Complete genome sequencing and evolutionary analysis of Indian isolates of Dengue virus type 2
•Complete genome of Indian DENV-2 was deciphered for the first time in this study.•The recent Indian DENV-2 revealed presence of many unique amino acid residues.•Genotype shift (American to Cosmopolitan) characterizes evolution of DENV-2 in India.•Circulation of a unique clade of DENV-2 in South Asi...
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| Veröffentlicht in: | Biochemical and biophysical research communications 2013-07, Vol.436 (3), p.478-485 |
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| creator | Dash, Paban Kumar Sharma, Shashi Soni, Manisha Agarwal, Ankita Parida, Manmohan Rao, P.V.Lakshmana |
| description | •Complete genome of Indian DENV-2 was deciphered for the first time in this study.•The recent Indian DENV-2 revealed presence of many unique amino acid residues.•Genotype shift (American to Cosmopolitan) characterizes evolution of DENV-2 in India.•Circulation of a unique clade of DENV-2 in South Asia was identified.
Dengue is the most important arboviral infection of global public health significance. It is now endemic in most parts of the South East Asia including India. Though Dengue virus type 2 (DENV-2) is predominantly associated with major outbreaks in India, complete genome information of Indian DENV-2 is not available. In this study, the full-length genome of five DENV-2 isolates (four from 2001 to 2011 and one from 1960), from different parts of India was determined. The complete genome of the Indian DENV-2 was found to be 10,670 bases long with an open reading frame coding for 3391 amino acids. The recent Indian DENV-2 (2001–2011) revealed a nucleotide sequence identity of around 90% and 97% with an older Indian DENV-2 (1960) and closely related Sri Lankan and Chinese DENV-2 respectively. Presence of unique amino acid residues and non-conservative substitutions in critical amino acid residues of major structural and non-structural proteins was observed in recent Indian DENV-2. Selection pressure analysis revealed positive selection in few amino acid sites of the genes encoding for structural and non-structural proteins. The molecular phylogenetic analysis based on comparison of both complete coding region and envelope protein gene with globally diverse DENV-2 viruses classified the recent Indian isolates into a unique South Asian clade within Cosmopolitan genotype. A shift of genotype from American to Cosmopolitan in 1970s characterized the evolution of DENV-2 in India. Present study is the first report on complete genome characterization of emerging DENV-2 isolates from India and highlights the circulation of a unique clade in South Asia. |
| doi_str_mv | 10.1016/j.bbrc.2013.05.130 |
| format | Article |
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Dengue is the most important arboviral infection of global public health significance. It is now endemic in most parts of the South East Asia including India. Though Dengue virus type 2 (DENV-2) is predominantly associated with major outbreaks in India, complete genome information of Indian DENV-2 is not available. In this study, the full-length genome of five DENV-2 isolates (four from 2001 to 2011 and one from 1960), from different parts of India was determined. The complete genome of the Indian DENV-2 was found to be 10,670 bases long with an open reading frame coding for 3391 amino acids. The recent Indian DENV-2 (2001–2011) revealed a nucleotide sequence identity of around 90% and 97% with an older Indian DENV-2 (1960) and closely related Sri Lankan and Chinese DENV-2 respectively. Presence of unique amino acid residues and non-conservative substitutions in critical amino acid residues of major structural and non-structural proteins was observed in recent Indian DENV-2. Selection pressure analysis revealed positive selection in few amino acid sites of the genes encoding for structural and non-structural proteins. The molecular phylogenetic analysis based on comparison of both complete coding region and envelope protein gene with globally diverse DENV-2 viruses classified the recent Indian isolates into a unique South Asian clade within Cosmopolitan genotype. A shift of genotype from American to Cosmopolitan in 1970s characterized the evolution of DENV-2 in India. Present study is the first report on complete genome characterization of emerging DENV-2 isolates from India and highlights the circulation of a unique clade in South Asia.