Phylogenetic and Molecular Clock Analysis of Dengue Serotype 1 and 3 from New Delhi, India

Afreen, Nazia; Naqvi, Irshad H.; Broor, Shobha; Ahmed, Anwar; Parveen, Shama

doi:10.1371/journal.pone.0141628

Cited by 37 publications

(39 citation statements)

References 27 publications

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“…Similarly 43% co-infection was reported from Davangere, Karnataka [5] and 57% from Thiruvananthapuram, Kerala [6], 32·5% from Moreh, Manipur [38] and 19% from Delhi [3]. Our earlier work reported 9% co-infections during 2011 [7], 14% during 2013 [2] and 18% during 4 years of study from 2011-14 [39] in Delhi. Dual infection was also reported in other investigations from Delhi [4,40,41].…”

Section: Discussionsupporting

confidence: 63%

Occurrence of co-infection with dengue viruses during 2014 in New Delhi, India

et al. 2016

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SUMMARYDengue fever is an arthropod-borne viral infection that has become endemic in several parts of India including Delhi. We studied occurrence of co-infection with dengue viruses during an outbreak in New Delhi, India in 2014. For the present study, blood samples collected from symptomatic patients were analysed by RT-PCR. Eighty percent of the samples were positive for dengue virus. The result showed that DENV-1 (77%) was the predominant serotype followed by DENV-2 (60%). Concurrent infection with more than one serotype was identified in 43% of the positive samples. Phylogenetic analysis clustered DENV-1 strains with the American African and DENV-2 strains in Cosmopolitan genotypes. Four common amino-acid mutations were identified in the envelope gene of DENV-1 sequences (F337I, A369T, V380I and L402F) and one common mutation (N390S) in the DENV-2 sequences. Further analysis revealed purifying selection in both the serotypes. A significant number of patients were co-infected with DENV-1 and DENV-2 serotypes. Although we do not have direct evidence to demonstrate co-evolution of these two stereotypes, nonetheless their simultaneous occurrence does indicate that they are favoured by evolutionary forces. An ongoing surveillance and careful analysis of future outbreaks will strengthen the concept of co-evolution or otherwise. Whether the concurrent dengue viral infection is correlated with disease severity in a given population is another aspect to be pursued. This study is envisaged to be useful for future reference in the context of overall epidemiology.

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Section: Discussionsupporting

confidence: 63%

Occurrence of co-infection with dengue viruses during 2014 in New Delhi, India

et al. 2016

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“…Den-3 strain circulating in this area grouped into genotype III, which is also known to associate with severe dengue [39]. Very less genetic information is available in case of Den-4 from India and the studies carried out during 2011-14 in Delhi also failed to find a single patient with Den-4 [36]. But in our study, Den-4 was detected in 33% of infected patients and found to be grouped into genotype I C. The results showed its close relatedness to the Den-4 strain characterised from Pune, India, in 2009 with high percent similarity at nucleotide level (Fig.…”

Section: Discussionmentioning

confidence: 99%

Co-circulation and co-infections of all dengue virus serotypes in Hyderabad, India 2014

et al. 2017

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The burden of dengue virus infections increased globally during recent years. Though India is considered as dengue hyper-endemic country, limited data are available on disease epidemiology. The present study includes molecular characterization of dengue virus strains occurred in Hyderabad, India, during the year 2014. A total of 120 febrile cases were recruited for this study, which includes only children and 41 were serologically confirmed for dengue positive infections using non-structural (NS1) and/or IgG/IgM ELISA tests. RT-PCR, nucleotide sequencing and evolutionary analyses were carried out to identify the circulating serotypes/genotypes. The data indicated a high percent of severe dengue (63%) in primary infections. Simultaneous circulation of all four serotypes and co-infections were observed for the first time in Hyderabad, India. In total, 15 patients were co-infected with more than one dengue serotype and 12 (80%) of them had severe dengue. One of the striking findings of the present study is the identification of serotype Den-1 as the first report from this region and this strain showed close relatedness to the Thailand 1980 strains but not to any of the strains reported from India until now. Phylogenetically, all four strains of the present study showed close relatedness to the strains, which are reported to be high virulent.

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“…A hitherto unpublished sequence from Tamil Nadu (Vellore 2015) aligned as G-I (Asian). (Tripathi et al, 2012;Afreen et al, 2015;Cecilia et al, 2017;Pooja et al, 2017;Yergolkar et al, 2017) Kerala also had genotype I (Asian) circulating (2014,2015).…”

Section: Denv-1 Genotypesmentioning

confidence: 98%

“…Indian DENV-3 genotypes are G-I II from the earliest DENV-3 strain (Vellore, 1966). Later viruses include multiple strains of G III from across the country (Figures 9 and 10) (Bedi et al, 2013;Tripathi et al, 2013;Afreen et al, 2015;Angel et al, 2016).…”

Section: Denv-3 Genotypesmentioning

confidence: 99%

Phylogenetic analysis of partial pre-membrane and envelope sequences of dengue viruses circulating in India

Kasirajan

Mammen

Kannangai

et al. 2019

International Journal of Infectious Diseases

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A B S T R A C TObjective: Phylogenetic characteristics of circulating Indian dengue viruses (DENV) were analysed using partial pre-membrane (PrM) and envelope (E) sequences. An immunodominant region was analysed for mutations, and alignment with common DENV PCR primers and probes was determined. Methods: Published Indian PrM and E DENV sequences were analysed with hitherto unpublished PrM sequences from this study site. Alignments of DENV were checked for mutations in an immunodominant region and against the commonly used PCR primers and probes. Results: All four serotypes of DENV circulate in India. Genotype (G) GIII and GI of DENV-1 co-circulated in the south with significant PrM mutations before and after 2012. DENV-2 American genotype was first reported after which the Cosmopolitan genotype co-circulated with it in the southwest. The Cosmopolitan strain has been the only DENV-2 genotype circulating, although an Asian American genotype was recently reported. Significant mutations were found in the E region of DENV-2 strains. DENV-3 strains were GIII across the country. DENV-4 GI from the south and west has now spread across India. No significant mutations were found for DENV-3 or DENV-4. Indian strains showed mutations in an immunodominant region of the E gene and in the regions targeted by commonly used PCR primers and probes. Conclusions: The genetic variability of Indian DENV with co-circulation of multiple genotypes suggests that genotype surveillance is crucial to determining the composition of dengue vaccines and understanding their contribution to epidemiology, virus fitness and pathogenesis. Some mutations seen in an immunodominant region of the E gene may allow these viruses to evade host immune cells. The mutations in the regions targeted by commonly used primers and probes necessitate higher degeneracy.

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Phylogenetic and Molecular Clock Analysis of Dengue Serotype 1 and 3 from New Delhi, India

Cited by 37 publications

References 27 publications

Occurrence of co-infection with dengue viruses during 2014 in New Delhi, India

Occurrence of co-infection with dengue viruses during 2014 in New Delhi, India

Co-circulation and co-infections of all dengue virus serotypes in Hyderabad, India 2014

Phylogenetic analysis of partial pre-membrane and envelope sequences of dengue viruses circulating in India

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