Emergence of new genotypes and lineages of dengue viruses during the 2012–15 epidemics in southern India. (July 2019)

• Record Type: Journal Article
• Authors: Ahamed, Syed Fazil; Rosario, Vivek; Britto, Carl; Dias, Mary; Nayak, Kaustuv; Chandele, Anmol; Kaja, Murali-Krishna; Shet, Anita
• Is Part Of: International journal of infectious diseases. Volume 84(2019)
• Page Start: S34
• Page End: S43
• Publication Date: 2019-07
• Subjects: Dengue virus -- Serotyping -- Sequencing -- Phylogenetics -- Genotypes -- Lineages; Communicable diseases -- Periodicals; Communicable Diseases -- Periodicals; Communicable diseases; Periodicals; Electronic journals; 616.9
• DOI: 10.1016/j.ijid.2019.01.014
• Languages: English
• ISSNs: 1201-9712

Abstract

Highlights: Co-circulation of all four DENV serotypes seen in 2012–2015 dengue outbreaks in southern India. Genotype GI of DENV-1 replaced GIII in 2014–15, possibly accounting for DENV-1 predominance. Novel findings include identification of DENV-2 'GIVc' (new lineage), and two clades of DENV-4 GIC. These genotypic variations may have contributed towards recent dengue outbreaks in southern India. Abstract: Objectives: To genotypically characterize dengue virus (DENV) isolates among dengue-infected children from 2012–13/2014–15 outbreaks in southern India. Methods: Children hospitalized with suspected dengue were tested for dengue RT-PCR targeting Capsid-preMembrane (C-prM) and Envelope (Env) regions. Following virologic confirmation (n = 612), a representative selection of DENV isolates (n = 99) were sequenced for C-prM, aligned using ClustalW and subjected to phylogenetic analysis by maximum-likelihood method in MEGA6. Results: In 2012–13 (n = 113), DENV-3 (44, 38.9%) and DENV-2 (43, 38.1%) predominated; DENV-1 (22, 19.5%) and DENV-4 (1, 0.9%) were less common. The pattern changed in 2014–15 (n = 499), when DENV-1 (329, 65.7%) predominated, followed by DENV-2 (97, 21.2%), DENV-3 (36, 6.7%) and DENV-4 (10, 2.0%). Multiple-serotype co-infections occurred in 2.7% and 5.4% in 2012–13 and 2014–15, respectively. Genotype III (GIII) of DENV-1 predominated (85.7%) in 2012–13, ceding to GI predominance (80.8%) in 2014–15. Among DENV-2, 71.9% (23/32) showed distinct clustering suggesting a new lineage, 'GIVc'. All tested DENV-4 were GIC, whose clustering pattern showed the emergence of two distinct clades. Conclusions: New genotypic/lineage variations in DENV-1 and DENV-2 may have influenced the magnitude and severity of dengue epidemics in southern India during this period. These findings emphasize the role of active surveillance of DENV serotypes/genotypes in aiding outbreak control and vaccine studies.