Valine/isoleucine variants drive selective pressure in the VP1 sequence of EV-A71 enteroviruses
Abstract Background In 2011–2012, Northern Vietnam experienced its first large scale hand foot and mouth disease (HFMD) epidemic. In 2011, a major HFMD epidemic was also reported in South Vietnam with fatal cases. This 2011–2012 outbreak was the first one to occur in North Vietnam providing grounds...
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| Format: | Article |
| Language: | English |
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BMC
2017-05-01
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| Series: | BMC Infectious Diseases |
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| Online Access: | http://link.springer.com/article/10.1186/s12879-017-2427-4 |
| _version_ | 1818878763874648064 |
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| author | Nghia Ngu Duy Le Thi Thanh Huong Patrice Ravel Le Thi Song Huong Ankit Dwivedi October Michael Sessions Yan’An Hou Robert Chua Guilhem Kister Aneta Afelt Catherine Moulia Duane J. Gubler Vu Dinh Thiem Nguyen Thi Hien Thanh Christian Devaux Tran Nhu Duong Nguyen Tran Hien Emmanuel Cornillot Laurent Gavotte Roger Frutos |
| author_facet | Nghia Ngu Duy Le Thi Thanh Huong Patrice Ravel Le Thi Song Huong Ankit Dwivedi October Michael Sessions Yan’An Hou Robert Chua Guilhem Kister Aneta Afelt Catherine Moulia Duane J. Gubler Vu Dinh Thiem Nguyen Thi Hien Thanh Christian Devaux Tran Nhu Duong Nguyen Tran Hien Emmanuel Cornillot Laurent Gavotte Roger Frutos |
| author_sort | Nghia Ngu Duy |
| collection | DOAJ |
| description | Abstract Background In 2011–2012, Northern Vietnam experienced its first large scale hand foot and mouth disease (HFMD) epidemic. In 2011, a major HFMD epidemic was also reported in South Vietnam with fatal cases. This 2011–2012 outbreak was the first one to occur in North Vietnam providing grounds to study the etiology, origin and dynamic of the disease. We report here the analysis of the VP1 gene of strains isolated throughout North Vietnam during the 2011–2012 outbreak and before. Methods The VP1 gene of 106 EV-A71 isolates from North Vietnam and 2 from Central Vietnam were sequenced. Sequence alignments were analyzed at the nucleic acid and protein level. Gene polymorphism was also analyzed. A Factorial Correspondence Analysis was performed to correlate amino acid mutations with clinical parameters. Results The sequences were distributed into four phylogenetic clusters. Three clusters corresponded to the subgenogroup C4 and the last one corresponded to the subgenogroup C5. Each cluster displayed different polymorphism characteristics. Proteins were highly conserved but three sites bearing only Isoleucine (I) or Valine (V) were characterized. The isoleucine/valine variability matched the clusters. Spatiotemporal analysis of the I/V variants showed that all variants which emerged in 2011 and then in 2012 were not the same but were all present in the region prior to the 2011–2012 outbreak. Some correlation was found between certain I/V variants and ethnicity and severity. Conclusions The 2011–2012 outbreak was not caused by an exogenous strain coming from South Vietnam or elsewhere but by strains already present and circulating at low level in North Vietnam. However, what triggered the outbreak remains unclear. A selective pressure is applied on I/V variants which matches the genetic clusters. I/V variants were shown on other viruses to correlate with pathogenicity. This should be investigated in EV-A71. I/V variants are an easy and efficient way to survey and identify circulating EV-A71 strains. |
| first_indexed | 2024-12-19T14:19:21Z |
| format | Article |
| id | doaj.art-1b9eafd96b5443bf8db7ec9e336dc06d |
| institution | Directory Open Access Journal |
| issn | 1471-2334 |
| language | English |
| last_indexed | 2024-12-19T14:19:21Z |
| publishDate | 2017-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Infectious Diseases |
