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

Afreen N, Naqvi IH, Broor S, Ahmed A, Parveen S - PLoS ONE (2015)

Bottom Line: All DENV-3 strains were found to belong to Genotype III.Bayesian skyline plots were constructed for Indian DENV-1 and 3 strains which showed a decrease in population size since 2005 in case of DENV- 1 strains while no change was observed in recent years in case of DENV-3 strains.In addition, it will also assist in tracking the movement and evolution of this emerging virus.

View Article: PubMed Central - PubMed

Affiliation: Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.

ABSTRACT
Dengue fever is the most prevalent arboviral disease in the tropical and sub-tropical regions of the world. The present report describes molecular detection and serotyping of dengue viruses in acute phase blood samples collected from New Delhi, India. Phylogenetic and molecular clock analysis of dengue virus serotype 1 and 3 strains were also investigated. Dengue virus infection was detected in 68.87% out of 604 samples tested by RT-PCR between 2011 & 2014. Dengue serotype 1 was detected in 25.48% samples, dengue serotype 2 in 79.56% samples and dengue serotype 3 in 11.29% samples. Dengue serotype 4 was not detected. Co-infection by more than one dengue serotype was detected in 18.26% samples. Envelope gene of 29 DENV-1 and 14 DENV-3 strains were sequenced in the study. All the DENV-1 strains grouped with the American African genotype. All DENV-3 strains were found to belong to Genotype III. Nucleotide substitution rates of dengue 1 and 3 viruses were determined in the study. Time to the most recent common ancestor (TMRCA) of dengue 1 viruses was determined to be 132 years. TMRCA of DENV-3 viruses was estimated to be 149 years. Bayesian skyline plots were constructed for Indian DENV-1 and 3 strains which showed a decrease in population size since 2005 in case of DENV- 1 strains while no change was observed in recent years in case of DENV-3 strains. The study also revealed a change in the dominating serotype in Delhi, India in recent years. The study will be helpful in formulating control strategies for the outbreaks. In addition, it will also assist in tracking the movement and evolution of this emerging virus.

No MeSH data available.


Related in: MedlinePlus

Maximum likelihood phylogenetic tree of DENV-1 strains.The strains sequenced in the study are marked by diamonds. Numbers on nodes indicate bootstrap support generated by 1000 replicates. Bootstrap values of >70 are shown.
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pone.0141628.g001: Maximum likelihood phylogenetic tree of DENV-1 strains.The strains sequenced in the study are marked by diamonds. Numbers on nodes indicate bootstrap support generated by 1000 replicates. Bootstrap values of >70 are shown.

Mentions: E gene segments of 29 DENV-1 strains were sequenced in the present study. Twenty five strains were sequenced in 2013 while 4 strains were sequenced in 2014. The study sequences were deposited in the GenBank database with following accession numbers; GenBank: KJ729163-KJ729172 and KR091047- KR091065. Sequencing and phylogenetic analysis of the sequences with accession numbers KJ729163-KJ729172 have been described in our previous paper [7]. A 353 bp (117 amino acid) region of envelope gene corresponding to 1921–2273 bp of the DENV-1 genome and 332–448 amino acid of the E protein (numbering based on the prototype Nauru strain; GenBank Accession Number: U88535) was aligned. The study strains were found to group together with the American African Genotype (Fig 1) on phylogenetic analysis by Maximum Likelihood method. Patil et al. have described four lineages of Indian strains i.e. India I, II, III and Afro-India [17]. Strains of the present study clustered in Lineage India II of Patil et al. which is considered as an in situ evolving lineage. Six mutations i.e. PheE339Ile, SerE341Thr, AlaE371Thr, Val E382Ile, IleE438Val, Ile E441Val were detected in the study strains in comparison to the prototype strain. All these mutations were shown by earlier published sequences [18]. The study sequences showed nucleotide distance of up to 0.3% amongst themselves while amino acid sequences were identical. Strains from 2014 were identical to the predominant strain of 2013. The study strains were similar to recent strains reported from India, China, Bangladesh and Singapore (Fig 1).