</description><identifier>ISSN: 0006-291X</identifier><identifier>EISSN: 1090-2104</identifier><identifier>DOI: 10.1016/j.bbrc.2013.05.130</identifier><identifier>PMID: 23756811</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>60 APPLIED LIFE SCIENCES ; Amino Acid Substitution ; AMINO ACIDS ; Base Sequence ; Complete genome ; Dengue Virus - classification ; Dengue Virus - genetics ; Dengue Virus - isolation & purification ; Dengue virus type 2 ; DENV-2 ; EPIDEMIOLOGY ; Evolution, Molecular ; Genetic Variation ; Genome, Viral ; Genotype ; Humans ; India ; Molecular epidemiology ; NUCLEOTIDES ; Open Reading Frames ; Phylogeny ; PROTEINS ; PUBLIC HEALTH ; RNA, Viral - analysis ; RNA, Viral - genetics ; Selection pressure ; Selection, Genetic ; Sequence Analysis, RNA ; Sequence Homology, Nucleic Acid ; Viral Envelope Proteins - genetics ; VIRUSES</subject><ispartof>Biochemical and biophysical research communications, 2013-07, Vol.436 (3), p.478-485</ispartof><rights>2013 Elsevier Inc.</rights><rights>Copyright © 2013 Elsevier Inc. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c417t-5932900c76748259e6abd3b0e381600c692c174d7377f85adf87f2fe081f0e5a3</citedby><cites>FETCH-LOGICAL-c417t-5932900c76748259e6abd3b0e381600c692c174d7377f85adf87f2fe081f0e5a3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0006291X13009480$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>230,314,776,780,881,3536,27903,27904,65309</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23756811$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/biblio/22239654$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Dash, Paban Kumar</creatorcontrib><creatorcontrib>Sharma, Shashi</creatorcontrib><creatorcontrib>Soni, Manisha</creatorcontrib><creatorcontrib>Agarwal, Ankita</creatorcontrib><creatorcontrib>Parida, Manmohan</creatorcontrib><creatorcontrib>Rao, P.V.Lakshmana</creatorcontrib><title>Complete genome sequencing and evolutionary analysis of Indian isolates of Dengue virus type 2</title><title>Biochemical and biophysical research communications</title><addtitle>Biochem Biophys Res Commun</addtitle><description>•Complete genome of Indian DENV-2 was deciphered for the first time in this study.•The recent Indian DENV-2 revealed presence of many unique amino acid residues.•Genotype shift (American to Cosmopolitan) characterizes evolution of DENV-2 in India.•Circulation of a unique clade of DENV-2 in South Asia was identified.
Dengue is the most important arboviral infection of global public health significance. It is now endemic in most parts of the South East Asia including India. Though Dengue virus type 2 (DENV-2) is predominantly associated with major outbreaks in India, complete genome information of Indian DENV-2 is not available. In this study, the full-length genome of five DENV-2 isolates (four from 2001 to 2011 and one from 1960), from different parts of India was determined. The complete genome of the Indian DENV-2 was found to be 10,670 bases long with an open reading frame coding for 3391 amino acids. The recent Indian DENV-2 (2001–2011) revealed a nucleotide sequence identity of around 90% and 97% with an older Indian DENV-2 (1960) and closely related Sri Lankan and Chinese DENV-2 respectively. Presence of unique amino acid residues and non-conservative substitutions in critical amino acid residues of major structural and non-structural proteins was observed in recent Indian DENV-2. Selection pressure analysis revealed positive selection in few amino acid sites of the genes encoding for structural and non-structural proteins. The molecular phylogenetic analysis based on comparison of both complete coding region and envelope protein gene with globally diverse DENV-2 viruses classified the recent Indian isolates into a unique South Asian clade within Cosmopolitan genotype. A shift of genotype from American to Cosmopolitan in 1970s characterized the evolution of DENV-2 in India. Present study is the first report on complete genome characterization of emerging DENV-2 isolates from India and highlights the circulation of a unique clade in South Asia.