converted to the amino acid sequence and genetic variations in comparison to the reference genomes were evaluated. The results showed that there was a higher number of positive cases in males (58%) than in females (42%). The most affected age group was 21-30. The study suggested that the dominant serotype in the population of Karachi was DENV-1 (78.33%), followed by DENV- 2 (15%) and DENV-3 (6.66%). Overall, the acquired data provide the information about genetic variation in the C-prM region of dengue virus in Karachi, Pakistan.