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

Afreen N, Naqvi IH, Broor S, Ahmed A, Parveen S - PLoS ONE (2015)

Maximum likelihood phylogenetic tree of DENV-1 strains.The strains sequenced in the study are marked by diamonds. Numbers on nodes indicate bootstrap support generated by 1000 replicates. Bootstrap values of >70 are shown.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4633233&req=5

pone.0141628.g001: Maximum likelihood phylogenetic tree of DENV-1 strains.The strains sequenced in the study are marked by diamonds. Numbers on nodes indicate bootstrap support generated by 1000 replicates. Bootstrap values of >70 are shown.
Mentions: E gene segments of 29 DENV-1 strains were sequenced in the present study. Twenty five strains were sequenced in 2013 while 4 strains were sequenced in 2014. The study sequences were deposited in the GenBank database with following accession numbers; GenBank: KJ729163-KJ729172 and KR091047- KR091065. Sequencing and phylogenetic analysis of the sequences with accession numbers KJ729163-KJ729172 have been described in our previous paper [7]. A 353 bp (117 amino acid) region of envelope gene corresponding to 1921–2273 bp of the DENV-1 genome and 332–448 amino acid of the E protein (numbering based on the prototype Nauru strain; GenBank Accession Number: U88535) was aligned. The study strains were found to group together with the American African Genotype (Fig 1) on phylogenetic analysis by Maximum Likelihood method. Patil et al. have described four lineages of Indian strains i.e. India I, II, III and Afro-India [17]. Strains of the present study clustered in Lineage India II of Patil et al. which is considered as an in situ evolving lineage. Six mutations i.e. PheE339Ile, SerE341Thr, AlaE371Thr, Val E382Ile, IleE438Val, Ile E441Val were detected in the study strains in comparison to the prototype strain. All these mutations were shown by earlier published sequences [18]. The study sequences showed nucleotide distance of up to 0.3% amongst themselves while amino acid sequences were identical. Strains from 2014 were identical to the predominant strain of 2013. The study strains were similar to recent strains reported from India, China, Bangladesh and Singapore (Fig 1).

Bottom Line: All DENV-3 strains were found to belong to Genotype III.Bayesian skyline plots were constructed for Indian DENV-1 and 3 strains which showed a decrease in population size since 2005 in case of DENV- 1 strains while no change was observed in recent years in case of DENV-3 strains.In addition, it will also assist in tracking the movement and evolution of this emerging virus.

View Article: PubMed Central - PubMed

Affiliation: Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.

ABSTRACT
Dengue fever is the most prevalent arboviral disease in the tropical and sub-tropical regions of the world. The present report describes molecular detection and serotyping of dengue viruses in acute phase blood samples collected from New Delhi, India. Phylogenetic and molecular clock analysis of dengue virus serotype 1 and 3 strains were also investigated. Dengue virus infection was detected in 68.87% out of 604 samples tested by RT-PCR between 2011 & 2014. Dengue serotype 1 was detected in 25.48% samples, dengue serotype 2 in 79.56% samples and dengue serotype 3 in 11.29% samples. Dengue serotype 4 was not detected. Co-infection by more than one dengue serotype was detected in 18.26% samples. Envelope gene of 29 DENV-1 and 14 DENV-3 strains were sequenced in the study. All the DENV-1 strains grouped with the American African genotype. All DENV-3 strains were found to belong to Genotype III. Nucleotide substitution rates of dengue 1 and 3 viruses were determined in the study. Time to the most recent common ancestor (TMRCA) of dengue 1 viruses was determined to be 132 years. TMRCA of DENV-3 viruses was estimated to be 149 years. Bayesian skyline plots were constructed for Indian DENV-1 and 3 strains which showed a decrease in population size since 2005 in case of DENV- 1 strains while no change was observed in recent years in case of DENV-3 strains. The study also revealed a change in the dominating serotype in Delhi, India in recent years. The study will be helpful in formulating control strategies for the outbreaks. In addition, it will also assist in tracking the movement and evolution of this emerging virus.

No MeSH data available.


Related in: MedlinePlus