Molecular characterization of dengue virus reveals regional diversification of serotype 2 in Colombia.
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ABSTRACT:
SUBMITTER: Laiton-Donato K
PROVIDER: S-EPMC6505283 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:In 2015, a dengue outbreak with 1,067 reported cases occurred in Xishuangbanna, a city in China that borders Burma and Laos. To characterize the virus, the complete genome sequence was obtained and phylogenetic, mutation, substitution and recombinant analyses were performed. DENV-NS1 positive serum samples were collected from dengue fever patients, and complete genome sequences were obtained through RT-qPCR from these serum samples. Phylogenetic trees were then constructed by maximum likelihood phylogeny test (MEGA7.0), followed by analysis of nucleotide mutation and amino acid substitution. The recombination events among DENVs were also analyzed by RDP4 package. The diversity analysis of secondary structure for translated viral proteins was also performed. The complete genome sequences of four amplified viruses (YNXJ10, YNXJ12, YNXJ13, and YNXJ16) were 10,742, 10,742, 10,741, and 10,734 nucleotides in length, and phylogenetic analysis classified the viruses as cosmopolitan genotype of DENV-2. All viruses were close to DENV Singapore 2013 (KX380828.1) and the DENV China 2013 (KF479233.1). In comparison to DENV-2SS (M29095), the total numbers of base substitutions were 712 nt (YNXJ10), 809 nt (YNXJ12), 772 nt (YNXJ13), and 841 nt (YNXJ16), resulting in 109, 171, 130, and 180 amino acid substitutions in translated regions, respectively. In addition, compared with KX380828.1, there were 44, 105, 64, and 116 amino acid substitutions in translated regions, respectively. The highest mutation rate occurred in the prM region, and the lowest mutation rate occurred in the NS4B region. Most of the recombination events occurred in the prM, E and NS2B/3 regions, which corresponded with the mutation frequency of the related portion. Secondary structure prediction within the 3,391 amino acids of DENV structural proteins showed there were 7 new possible nucleotide-binding sites and 6 lost sites compared to DENV-2SS. In addition, 41 distinct amino acid changes were found in the helix regions, although the distribution of the exposed and buried regions changed only slightly. Our findings may help to understand the intrinsic geographical relatedness of DENV-2 and contributes to the understanding of viral evolution and its impact on the epidemic potential and pathogenicity of DENV.
| S-EPMC6030573 | biostudies-literature
Project description:The number of sporadic and epidemic dengue fever cases have reportedly been increasing in recent years in some West African countries, such as Senegal and Mali. The first epidemic of laboratory-confirmed dengue occurred in Nouakchott, the capital city of Mauritania situated in the Saharan desert, in 2014. On-site diagnosis of dengue fever was established using a rapid diagnostic test for dengue. In parallel, the presence of Aedes aegypti mosquitoes in the city was confirmed. The initial diagnosis was confirmed by RT-PCR, which showed that all samples from the 2014 dengue epidemic in Nouakchott were dengue virus serotype 2 (DENV-2). The whole genome or envelope protein gene of these strains, together with other DENV-2 strains obtained from travelers returning from West African countries to France between 2016 and 2019 (including two Mauritanian strains in 2017 and 2018), were sequenced. Phylogenetic analysis suggested a recent emergence of an epidemic strain from the cosmopolitan genotype belonging to West African cosmopolitan lineage II, which is genetically distinct from African sylvatic genotype. The origin of this DENV-2 lineage is still unknown, but our data seem to suggest a recent and rapid dispersion of the epidemic strain throughout the region. More complete genome sequences of West African DENV-2 are required for a better understanding of the dynamics of its circulation. Arboviral surveillance and outbreak forecasting are urgently needed in West Africa. Author summary In Africa, dengue viruses 1 to 4 are transmitted to primates by Aedes mosquitoes in a sylvatic cycle or an urban/epidemic cycle involving humans. Infection in humans may be asymptomatic or may range from mild flu-like illness to severe hemorrhagic fever. The dengue viruses have a pantropical distribution, mostly in urbanized areas where vectors have become well adapted. This report shows dengue can also emerge in desert areas, as seen for the first time in an outbreak in 2014 in Nouakchott, Mauritania, where climatic, environmental, and human behavioral changes favor the emergence of Aedes mosquitoes. Dengue virus 2 was found in multiple human samples collected during the outbreak. Genomic analysis of dengue virus 2 isolates from the Mauritanian outbreak and from infected travelers revealed the rapid emergence of a specific “West African epidemic strain” of the virus throughout West Africa during the last decade, which is distinct from other strains found elsewhere and from historical or sylvatic strains. More genomic data would help us understand the circulation of dengue virus in West Africa, to help forecast and mitigate outbreaks in this region.
