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Roy P, Dey S, Nandy A, Basak SC, Das S. Base Distribution in Dengue Nucleotide Sequences Differs Significantly from Other Mosquito-Borne Human-Infecting Flavivirus Members. Curr Comput Aided Drug Des 2018; 15:29-44. [PMID: 30062973 DOI: 10.2174/1573409914666180731090005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/02/2018] [Accepted: 07/25/2018] [Indexed: 11/22/2022]
Abstract
INTRODUCTION Among the mosquito-borne human-infecting flavivirus species that include Zika, West Nile, yellow fever, Japanese encephalitis and Dengue viruses, the Zika virus is found to be closest to Dengue virus, sharing the same clade in the Flavivirus phylogenetic tree. We consider these five flaviviruses and on closer examination in our analyses, the nucleotide sequences of the Dengue viral genes (envelope and NS5) and genomes are seen to be quite widely different from the other four flaviviruses. We consider the extent of this distinction and determine the advantage and/or disadvantage such differences may confer upon the Dengue viral pathogenesis. METHODS We have primarily used a 2D graphical representation technique to show the differences in base distributions in these five flaviviruses and subsequently, obtained quantitative estimates of the differences. Similarity/dissimilarity between the viruses based on the genes were also determined which showed that the differences with the Dengue genes are more pronounced. RESULTS We found that the Dengue viruses compared to the other four flaviviruses spread rapidly worldwide and became endemic in various regions with small alterations in sequence composition relative to the host populations as revealed by codon usage biases and phylogenetic examination. CONCLUSION We conclude that the Dengue genes are indeed more widely separated from the other aforementioned mosquito-borne human-infecting flaviviruses due to excess adenine component, a feature that is sparse in the literature. Such excesses have a bearing on drug and vaccine, especially peptide vaccine, development and should be considered appropriately.
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Affiliation(s)
- Proyasha Roy
- Centre for Interdisciplinary Research and Education, 404B Jodhpur Park, Kolkata 700058, India
| | - Sumanta Dey
- Centre for Interdisciplinary Research and Education, 404B Jodhpur Park, Kolkata 700058, India
| | - Ashesh Nandy
- Centre for Interdisciplinary Research and Education, 404B Jodhpur Park, Kolkata 700058, India
| | - Subhash C Basak
- Department of Chemistry and Biochemistry, Duluth-Natural Resources Research Institute, University of Minnesota Duluth, 5013 Miller Trunk Highway, Duluth, MN 55811, United States
| | - Sukhen Das
- Department of Physics, Jadavpur University, Jadavpur, Kolkata 700032, India
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Tan KK, Zulkifle NI, Sulaiman S, Pang SP, NorAmdan N, MatRahim N, Abd-Jamil J, Shu MH, Mahadi NM, AbuBakar S. Emergence of the Asian lineage dengue virus type 3 genotype III in Malaysia. BMC Evol Biol 2018; 18:58. [PMID: 29699483 PMCID: PMC5921268 DOI: 10.1186/s12862-018-1175-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/11/2018] [Indexed: 01/16/2023] Open
Abstract
Background Dengue virus type 3 genotype III (DENV3/III) is associated with increased number of severe infections when it emerged in the Americas and Asia. We had previously demonstrated that the DENV3/III was introduced into Malaysia in the late 2000s. We investigated the genetic diversity of DENV3/III strains recovered from Malaysia and examined their phylogenetic relationships against other DENV3/III strains isolated globally. Results Phylogenetic analysis revealed at least four distinct DENV3/III lineages. Two of the lineages (DENV3/III-B and DENV3/III-C) are current actively circulating whereas the DENV3/III-A and DENV3/III-D were no longer recovered since the 1980s. Selection pressure analysis revealed strong evidence of positive selection on a number of amino acid sites in PrM, E, NS1, NS2a, NS2b, NS3, NS4a, and NS5. The Malaysian DENV3/III isolates recovered in the 1980s (MY.59538/1987) clustered into DENV3/III-B, which was the lineage with cosmopolitan distribution consisting of strains actively circulating in the Americas, Africa, and Asia. The Malaysian isolates recovered after the 2000s clustered within DENV3/III-C. This DENV3/III-C lineage displayed a more restricted geographical distribution and consisted of isolates recovered from Asia, denoted as the Asian lineage. Amino acid variation sites in NS5 (NS5–553I/M, NS5–629 T, and NS5–820E) differentiated the DENV3/III-C from other DENV3 viruses. The codon 629 of NS5 was identified as a positively selected site. While the NS5-698R was identified as unique to the genome of DENV3/III-C3. Phylogeographic results suggested that the recent Malaysian DENV3/III-C was likely to have been introduced from Singapore in 2008 and became endemic. From Malaysia, the virus subsequently spread into Taiwan and Thailand in the early part of the 2010s and later reintroduced into Singapore in 2013. Conclusions Distinct clustering of the Malaysian old and new DENV3/III isolates suggests that the currently circulating DENV3/III in Malaysia did not descend directly from the strains recovered during the 1980s. Phylogenetic analyses and common genetic traits in the genome of the strains and those from the neighboring countries suggest that the Malaysian DENV3/III is likely to have been introduced from the neighboring regions. Malaysia, however, serves as one of the sources of the recent regional spread of DENV3/III-C3 within the Asia region. Electronic supplementary material The online version of this article (10.1186/s12862-018-1175-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kim-Kee Tan
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia.,Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Nurul-Izzani Zulkifle
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Syuhaida Sulaiman
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Sui-Ping Pang
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - NurAsyura NorAmdan
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - NorAziyah MatRahim
