TY - JOUR
T1 - Emergence of new genotypes and lineages of dengue viruses during the 2012–15 epidemics in southern India
AU - Ahamed, Syed Fazil
AU - Rosario, V.
AU - Britto, Carl
AU - Dias, Mary
AU - Nayak, Kaustuv
AU - Chandele, A.
AU - Kaja, Murali Krishna
AU - Shet, A.
N1 - Funding Information:
We acknowledge financial support by the Department of Biotechnology (DBT), Ministry of Science and Technology, Government of India, No: BT/PR8470/MED/29/726/2013 (A Shet), and partial support from ICIDR 1UO1A/115654 (R. Ahmed). This article is part of a supplement entitled ?Dengue Fever in India? which is sponsored by the Department of Biotechnology, Government of India, and collated by the Translational Health Science and Technology Institute. We thank our colleagues Ms. Shalini Kotabagi for technical assistance and Mrs. Karthika Arumugam for statistical help, study nurse Mrs. Sheeba and phlebotomist Mr. Prem Kumar for patient recruitment and specimen collection. We thank Dr. Malali Gowda (Professor, TDU, Bangalore) and Dr. Subrahmanya Kumar (Assistant Professor, TDU, Bangalore) for their valuable comments. We are very grateful to our study children and their caregivers for participating in this study.
Funding Information:
We acknowledge financial support by the Department of Biotechnology (DBT), Ministry of Science and Technology, Government of India , No: BT/PR8470/MED/29/726/2013 (A Shet), and partial support from ICIDR 1UO1A/115654 (R. Ahmed).
Publisher Copyright:
© 2019
PY - 2019/7
Y1 - 2019/7
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.
KW - Dengue virus
KW - Genotypes
KW - Lineages
KW - Phylogenetics
KW - Sequencing
KW - Serotyping
UR - http://www.scopus.com/inward/record.url?scp=85061455682&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85061455682&partnerID=8YFLogxK
U2 - 10.1016/j.ijid.2019.01.014
DO - 10.1016/j.ijid.2019.01.014
M3 - Article
C2 - 30639622
AN - SCOPUS:85061455682
VL - 84
SP - S34-S43
JO - International Journal of Infectious Diseases
JF - International Journal of Infectious Diseases
SN - 1201-9712
ER -