ABSTRACT
In Brazil, detection of the HIV-1 sub-subtype F1 has decreased with a simultaneous increase in detection of the recombinant FB and FC forms. In previous HIV-1 env molecular epidemiology studies in Rio de Janeiro, 11.4% of the detected sequences were of the F1 sub-subtype. With the goal of re-estimating the prevalence of the HIV-1 F1 sub-subtype, we performed extended analyses of these samples by examining five genomic regions, resulting in 3.3% being confirmed as F1. Moreover, genomic analysis of 11 of the 21 samples identified as F1 confirmed that nine were F1 and two were BF1. Considering the number of samples assayed, the prevalence of F1 was quite low, which supports the use of different genomic regions for the assessment of HIV-1 classification in countries where several subtypes and recombinant forms co-circulate.
Subject(s)
Humans , HIV Infections/epidemiology , HIV Infections/virology , HIV-1/genetics , Genome, Viral/genetics , Phylogeny , Brazil/epidemiology , DNA Mutational Analysis , Base Sequence , Molecular Epidemiology , GenotypeABSTRACT
We investigated the molecular characteristics of the full-length genome of 5 dengue serotype 4 virus (DENV-4) strains isolated in Yunnan Province,China,2015 and their molecular epidemiological feature.Isolation of dengue virus was using C6/36 cell culture method.Viral RNA was extracted from virus isolates,then the full-length genome was amplified by RT-PCR.The homology and phylogenetic analysis was made on the nucleotide and deduced amino acid sequences by bioinfor matics softwares including ClastalX1.83 and MEGA6 etc.Results showed that five strains of DENV-4 isolated from dengue fe ver cases in Ruili City of Yunnan Province in 2015,of these,2 strains from indigenous cases,3 from imported cases from Lashio and Nam Can cities of Myanmar to Ruili of China.RT-PCR and sequencing indicated that the full-length genes (10 661 nt) of 5 DENV-4 strains were obtained,and their open reading frame (103-10 264) were coded 3 386 amino acid residues.Phylogenetic tree and homology analysis based on the comeplete genome or structural and non-structural protein genes showed that the 5 DENV 4 isolates were highly homologous and gathered in an evolution as well as they have a closer genetic relationship with the DENV-4 genotype Ⅰ (G-Ⅰ) strains isolated from Thailand.Results indicated that the Yunnan strains belonged to G-Ⅰ.Yunnan strains and Thailand strains compared with DENV 4 prototype strain (H241,Philippines 1956) and Guangzhou strain (B5,1990) of China and showed low homology and evolutionary relationship.When Yunnan strains compared with H241 strain,there were 21 and 45 different sites in amino acid of structural and non-structural proteins,respectively.This is the first time in Yunnan to obtain full-length genomes sequence of DENV-4 and they have closer evolutionary relationship with DENV 4G-Ⅰ strains from Southeast Asia region in recent years.The autochthonous DENV-4 epidemic in Yunnan was detected for the first time,and the virus transmission sources were from neighboring northern Myanmar.It is necessary to further study that change of the amino acid sites of Yunnan strains of DENV-4 is related to its antigenicity and virulence.
ABSTRACT
We investigated the molecular characteristics of the full-length genome of 14 dengue serotype 1 virus (DENV-1)strains isolated in Sino-Myanmar border region in Yunnan Province,China during 2013-2015.Isolation of dengue virus was using C6/36 cell culture method.Viral RNA was extracted from virus isolates,and then the full-length genome was amplified by RT-PCR.The homology and phylogenetic analysis was made on the nucleotide and deduced amino acid sequences by bioinformatics software including ClastalX1.83 and MEGA6 etc.Results showed that fourteen strains of DENV-1 isolated from dengue fever cases,of these,9 strains from Ruili City of Dehong Prefecture,3 from Lincang Prefecture,2 from Kunming City.RT-PCR and sequencing indicated that the full-length genes (10 735 nt) of 14 DENV-1 strains were obtained,and their open reading frame (95-10 271) were coded 3 392 amino acid residues.The genotypes of DENV-1 were revealed by homology and phylogenetic analysis based on structural and non-structural proteins.Thirteen were genotype Ⅰ (G-Ⅰ) (7 from indigenous cases in Ruili and Lincang and 6 from imported case from Myanmar to Ruili,Lincang and Kunming),and 1 G-Ⅲ from imported case from India to Kunming.The phylogenic analysis indicated that the 13 isolates from Yunnan divided into 2 phylogenic subgroups,and they had a closer genetic relationship with the strains isolated from Southeast Asia.The gene sequences of the 13 G-Ⅰ strains have been acquired,the rate of their nucleotide homology and amino acid homology were 97.02 ％-100 ％ and 98.78 ％100 ％ respectively.Compared with 6 strains from Southeast Asia,nucleotide homology and amino acid homology were 96.53％-99.53％ and 97.33％-100％ respectively.Compared with prototype strain (US_Hawaii) of DENV-1,nucleotide homology and amino acid homology were 93.76％-94.45 ％ and 95.86 ％-96.91％ respectively.Compared with US_Hawaii strain,there were 44 and 150 different sites in amino acid of structural and non-structural proteins,respectively.The G-1 of DENV-1 have been popular in Sino-Myanmar border region in Yunnan,2013-2015.They have genetic diversity but multiple transmission sources were from Myanmar,and should strengthen control cross-border spread of dengue fever in this region.It is necessary to further study that change of the amino acid sites of Yunnan strains of DENV-1 is related to its antigenicity and pathogenicity.
