Evolutionary Analysis of Dengue Serotype 2 Viruses Using Phylogenetic and Bayesian Methods from New Delhi, India

Afreen, Nazia; Naqvi, Irshad H.; Broor, Shobha; Ahmed, Anwar; Kazim, Syed Naqui; Dohare, Ravins; Kumar, Manoj; Parveen, Shama

doi:10.1371/journal.pntd.0004511

Cited by 44 publications

(57 citation statements)

References 36 publications

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“…Our Bayesian skyline plots showed the demographic history of DENV-2, a decay was observed during 2005–2009. While population size of Indian Cosmopolitan strains remained almost constant in the period 2005 to 200941, the changes in genetic diversity of other genotypes may resulted in the decay of DENV-2 population size. Furthermore, the event of exponential increase in global dengue cases during 1976–1977 was not detected by the DENV-2 BSP analysis, it is possible that the increase of cases is due to other three DENV serotypes.…”

Section: Discussionmentioning

confidence: 99%

Global evolutionary history and spatio-temporal dynamics of dengue virus type 2

Wei

2017

Sci Rep

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DENV-2 spread throughout the tropical and subtropical regions globally, which is implicated in deadly outbreaks of DHF and DSS. Since dengue cases have grown dramatically in recent years, about half of the world’s population is now at risk. Our timescale analysis indicated that the most recent common ancestor existed about 100 years ago. The rate of nucleotide substitution was estimated to be 8.94 × 10−4 subs/site/year. Selection pressure analysis showed that two sites 160 and 403 were under positive selection, while E gene is mainly shaped by stronger purifying selection. BSP analysis showed that estimating effective population size from samples of sequences has undergone three obvious increases, additionally, Caribbean and Puerto Rico maintained higher levels of genetic diversity relative to other 6 representative geographical populations using GMRF method. The phylogeographic analysis indicated that two major transmission routes are from South America to Caribbean and East&SouthAsia to Puerto Rico. The trunk reconstruction confirmed that the viral evolution spanned 50 years occurred primarily in Southeast Asia and East&South Asia. In addition, phylogeographic association-trait analysis indicated that the viral phenotypes are highly correlated with phylogeny in Nicaragua and Puerto Rico (P < 0.05).

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Section: Discussionmentioning

confidence: 99%

Global evolutionary history and spatio-temporal dynamics of dengue virus type 2

Wei

2017

Sci Rep

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“…We identified a number of amino-acid mutations in this region. These mutations may alter the local secondary structure of the E protein which might affect the structure-function relationship [44]. One such recently reported mutation (T404I) was identified in two study DENV-2 strains.…”

Section: Discussionmentioning

confidence: 99%

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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“…From 1974, the genotypes circulating aligned with the Cosmopolitan genotype in Kerala, which had both genotypes circulating between 1971 and 1980. The Cosmopolitan genotype was the DENV-2 strain circulating between 1983 to the present time across India (Dash et al, 2004;Afreen et al, 2016;Yergolkar et al, 2017). An Asian American genotype was described from Maharashtra in 2017.…”

Section: Denv-2 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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Evolutionary Analysis of Dengue Serotype 2 Viruses Using Phylogenetic and Bayesian Methods from New Delhi, India

Cited by 44 publications

References 36 publications

Global evolutionary history and spatio-temporal dynamics of dengue virus type 2

Global evolutionary history and spatio-temporal dynamics of dengue virus type 2

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

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

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