</description><subject>60 APPLIED LIFE SCIENCES</subject><subject>Amino Acid Substitution</subject><subject>AMINO ACIDS</subject><subject>Base Sequence</subject><subject>Complete genome</subject><subject>Dengue Virus - classification</subject><subject>Dengue Virus - genetics</subject><subject>Dengue Virus - isolation & purification</subject><subject>Dengue virus type 2</subject><subject>DENV-2</subject><subject>EPIDEMIOLOGY</subject><subject>Evolution, Molecular</subject><subject>Genetic Variation</subject><subject>Genome, Viral</subject><subject>Genotype</subject><subject>Humans</subject><subject>India</subject><subject>Molecular epidemiology</subject><subject>NUCLEOTIDES</subject><subject>Open Reading Frames</subject><subject>Phylogeny</subject><subject>PROTEINS</subject><subject>PUBLIC HEALTH</subject><subject>RNA, Viral - analysis</subject><subject>RNA, Viral - genetics</subject><subject>Selection pressure</subject><subject>Selection, Genetic</subject><subject>Sequence Analysis, RNA</subject><subject>Sequence Homology, Nucleic Acid</subject><subject>Viral Envelope Proteins - genetics</subject><subject>VIRUSES</subject><issn>0006-291X</issn><issn>1090-2104</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkUFv1DAQhS1ERbeFP8ABWeLCJenYTpxY4oIWCpUqcQGJE5bjTBavEnuJnZX239dhC0d6Gunpe2808wh5zaBkwOTNvuy62ZYcmCihLpmAZ2TDQEHBGVTPyQYAZMEV-3FJrmLcAzBWSfWCXHLR1LJlbEN-bsN0GDEh3aEPE9KIvxf01vkdNb6neAzjklzwZj5lwYyn6CINA73zvTOeuhhGk_CP9BH9bkF6dPMSaTodkPKX5GIwY8RXj_OafL_99G37pbj_-vlu--G-sBVrUlErwRWAbWRTtbxWKE3Xiw5QtExmXSpuWVP1jWiaoa1NP7TNwAeElg2AtRHX5O05N8TkdLQuof1lg_dok-acCyXrKlPvztRhDvnKmPTkosVxNB7DEjWTMm_PS9TTqFAK6ir_OaP8jNo5xDjjoA-zm_K_NAO9FqX3ei1Kr0VpqLMXsunNY_7STdj_s_xtJgPvzwDmtx0dzutVuRjs3bwe1Qf3v_wHO2yitw</recordid><startdate>20130705</startdate><enddate>20130705</enddate><creator>Dash, Paban Kumar</creator><creator>Sharma, Shashi</creator><creator>Soni, Manisha</creator><creator>Agarwal, Ankita</creator><creator>Parida, Manmohan</creator><creator>Rao, P.V.Lakshmana</creator><general>Elsevier Inc</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>7T2</scope><scope>7TM</scope><scope>7U2</scope><scope>7U9</scope><scope>C1K</scope><scope>F1W</scope><scope>H94</scope><scope>H95</scope><scope>H97</scope><scope>L.G</scope><scope>OTOTI</scope></search><sort><creationdate>20130705</creationdate><title>Complete genome sequencing and evolutionary analysis of Indian isolates of Dengue virus type 2</title><author>Dash, Paban Kumar ; 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Dengue is the most important arboviral infection of global public health significance. It is now endemic in most parts of the South East Asia including India. Though Dengue virus type 2 (DENV-2) is predominantly associated with major outbreaks in India, complete genome information of Indian DENV-2 is not available. In this study, the full-length genome of five DENV-2 isolates (four from 2001 to 2011 and one from 1960), from different parts of India was determined. The complete genome of the Indian DENV-2 was found to be 10,670 bases long with an open reading frame coding for 3391 amino acids. The recent Indian DENV-2 (2001–2011) revealed a nucleotide sequence identity of around 90% and 97% with an older Indian DENV-2 (1960) and closely related Sri Lankan and Chinese DENV-2 respectively. Presence of unique amino acid residues and non-conservative substitutions in critical amino acid residues of major structural and non-structural proteins was observed in recent Indian DENV-2. Selection pressure analysis revealed positive selection in few amino acid sites of the genes encoding for structural and non-structural proteins. The molecular phylogenetic analysis based on comparison of both complete coding region and envelope protein gene with globally diverse DENV-2 viruses classified the recent Indian isolates into a unique South Asian clade within Cosmopolitan genotype. A shift of genotype from American to Cosmopolitan in 1970s characterized the evolution of DENV-2 in India. Present study is the first report on complete genome characterization of emerging DENV-2 isolates from India and highlights the circulation of a unique clade in South Asia.</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>23756811</pmid><doi>10.1016/j.bbrc.2013.05.130</doi><tpages>8</tpages></addata></record> |
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| subjects | 60 APPLIED LIFE SCIENCES Amino Acid Substitution AMINO ACIDS Base Sequence Complete genome Dengue Virus - classification Dengue Virus - genetics Dengue Virus - isolation & purification Dengue virus type 2 DENV-2 EPIDEMIOLOGY Evolution, Molecular Genetic Variation Genome, Viral Genotype Humans India Molecular epidemiology NUCLEOTIDES Open Reading Frames Phylogeny PROTEINS PUBLIC HEALTH RNA, Viral - analysis RNA, Viral - genetics Selection pressure Selection, Genetic Sequence Analysis, RNA Sequence Homology, Nucleic Acid Viral Envelope Proteins - genetics VIRUSES |
| title | Complete genome sequencing and evolutionary analysis of Indian isolates of Dengue virus type 2 |
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