| spelling | doaj.art-1b9eafd96b5443bf8db7ec9e336dc06d2022-12-21T20:17:51ZengBMCBMC Infectious Diseases1471-23342017-05-0117111210.1186/s12879-017-2427-4Valine/isoleucine variants drive selective pressure in the VP1 sequence of EV-A71 enterovirusesNghia Ngu Duy0Le Thi Thanh Huong1Patrice Ravel2Le Thi Song Huong3Ankit Dwivedi4October Michael Sessions5Yan’An Hou6Robert Chua7Guilhem Kister8Aneta Afelt9Catherine Moulia10Duane J. Gubler11Vu Dinh Thiem12Nguyen Thi Hien Thanh13Christian Devaux14Tran Nhu Duong15Nguyen Tran Hien16Emmanuel Cornillot17Laurent Gavotte18Roger Frutos19National Institute of Hygiene and EpidemiologyNational Institute of Hygiene and EpidemiologyInstitut de Recherche en Cancérologie de Montpellier (U1194), Campus Val d’AurelleHai Phong Preventive Medicine CenterInstitut de Biologie Computationnelle, MMVEDUKE-NUS Graduate Medical SchoolDUKE-NUS Graduate Medical SchoolDUKE-NUS Graduate Medical SchoolFaculty of Pharmacy, University of MontpellierFaculty of Geography and Regional Studies, University of WarsawUniversity of Montpellier, ISEMDUKE-NUS Graduate Medical SchoolNational Institute of Hygiene and EpidemiologyNational Institute of Hygiene and EpidemiologyInstitut de Recherche pour le Développement (IRD)National Institute of Hygiene and EpidemiologyNational Institute of Hygiene and EpidemiologyInstitut de Recherche en Cancérologie de Montpellier (U1194), Campus Val d’AurelleUniversity of Montpellier, ISEMCirad, UMR 17, Intertryp, TA-A17/G, Campus International de BaillarguetAbstract Background In 2011–2012, Northern Vietnam experienced its first large scale hand foot and mouth disease (HFMD) epidemic. In 2011, a major HFMD epidemic was also reported in South Vietnam with fatal cases. This 2011–2012 outbreak was the first one to occur in North Vietnam providing grounds to study the etiology, origin and dynamic of the disease. We report here the analysis of the VP1 gene of strains isolated throughout North Vietnam during the 2011–2012 outbreak and before. Methods The VP1 gene of 106 EV-A71 isolates from North Vietnam and 2 from Central Vietnam were sequenced. Sequence alignments were analyzed at the nucleic acid and protein level. Gene polymorphism was also analyzed. A Factorial Correspondence Analysis was performed to correlate amino acid mutations with clinical parameters. Results The sequences were distributed into four phylogenetic clusters. Three clusters corresponded to the subgenogroup C4 and the last one corresponded to the subgenogroup C5. Each cluster displayed different polymorphism characteristics. Proteins were highly conserved but three sites bearing only Isoleucine (I) or Valine (V) were characterized. The isoleucine/valine variability matched the clusters. Spatiotemporal analysis of the I/V variants showed that all variants which emerged in 2011 and then in 2012 were not the same but were all present in the region prior to the 2011–2012 outbreak. Some correlation was found between certain I/V variants and ethnicity and severity. Conclusions The 2011–2012 outbreak was not caused by an exogenous strain coming from South Vietnam or elsewhere but by strains already present and circulating at low level in North Vietnam. However, what triggered the outbreak remains unclear. A selective pressure is applied on I/V variants which matches the genetic clusters. I/V variants were shown on other viruses to correlate with pathogenicity. This should be investigated in EV-A71. I/V variants are an easy and efficient way to survey and identify circulating EV-A71 strains.http://link.springer.com/article/10.1186/s12879-017-2427-4VP1HFMDEnterovirusEV-A71Vietnam |
| spellingShingle | Nghia Ngu Duy Le Thi Thanh Huong Patrice Ravel Le Thi Song Huong Ankit Dwivedi October Michael Sessions Yan’An Hou Robert Chua Guilhem Kister Aneta Afelt Catherine Moulia Duane J. Gubler Vu Dinh Thiem Nguyen Thi Hien Thanh Christian Devaux Tran Nhu Duong Nguyen Tran Hien Emmanuel Cornillot Laurent Gavotte Roger Frutos Valine/isoleucine variants drive selective pressure in the VP1 sequence of EV-A71 enteroviruses BMC Infectious Diseases VP1 HFMD Enterovirus EV-A71 Vietnam |
| title | Valine/isoleucine variants drive selective pressure in the VP1 sequence of EV-A71 enteroviruses |
| title_full | Valine/isoleucine variants drive selective pressure in the VP1 sequence of EV-A71 enteroviruses |
| title_fullStr | Valine/isoleucine variants drive selective pressure in the VP1 sequence of EV-A71 enteroviruses |
| title_full_unstemmed | Valine/isoleucine variants drive selective pressure in the VP1 sequence of EV-A71 enteroviruses |
| title_short | Valine/isoleucine variants drive selective pressure in the VP1 sequence of EV-A71 enteroviruses |
| title_sort | valine isoleucine variants drive selective pressure in the vp1 sequence of ev a71 enteroviruses |
| topic | VP1 HFMD Enterovirus EV-A71 Vietnam |
| url | http://link.springer.com/article/10.1186/s12879-017-2427-4 |
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