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Juraina Abd-Jamil
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Meng-Hooi Shu
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Nor Muhammad Mahadi
- Malaysia Genome Institute, Ministry of Science, Technology and Innovation, Jalan Bangi, 43000, Kajang, Selangor, Malaysia
| | - Sazaly AbuBakar
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia. .,Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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Vazeille M, Gaborit P, Mousson L, Girod R, Failloux AB. Competitive advantage of a dengue 4 virus when co-infecting the mosquito Aedes aegypti with a dengue 1 virus. BMC Infect Dis 2016; 16:318. [PMID: 27390932 PMCID: PMC4939008 DOI: 10.1186/s12879-016-1666-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 06/14/2016] [Indexed: 01/30/2023] Open
Abstract
Background Dengue viruses (DENV) are comprised in four related serotypes (DENV-1 to 4) and are critically important arboviral pathogens affecting human populations in the tropics. South American countries have seen the reemergence of DENV since the 1970’s associated with the progressive re-infestation by the mosquito vector, Aedes aegypti. In French Guiana, DENV is now endemic with the co-circulation of different serotypes resulting in viral epidemics. Between 2009 and 2010, a predominant serotype change occurred from DENV-1 to DENV-4 suggesting a competitive displacement. The aim of the present study was to evaluate the potential role of the mosquito in the selection of the new epidemic serotype. Methods To test this hypothesis of competitive displacement of one serotype by another in the mosquito vector, we performed mono- and co-infections of local Ae. aegypti collected during the inter-epidemic period with both viral autochthonous epidemic serotypes and compared infection, dissemination and transmission rates. We performed oral artificial infections of F1 populations in BSL-3 conditions and analyzed infection, dissemination and transmission rates. Results When two populations of Ae. aegypti from French Guiana were infected with either serotype, no significant differences in dissemination and transmission were observed between DENV-1 and DENV-4. However, in co-infection experiments, a strong competitive advantage for DENV-4 was seen at the midgut level leading to a much higher dissemination of this serotype. Furthermore only DENV-4 was present in Ae. aegypti saliva and therefore able to be transmitted. Conclusions In an endemic context, mosquito vectors may be infected by several DENV serotypes. Our results suggest a possible competition between serotypes at the midgut level in co-infected mosquitoes leading to a drastically different transmission potential and, in this case, favoring the competitive displacement of DENV-1 by DENV-4. This phenomenon was observed despite a similar replicative fitness in mono-infections conditions.
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Affiliation(s)
- Marie Vazeille
- Institut Pasteur, Department of Virology, Arboviruses and Insect Vectors, 25 rue du Dr Roux, 75724, Paris Cedex 15, France
| | - Pascal Gaborit
- Medical Entomology Unit, Institut Pasteur of French Guiana, Cayenne, French Guiana
| | - Laurence Mousson
- Institut Pasteur, Department of Virology, Arboviruses and Insect Vectors, 25 rue du Dr Roux, 75724, Paris Cedex 15, France
| | - Romain Girod
- Medical Entomology Unit, Institut Pasteur of French Guiana, Cayenne, French Guiana
| | - Anna-Bella Failloux
- Institut Pasteur, Department of Virology, Arboviruses and Insect Vectors, 25 rue du Dr Roux, 75724, Paris Cedex 15, France.
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Kolondam B, Rao P, Sztuba-Solinska J, Weber PH, Dzianott A, Johns MA, Bujarski JJ. Co-infection with two strains of Brome mosaic bromovirus reveals common RNA recombination sites in different hosts. Virus Evol 2015; 1:vev021. [PMID: 27774290 PMCID: PMC5014487 DOI: 10.1093/ve/vev021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have previously reported intra-segmental crossovers in Brome mosaic virus (BMV) RNAs. In this work, we studied the homologous recombination of BMV RNA in three different hosts: barley (Hordeum vulgare), Chenopodium quinoa, and Nicotiana benthamiana that were co-infected with two strains of BMV: Russian (R) and Fescue (F). Our work aimed at (1) establishing the frequency of recombination, (2) mapping the recombination hot spots, and (3) addressing host effects. The F and R nucleotide sequences differ from each other at many translationally silent nucleotide substitutions. We exploited this natural variability to track the crossover sites. Sequencing of a large number of cDNA clones revealed multiple homologous crossovers in each BMV RNA segment, in both the whole plants and protoplasts. Some recombination hot spots mapped at similar locations in different hosts, suggesting a role for viral factors, but other sites depended on the host. Our results demonstrate the chimeric ('mosaic') nature of the BMV RNA genome.
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Affiliation(s)
- Beivy Kolondam
- Department of Biological Sciences and Plant Molecular Biology Center, Northern Illinois University, DeKalb, IL 60115, USA and
| | - Parth Rao
- Department of Biological Sciences and Plant Molecular Biology Center, Northern Illinois University, DeKalb, IL 60115, USA and
| | - Joanna Sztuba-Solinska
- Department of Biological Sciences and Plant Molecular Biology Center, Northern Illinois University, DeKalb, IL 60115, USA and
| | - Philipp H Weber
- Department of Biological Sciences and Plant Molecular Biology Center, Northern Illinois University, DeKalb, IL 60115, USA and
| | - Aleksandra Dzianott
- Department of Biological Sciences and Plant Molecular Biology Center, Northern Illinois University, DeKalb, IL 60115, USA and
| | - Mitrick A Johns
- Department of Biological Sciences and Plant Molecular Biology Center, Northern Illinois University, DeKalb, IL 60115, USA and
| | - Jozef J Bujarski
- Department of Biological Sciences and Plant Molecular Biology Center, Northern Illinois University, DeKalb, IL 60115, USA and; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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