Comparative analysis of full genomic sequences among different genotypes of dengue virus type 3 (original) (raw)
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Virology Journal, 2009
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.
Future Virology, 2018
This study was aimed to amplify, characterize and analyze complete genomes of dengue virus serotype-2 (DENV-2) Pakistani isolates.Patients & methods: Complete genomes of DENV-2 (n = 4) in nine overlapping fragments from two dengue outbreaks (2011 and 2013) were sequenced; deposited in Gen-Bank (Punjab Isolates: KM217157 and KM217156; Swat Isolates: KM217158 and KJ701507) and characterized using specific primers, we designed. Results: Analysis clustered Pakistani isolates with the cosmopolitan genotypes and further indicated that codons 65 of C, 155 of PrM, 203 of E and 254 of NS1 genes were under negative selection pressure. A substitution of alanine with proline in NS5 gene at nucleotide position 885 in Swat isolates was observed. Conclusion: DENV-2 is spreading to other parts of Pakistan with the possible adaptability of the virus molecularly.
2019
Since their discovery and sequencing 40 years ago, the DENV genotypes have shown an extreme coherence regarding the serotype class they code for. Considering the RNA virus mutation rate, we used Timed Markov Model to explore the transmission possibilities of mutated viruses and the statistical eventualities of new serotype emergence. We find that around 1 000 years are required for a new serotype to emerge, in line with phylogenetic analysis of the Dengue serotypes. Our work provides a mechanistic explanation of the strictness and low probability of a new Dengue virus serotype occurrence.Author summaryRecent Dengue virus global spread has drawn the attention of the Public Health Policy makers in developing countries and developed countries as well. The infection gravity and the hemorrhagic dengue syndromes have been related with the absence or presence of previous DENV immunity. Therefore, the emergence of a new DENV serotype and its spread constitute a matter of concern. Here, we c...
Phylogenetic analyses of DENV-3 isolated from field-caught mosquitoes in Thailand
Virus research, 2018
Dengue virus serotype 3 (DENV-3) can cause all forms of dengue diseases and is a predominant serotype in many countries. This serotype is classified into five genotypes: I-V. Genotypes I-III have widely spread throughout the world, whereas genotypes IV and V are rare. Despite the impact on the spread of dengue diseases, only a few studies have reported the characteristics of DENV present in mosquito vectors. Hence, this study aimed to identify DENV-3 genotypes and reveal genetic variation of this virus presented in field-caught mosquitoes collected from endemic areas in Thailand during 2011-2015. First, we examined the effectiveness of the E gene sequence on DENV-3 genotyping, with results supporting the use of this gene for genotype identification. Then, we sequenced this gene in ten DENV-3 strains isolated from mosquitoes. The results showed that eight and two samples were genotypes III and V, respectively, and that they are closely related to DENV-3 isolated from Southeast and Ea...
2009
We have investigated the genetic diversity of DENV-3 isolated during an outbreak of dengue haemorrhagic fever (DHF) in the city of Palembang, south Sumatra, Indonesia. Four viruses were isolated from patients with different disease severities. Amino acid differences were detected at 40 positions throughout the structural and non-structural proteins, except for the preM protein. Of the 40 positions, amino acids were conserved at 24 positions among three DSS/DHF strains, and the DF strain possessed different amino acids at these positions. Five nucleotide substitutions were identified on 3’ UTR. In monocyte cell line, U937, the three DSS/DHF strains were able to propagate to higher levels compared to the DF strain. These preliminary results showed that the DSS/DHF strains have unique amino acid residues that are different from the DF strain and have better ability to propagate to a higher level in human monocytes. These characteristics of the DSS/DHF strains may contribute to enhanced...
Molecular Investigation of DENV serotypes in the dengue outbreak of 2022 in Nepal
IntroductionDengue, a viral infection highly prevalent in tropical regions, exhibits local variations in risk that are influenced by a combination of climatic, socioeconomic, and environmental factors. The disease is caused by four distinct yet closely related serotypes of the dengue virus: DENV-1, DENV-2, DENV-3, and DENV-4.ObjectivesThe objective of this study is to identify the different serotypes of dengue virus responsible for the 2022 outbreak in Nepal, where dengue has been prevalent since 2006 but with limited availability of molecular information on the serotypes.MethodologySerum samples from suspected dengue patients visiting Dhulikhel Hospital were analyzed using Dengue Ag and IgM/IgG Ab Kit test, for the presence of IgG/IgM antibodies or NS1 Ag. The positive samples were stored at -80 °C, and 89 samples were selected for further analysis. RNA was extracted from those positive samples using the Zymo Quick RNA Viral Kit, and RT-PCR was performed using the Sacace Dengue Rea...
