Emergence of new genotypes and lineages of dengue viruses during the 2012–15 epidemics in southern India

Syed Fazil Ahamed, Vivek Rosario, Carl Britto, Mary Dias, Kaustuv Nayak, Anmol Chandele, Murali Krishna Kaja, Anita Shet

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
JournalInternational Journal of Infectious Diseases
DOIs
StatePublished - Jan 1 2019

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Dengue Virus
India
Genotype
Dengue
Capsid
Disease Outbreaks
Cluster Analysis
Hospitalized Child
Coinfection

Keywords

  • Dengue virus
  • Genotypes
  • Lineages
  • Phylogenetics
  • Sequencing
  • Serotyping

ASJC Scopus subject areas

  • Microbiology (medical)
  • Infectious Diseases

Cite this

Emergence of new genotypes and lineages of dengue viruses during the 2012–15 epidemics in southern India. / Ahamed, Syed Fazil; Rosario, Vivek; Britto, Carl; Dias, Mary; Nayak, Kaustuv; Chandele, Anmol; Kaja, Murali Krishna; Shet, Anita.

In: International Journal of Infectious Diseases, 01.01.2019.

Research output: Contribution to journalArticle

Ahamed, Syed Fazil ; Rosario, Vivek ; Britto, Carl ; Dias, Mary ; Nayak, Kaustuv ; Chandele, Anmol ; Kaja, Murali Krishna ; Shet, Anita. / Emergence of new genotypes and lineages of dengue viruses during the 2012–15 epidemics in southern India. In: International Journal of Infectious Diseases. 2019.
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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.",
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AU - Ahamed, Syed Fazil

AU - Rosario, Vivek

AU - Britto, Carl

AU - Dias, Mary

AU - Nayak, Kaustuv

AU - Chandele, Anmol

AU - Kaja, Murali Krishna

AU - Shet, Anita

PY - 2019/1/1

Y1 - 2019/1/1

N2 - 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.

AB - 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.

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KW - Genotypes

KW - Lineages

KW - Phylogenetics

KW - Sequencing

KW - Serotyping

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