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Phylogenetic studies reveal existence of multiple lineages of a single genotype of DENV-1 (genotype III) in India during 1956-2007.

Kukreti H, Dash PK, Parida M, Chaudhary A, Saxena P, Rautela RS, Mittal V, Chhabra M, Bhattacharya D, Lal S, Rao PV, Rai A - Virol. J. (2009)

Bottom Line: For comparison, we retrieved 11 other Indian and 70 global reference sequences from NCBI database, making sure that Indian and global isolates from all decades are available for comparative analysis.The region was found to be AT rich with no insertion or deletion.Majority of the nucleotide substitutions were silent, except 3 non-conservative amino acid changes (I --> T, A --> T and L --> S at amino acid positions 59,114 and 155 respectively) in the Indian DENV-1 sequences, sequenced in this study.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Institute of Communicable Diseases, Delhi, India. himani_kukreti@yahoo.co.in

ABSTRACT

Background: Dengue virus type 1 (DENV-1) have been mostly circulating silently with dominant serotypes DENV-2 and DENV-3 in India. However recent times have marked an increase in DENV-1 circulation in yearly outbreaks. Many studies have not been carried out on this virus type, leaving a lacunae pertaining to the circulating genotypes, since its earliest report in India. In the present study, we sequenced CprM gene junction of 13 DENV-1 isolated from Delhi and Gwalior (North India) between 2001-2007 and one 1956 Vellore isolate as reference. For comparison, we retrieved 11 other Indian and 70 global reference sequences from NCBI database, making sure that Indian and global isolates from all decades are available for comparative analysis.

Results: The region was found to be AT rich with no insertion or deletion. Majority of the nucleotide substitutions were silent, except 3 non-conservative amino acid changes (I --> T, A --> T and L --> S at amino acid positions 59,114 and 155 respectively) in the Indian DENV-1 sequences, sequenced in this study. Except two 1997-98 Delhi isolates, which group in genotype I; all other Indian isolates group in genotype III. All Indian genotype III DENV-1 exhibited diversity among them, giving rise to at least 4 distinct lineages (India 1-4) showing proximity to isolates from diverse geographic locations.

Conclusion: The extensive phylogenetic analysis revealed consistent existence of multiple lineages of DENV-1 genotype III during the last 5 decades in India.

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Related in: MedlinePlus

Amino acid alignment of CprM gene junction sequences of all Indian and global DENV-1 showing changes in comparison to the consensus sequence. The Indian sequences that are sequenced in this study are in bold. The numbering of amino acid position corresponds to the ORF of DEN-1 strain "Singapore 8114/93" (GenBank Acc. No. AY762084). Dot (.) indicates amino acid similarities with the consensus.
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Figure 1: Amino acid alignment of CprM gene junction sequences of all Indian and global DENV-1 showing changes in comparison to the consensus sequence. The Indian sequences that are sequenced in this study are in bold. The numbering of amino acid position corresponds to the ORF of DEN-1 strain "Singapore 8114/93" (GenBank Acc. No. AY762084). Dot (.) indicates amino acid similarities with the consensus.

Mentions: Thirteen serum samples found positive for DENV-1 during dengue outbreaks in northern India during 2001–2007 were included in this study. For sequence comparison and phylogenetic analysis we selected a 354 bp sequence (nucleotides 208–561) from CprM gene junction of 13 DENV-1 sequenced in this study and compared them with 11 representatives Indian and 70 other global geographically diverse DENV-1 sequences, spanning last 5 decades. All these sequences were aligned with the prototype Indian DENV-1 isolate (India-56 (Vellore) that was also sequenced in the study. This region was found to be AT rich and the AT composition of the Indian DENV-1 varied from 52.6–53.7%. The alignment did not reveal any base insertion or deletion, only substitutions which were mostly synonymous in nature. Deduced amino acid alignment of the Indian isolates sequenced in this study revealed that the non-synonymous nucleotide substitutions, gave rise to only 3 non-conservative amino acid changes i.e. isoleucine to threonine (Amino acid position 59) and leucine to serine (Amino acid position 155) as seen in some 2006 and 2007 Delhi isolates; and alanine to threonine (Amino acid position 114) as observed in 2001 Delhi and 2002 Gwalior isolates (amino acid alignment shown as Figure 1 and 2).