PLoS Neglected Tropical Diseases, 2013
In Brazil, dengue has been a major public health problem since its introduction in the 1980s. Phylogenetic studies constitute a valuable tool to monitor the introduction and spread of viruses as well as to predict the potential epidemiological consequences of such events. Aiming to perform the molecular characterization and phylogenetic analysis of DENV-2 during twenty years of viral activity in the country, viral strains isolated from patients presenting different disease manifestations (n = 34), representing six states of the country, from 1990 to 2010, were sequenced. Partial genome sequencing (genes C/prM/M/E) was performed in 25 DENV-2 strains and full-length genome sequencing (coding region) was performed in 9 strains. The percentage of similarity among the DENV-2 strains in this study and reference strains available in Genbank identified two groups epidemiologically distinct: one represented by strains isolated from 1990 to 2003 and one from strains isolated from 2007 to 2010. No consistent differences were observed on the E gene from strains isolated from cases with different clinical manifestations analyzed, suggesting that if the disease severity has a genetic origin, it is not only due to the differences observed on the E gene. The results obtained by the DENV-2 full-length genome sequencing did not point out consistent differences related to a more severe disease either. The analysis based on the partial and/or complete genome sequencing has characterized the Brazilian DENV-2 strains as belonging to the Southeast Asian genotype, however a distinction of two Lineages within this genotype has been identified. It was established that strains circulating prior DENV-2 emergence (1990)(1991)(1992)(1993)(1994)(1995)(1996)(1997)(1998)(1999)(2000)(2001)(2002)(2003) belong to Southeast Asian genotype, Lineage I and strains isolated after DENV-2 emergence in 2007 belong to Southeast Asian genotype, Lineage II. Furthermore, all DENV-2 strains analyzed presented an asparagine (N) in E 390 , previously identified as a probable genetic marker of virulence observed in DHF strains from Asian origin. The percentage of identity of the latter with the Dominican Republic strain isolated in 2001 combined to the percentage of divergence with the strains first introduced in the country in the 1990s suggests that those viruses did not evolve locally but were due to a new viral Lineage introduction in the country from the Caribbean. Citation: Faria NRdC, Nogueira RMR, de Filippis AMB, Simõ es JBS, Nogueira FdB, et al. (2013) Twenty Years of DENV-2 Activity in Brazil: Molecular Characterization and Phylogeny of Strains
PLOS ONE
Dengue fever is caused by dengue viruses (DENV) from the Flavivirus genus and is the most prevalent arboviral disease. DENV exists in four immunogenically distinct and genetically-related serotypes (DENV-1 to 4), each subdivided in genotypes. Despite the endemicity of all four DENV serotypes in Thailand, no prior study has characterized the circulation of DENV in the southern provinces of the country. To determine the genetic diversity of DENV circulating in Southern Thailand in 2015 and 2016, we investigated 46 viruses from 182 patients' sera confirmed positive for DENV by serological and Nested RT-PCR tests. Our dataset included 2 DENV-1, 20 DENV-2, 9 DENV-3 and 15 DENV-4. Phylogenetic analysis was performed on viral envelop sequences. This revealed that part of the identified genotypes from DENV-1 and DENV-4 had been predominant in Asia (genotype I for both serotypes), while genotype II for DENV-4 and the Cosmopolitan genotype DENV-2 were also circulating. Whereas DENV-3 genotype II had been predominantly detected in South East Asia during the previous decades, we found genotype III and genotype I in Southern Thailand. All DENV genotype identified in this study were closely related to contemporary strains circulating in Southeast Asian countries, emphasizing the regional circulation of DENV. These results provide new insights into the co-circulation of all four DENV serotypes in Southern Thailand, confirming the hyperendemicity of DENV in the region. These findings also suggest a new trend of dissemination for some DENV serotypes with a possible shift in genotype distribution; as recently observed in other Asian countries.
Journal of Microbiology, Immunology and Infection, 2010
BACKGROUND/PURPOSE: The re-emergence of an epidemic strain of dengue virus type-3 (DENV-3) in Delhi in 2003 and its persistence in subsequent years marked a changing trend in dengue virus circulation in this part of India. Its evolving phylogeny over the past decade has not been studied in detail as yet. METHODS: Reverse transcription polymerase chain reaction and sequencing of the CprM gene junction of DENV-3 from different outbreaks since 2003 was carried out. Thirty CprM DENV-3 sequences from this study were compared with 46 other previously reported CprM DENV-3 sequences from India and other countries. Multiple sequence alignment and phylogenetic trees were constructed to determine the extent of genetic heterogeneity and trace the phylogeny of DENV-3. RESULTS: Thirty CprM DENV-3 sequences (Accession numbers AY706096-99, DQ645945-52, EU181201-14, and EU846234-36) were submitted to GenBank. The CprM junction was found to be AT rich (approximately 53%). Nucleotide sequence alignment revealed only nucleotide substitutions. Phylogenetic analysis indicated sustained evolution of a distinct Indian lineage of DENV-3 genotype III in Delhi. CONCLUSION: Active circulation of DENV-3 genotype III over the last decade in Delhi was evident and worrying. This genotype has been implicated in several outbreaks in SouthEast Asia and other parts of the world.
International Journal of Infectious Diseases, 2008
Objectives: The sudden emergence of dengue virus type 1 (DENV-1) and its co-circulation with predominant DENV-3 was the hallmark of the 2006 dengue fever outbreak in Delhi. Viruses that circulated between 1996 and 2005 in the City have been well characterized, but the genomic diversity in 2006 strains is not known. The present study was undertaken to reveal the emerging molecular genotype(s) and evolutionary trend of the viruses responsible for the dengue fever outbreak in Delhi during 2006. Study design: The CprM gene junction of the DENV isolates from the 2006 Delhi dengue fever outbreak were subjected to nucleotide sequencing. Comparative phylogenetic analysis was done using DENV-1 and DENV-3 sequences retrieved from the global database. Results: Multiple sequence alignment revealed only substitutions, with no insertions or deletions. A dendrogram indicated emergence of a distinct lineage of DENV-1 (having similarity with the Comoros/Singapore 1993 and Delhi 1982 strains, but quite different from the Delhi 2005 lineage) and microevolution of the pre-circulating DENV-3. These findings point towards the circulation of two independent lineages of DENV-1 in Delhi during 2005 and 2006.