ABSTRACT
Encephalomyocarditis virus (EMCV) ,named JZ1202 ,was isolated from domesticated boar in Henan ,China . We performed the full-length genome sequencing and molecular characteristic analysis of the isolated strain .Results showed that the full-genome sequence of EMCV JZ1202 generated a sequence of 7 735 bp in length ,and had 81 .2%-99 .9% nucleotide identity with other reference strains from different animals ,but 99 .4% with Chinese reference from pig .The phylogenetic tree was constructed based on the full-length genome;ORF and VP1 gene sequences identified EMCV was divided into G1 ,G2 and G3 groups ;the strain JZ1202 belongs to G1 with other Chinese reference strains .Results identified that the EMCV infection could cause severe clinical symptoms in domesticated boar .Big regional differences exist in EMCV and the transmission is limit-ed in a range of area .However ,cross infection and prevalence of EMCV disease between domesticated boar and mice might ex-ist .Mutation of some amino acid may occurred in EMCV infected domesticated boar .
ABSTRACT
Objective Based on sequencing the full-length genomes of two Chinese Ferret-Badger, we analyzed the properties of rabies viruses genetic variation in molecular level to get information on prevalence and variation of rabies viruses in Zhejiang,and to enrich the genome database of rabies viruses street swains isolated from Chinese wildlife.Methods Overlapped fragments were amplified by RT-PCR and full-length genomes were assembled to analyze the nucleotide and deduced protein similarities and phylogenetic analyses of the N genes from Chinese Ferret-Badger,sika deer,vole,dog.Vaccine strains were then determined.Results The two full-length genomes were completely sequenced to find out that they had the same genetic structure with 11 923 nts including 58 nts-Leader, 1353 nts-NP,894 nts-PP,609 nts-MP,1575 nts-GP,6386 nts-LP, and 2,5,5 nts-intergenic regions (IORs),423 nts-Pseudogene-like sequence(ψ),70 nts-Trailer.Conclusion The two full-length genomes were in accordance with the propertms of Rhabdoviridae Lyssa virus by blast and multi-sequence alignment.Th nucleotide and amino acid sequences among Chinese strains had the highest similarity,especially among animals of the same species.Of the two full-length genomes,the similarity in amino acid level was dramatically higher than that in nucleotide level, so that the nucleotide mutations happened in these two genomes were most probably as synonymous mutations.Compared to the referenced rabies viruses,the lengths of the five protein coding regions did not show any changes or recombination,but only with a few-point mutations.It was evident that the five proteins appeared to be stable.The variation sites and types of the two ferret badgers genomes were similar to the referenced vaccine or street strains.The two strains were genotype 1 according to the multi-sequence and phyiogenetic analyses,which possessing the distinct geographyphic characteristics of China.All the evidence suggested a cue that these two ferret badgers rabies viruses were likely to be street virus that already circulating in wildlife.
ABSTRACT
The duck circovirus (DuCV) infection in sick ducks from Fujian Province was investigated. The liver samples of 43 sick Muscovy ducks with infectious serositis were collected from 12 duck farms in Fujian Province.Based on the published sequences of DuCV, two primers were designed for the detection of DuCV and four pairs of primers were designed to amplify four overlapping fragments that cover the complete genome of DuCV. The specific PCR products were amplified from positive samples. The fragments were then cloned into pMD18-T vector and sequenced, and the full length genomic sequence of the FJ0601 isolate of DuCV was obtained. PCR analysis showed that the proportion of ducks which were positive for circovirus was 79% and 10 out of the 12 farms were positive. Sequence analysis showed that the complete genome of DuCV-FJ0601 was 1988 bp and possessed features common to the family Circoviridae which included a stem-loop structure and the Rep protein motifs. Homology analysis showed that FJ0601 isolate of DuCV had 97.3%～97.5% nucleotide sequence identity to all the four Taiwan isolates (TC1/2002, TC2/2002, TC3/2002, TC4/2002), 82.9% identity to the America (33753-52) isolate and 82.3% identity to the Germany isolate. Phylogenetic analysis with Clustal W, however,showed that FJ0601 isolate of DuCV was on a common branch with Taiwan isolates, and Germany and America isolates belonged to the other branch.
ABSTRACT
Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most important animal pathogens in swine industry worldwide. In this study, we isolated the large-plaque forming variant virus designated PL97-1/LP1 from the parental strain PL97-1, the first Korean strain of PRRSV, isolated from the serum of an infected pig in 1997. We found that the 15411-nucleotide genome of PL97-1/LP1 consisted of a 189-nucleotide 5' untranslated region (UTR), a 15071-nucleotide protein-coding region, and a 151-nucleotide 3'UTR, followed by a poly (A) tail of about 50~60 nucleotides in size. The 5'-end of PL97-1/LP1 began with ATGACGTAT. Comparison of the PL97-1/LP1 genome with the 11 fully sequenced PRRSV genomes currently available revealed sequence similarity from 99.6~99.7% (the North American VR-2332 and two VR-2332-derived vaccine strains MLV RespPRRS/Repro and RespPRRS MLV) to 62.0% (the Dutch Lelystad strain). Phylogenetc analysis revealed that PL97-1/LP1 is most closely related to the North American genotype VR-2332, two VR-2332-derived vaccine strains, and Chinese BJ-4. It is distantly related to the European genotype Lelystad. The entire nucleotide sequence of PL97-1/LP1 was identical to that of the parental virus PL97-1 except for three silent nucleotide substitutions, one in ORF1a (U4230C), one in ORF1b (C10977U), and one in ORF5 (U13976A). This nucleotide sequence has been submitted to the GenBank database under the accession number AY612613.