Phylogenetic studies reveal existence of multiple lineages of a single genotype of DENV-1 (genotype III) in India during 1956-2007.

Kukreti H, Dash PK, Parida M, Chaudhary A, Saxena P, Rautela RS, Mittal V, Chhabra M, Bhattacharya D, Lal S, Rao PV, Rai A - Virol. J. (2009)

Amino acid alignment of CprM gene junction sequences of all Indian and global DENV-1 showing changes in comparison to the consensus sequence. The Indian sequences that are sequenced in this study are in bold. The numbering of amino acid position corresponds to the ORF of DEN-1 strain "Singapore 8114/93" (GenBank Acc. No. AY762084). Dot (.) indicates amino acid similarities with the consensus.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2667167&req=5

Figure 1: Amino acid alignment of CprM gene junction sequences of all Indian and global DENV-1 showing changes in comparison to the consensus sequence. The Indian sequences that are sequenced in this study are in bold. The numbering of amino acid position corresponds to the ORF of DEN-1 strain "Singapore 8114/93" (GenBank Acc. No. AY762084). Dot (.) indicates amino acid similarities with the consensus.
Mentions: Thirteen serum samples found positive for DENV-1 during dengue outbreaks in northern India during 2001–2007 were included in this study. For sequence comparison and phylogenetic analysis we selected a 354 bp sequence (nucleotides 208–561) from CprM gene junction of 13 DENV-1 sequenced in this study and compared them with 11 representatives Indian and 70 other global geographically diverse DENV-1 sequences, spanning last 5 decades. All these sequences were aligned with the prototype Indian DENV-1 isolate (India-56 (Vellore) that was also sequenced in the study. This region was found to be AT rich and the AT composition of the Indian DENV-1 varied from 52.6–53.7%. The alignment did not reveal any base insertion or deletion, only substitutions which were mostly synonymous in nature. Deduced amino acid alignment of the Indian isolates sequenced in this study revealed that the non-synonymous nucleotide substitutions, gave rise to only 3 non-conservative amino acid changes i.e. isoleucine to threonine (Amino acid position 59) and leucine to serine (Amino acid position 155) as seen in some 2006 and 2007 Delhi isolates; and alanine to threonine (Amino acid position 114) as observed in 2001 Delhi and 2002 Gwalior isolates (amino acid alignment shown as Figure 1 and 2).

Bottom Line: For comparison, we retrieved 11 other Indian and 70 global reference sequences from NCBI database, making sure that Indian and global isolates from all decades are available for comparative analysis.The region was found to be AT rich with no insertion or deletion.Majority of the nucleotide substitutions were silent, except 3 non-conservative amino acid changes (I --> T, A --> T and L --> S at amino acid positions 59,114 and 155 respectively) in the Indian DENV-1 sequences, sequenced in this study.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Institute of Communicable Diseases, Delhi, India. himani_kukreti@yahoo.co.in

ABSTRACT

Background: Dengue virus type 1 (DENV-1) have been mostly circulating silently with dominant serotypes DENV-2 and DENV-3 in India. However recent times have marked an increase in DENV-1 circulation in yearly outbreaks. Many studies have not been carried out on this virus type, leaving a lacunae pertaining to the circulating genotypes, since its earliest report in India. In the present study, we sequenced CprM gene junction of 13 DENV-1 isolated from Delhi and Gwalior (North India) between 2001-2007 and one 1956 Vellore isolate as reference. For comparison, we retrieved 11 other Indian and 70 global reference sequences from NCBI database, making sure that Indian and global isolates from all decades are available for comparative analysis.

Results: The region was found to be AT rich with no insertion or deletion. Majority of the nucleotide substitutions were silent, except 3 non-conservative amino acid changes (I --> T, A --> T and L --> S at amino acid positions 59,114 and 155 respectively) in the Indian DENV-1 sequences, sequenced in this study. Except two 1997-98 Delhi isolates, which group in genotype I; all other Indian isolates group in genotype III. All Indian genotype III DENV-1 exhibited diversity among them, giving rise to at least 4 distinct lineages (India 1-4) showing proximity to isolates from diverse geographic locations.

Conclusion: The extensive phylogenetic analysis revealed consistent existence of multiple lineages of DENV-1 genotype III during the last 5 decades in India.

Show MeSH
Related in: MedlinePlus