| S-EPMC8568173 | biostudies-literature
Project description:BACKGROUND:Dengue is the most common mosquito-borne infection worldwide and a serious threat to global public health. Sporadic dengue virus serotype 2 (DENV-2) imported cases from Myanmar have been documented almost every year in Yunnan Province of China since 2005. However, the complete genome sequences of DENV-2 isolates imported from Myanmar are not available. METHODS:The full-length genome of the DENV-2 strain (YNPE2), isolated from an imported case from Myanmar in 2013, was identified by the next-generation sequencing. The extreme ends of the viral genome were validated by 5'/3' RACE and Sanger sequencing. Furthermore, phylogenetic, recombination and selection pressure analyses were conducted for the molecular characterization of YNPE2 strain. RESULTS:Whole-genome sequencing revealed that the full-length sequence of YNPE2 strain was 10,724 bases, with an open reading frame encoding for 3391 amino acids. The YNPE2 strain had 99.0% nucleotide identity and 99.8% amino acid identity with two closely related strains, ThD2_0078_01 strain (DQ181797) and DENV-2/TH/BID-V2157/200 strain (FJ639832). The phylogenetic analysis suggested that the YNPE2 strain belonged to Asian I genotype and was likely derived from Thailand strain (DQ181797). Moreover, selection pressure analysis revealed two amino acid sites of the NS4B and NS5 proteins, with important evidence of positive selection. CONCLUSION:This study revealed the first complete genome sequence and molecular characterization of a DENV-2 strain (YNPE2) isolated from an imported case from Myanmar, thus providing a valuable reference genome source for future surveillance, epidemiology and vaccine development of DENV-2 virus in Yunnan, China.
| S-EPMC6102819 | biostudies-literature
Project description:A dengue virus serotype 1 (DENV-1) epidemic occurred from October to December 2018 in Xishuangbanna, Yunnan, Southwest China, neighboring Myanmar, Laos, and Vietnam. In this study, we investigated the molecular characteristics, evolution, and potential source of DENV from Xishuangbanna. The C (capsid), prM (premembrane), and E (envelope) genes of DENV isolated from 87 serum samples obtained from local patients were amplified and sequenced, and the sequences were evaluated by identification of mutations, phylogenetic and homologous recombination analysis, and secondary structure prediction. Phylogenetic analysis showed that all of the epidemic DENV strains from Xishuangbanna could be grouped in a branch with DENV-1 isolates, and were most similar to the Fujian 2005 (China, DQ193572) and Singapore 2016 (MF314188) strains. When compared with DENV-1SS (the standard strain), there were 31 non-synonymous mutations, but no obvious homologous recombination signal was found. Secondary structure prediction showed that some changes had occurred in a helical region in proteins of the MN123849 and MN123854 strains, but there were few changes in the disordered region. This study reveals the molecular characteristics of the structural genes of the Xishuangbanna epidemic strains in 2018 and provides a reference for molecular epidemiology, infection, and pathogenicity research and vaccine development.
