Sequencing and Phylogeny of Dengue virus serotype 1 circulating in Lucknow, India

Background: In India majority of the dengue outbreaks are attributed to DEN-2 and DEN-3. However, DEN-1 is increasingly being implicated as a major serotype during recent outbreaks in India, including the Delhi outbreak in 2006. In Lucknow we found a similar trend. We sequenced our strains to find out if similar strain is circulating here. In the present study, we sequenced C-prM gene junction of 5 DENV-1 isolated from Lucknow, India. For comparison, we retrieved 23 other Indian and 31 global reference sequences from NCBI database, making sure that Indian and global isolates from all decades are available for comparative analysis.Methods and Findings: 298 samples from clinically suspected cases were tested by IgM MAC ELISA, Viral culture and RT PCR, Real time PCR. 66 cases came out to be positive by various methods. Five serum samples found positive for DENV-1 RNA were further sequenced for analysis. On sequence analysis, we observed that the Lucknow DEN-1 sequences showed sequence similarity of 96.1%-97.8% (mean 96.95%) with the 1980 and 1993 sequences from Thailand and Comoros and 95.9%-97.85 (mean 96.85%) with the 1993 sequence from Singapore. On comparison of our sequences with the other Indian sequences, mean sequence divergence of 2.1%, 4.15% and 5.05% were observed with Gwalior 2002, Delhi 2006 and Vellore 1962-1964 respectively.Conclusion: DEN-1 isolates of this study clustered as a distinct subclade and signifies that a new lineage of DEN-1 has evolved.

Author(s): Sanjeev Tripathi, Vineeta Khare, Prashant Gupta*, Animesh Chatterjee, Mohhamed Yahiya Khan, Rashmi Kumar, T N Dhole

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