| S-EPMC7831630 | biostudies-literature
Project description: Not available
| S-EPMC2725812 | biostudies-literature
Project description:BackgroundDengue virus (DENV) infection caused by international visitors has become a public health concern in China. Although sporadic imported cases of DENV have been documented in Yunnan, China since 2000, a complete genome sequence of dengue virus serotype 3 (DENV-3) imported from Laos is still not available. Here, we report the first complete genome sequence and genomic characterization of a DENV-3 strain (YNPE3) isolated from a patient returned from Laos.MethodsViral isolation from the patient's serum was performed using mosquitoes C6/36 cells. Reverse transcriptase polymerase chain reaction (RT-PCR) was used for identification and serotyping of the virus. The complete sequence was determined by Sanger dideoxy sequencing. Homology analysis was implemented by NCBI-BLAST. Multiple sequence alignment was performed using MegAlign module of the Lasergene 7 software package DNASTAR. MFOLD software was used to predict the RNA secondary structure of 5' untranslated region (UTR) and 3' UTR. Phylogenetic analysis, which was based on envelope gene and complete coding sequence, was performed by Maximum-Likelihood method.ResultsRT-PCR analysis confirmed that the virus belonged to dengue virus serotype 3, which was named YNPE3 strain. The full-length genome of the YNPE3 strain was 10,627 nucleotides (nts) with an open reading frame (ORF) encoding 3390 amino acids. Strain YNPE3 shared 98.6-98.8% nucleotide identity with the closely related strains isolated in India (JQ922556, KU216209, KU216208). We observed the deletion of about 40 nts in the 5' UTR and 3' UTR of strain YNPE3, and 11 nts (ACGCAGGAAGT) insertion that was present in the 3' UTR of YNPE3. Compared with prototype strain H87, abundant amino acid substitutions in the YNPE3 strain were observed. Phylogenetic analysis revealed that the YNPE3 strain belonged to genotype III of DENV-3, and that it might be closely related with genotype III strains isolated in Laos and India.ConclusionsThis is the first report of the complete genome sequence and molecular characterization of a DENV-3 isolate imported from Laos. The presented results can further promote disease surveillance, and epidemiological and evolutionary studies of the DENV-3 in Yunnan province of China.
| S-EPMC6057004 | biostudies-literature
Project description:Dengue has been well recognized as a global public health threat, but only sporadic epidemics and imported cases were reported in recent decades in China. Since July 2014, an unexpected large dengue outbreak has occurred in Guangdong province, China, resulting in more than 40000 patients including six deaths. To clarify and characterize the causative agent of this outbreak, the acute phase serum from a patient diagnosed with severe dengue was subjected to virus isolation and high-throughput sequencing (HTS). Traditional real-time RT-PCR and HTS with Ion Torrent PGM detected the presence of dengue virus serotype 2 (DENV-2). A clinical DENV-2 isolate GZ05/2014 was obtained by culturing the patient serum in mosquito C6/36 cells. The complete genome of GZ05/2014 was determined and deposited in GenBank under the access number KP012546. Phylogenetic analysis based on the complete envelope gene showed that the newly DENV-2 isolate belonged to Cosmopolitan genotype and clustered closely with other Guangdong strains isolated in the past decade. No amino acid mutations that are obviously known to increase virulence or replication were identified throughout the genome of GZ05/2014. The high homology of Guangdong DENV-2 strains indicated the possibility of establishment of local DENV-2 circulation in Guangdong, China. These results help clarify the origin of this epidemic and predict the future status of dengue in China.
| S-EPMC7089550 | biostudies-literature
Project description:In 2008, dengue virus serotype 4 (DENV-4) emerged in northeastern Peru, causing a large outbreak and displacing DENV-3, which had predominated for the previous 6 years. Phylogenetic analysis of 2008 and 2009 isolates support their inclusion into DENV-4 genotype II, forming a lineage distinct from strains that had previously circulated in the region.
| S-EPMC2857240 | biostudies-literature
Project description: Not available
| S-EPMC3310685 | biostudies-literature
Project description:BACKGROUND: Dengue fever is perhaps the most important viral re-emergent disease especially in tropical and sub-tropical countries, affecting about 50 million people around the world yearly. In Colombia, dengue virus was first detected in 1971 and still remains as a major public health issue. Although four viral serotypes have been recurrently identified, dengue virus type 2 (DENV-2) has been involved in the most important outbreaks during the last 20 years, including 2010 when the fatality rate highly increased. As there are no major studies reviewing virus origin and genotype distribution in this country, the present study attempts to reconstruct the phylogenetic history of DENV-2 using a sequence analysis from a 224 bp PCR-amplified product corresponding to the carboxyl terminus of the envelope (E) gene from 48 Colombian isolates. RESULTS: As expected, the oldest isolates belonged to the American genotype (subtype V), but the strains collected since 1990 represent the American/Asian genotype (subtype IIIb) as previously reported in different American countries. Interestingly, the introduction of this genotype coincides with the first report of dengue hemorrhagic fever in Colombia at the end of 1989 and the increase of cases during the next years. CONCLUSION: After replacement of the American genotype, several lineages of American/Asian subtype have rapidly spread all over the country evolving in new clades. Nevertheless, the direct association of these new variants in the raise of lethality rate observed during the last outbreak has to be demonstrated.
| S-EPMC3349600 | biostudies-literature