Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 30.796
Filtrar
1.
Braz. j. biol ; 83: e247237, 2023. tab, graf
Artigo em Inglês | MEDLINE, LILACS, VETINDEX | ID: biblio-1339386

RESUMO

Abstract Novel coronavirus (nCoV) namely "SARS-CoV-2" is being found responsible for current PANDEMIC commenced from Wuhan (China) since December 2019 and has been described with epidemiological linkage to China in about 221 countries and territories until now. In this study we have characterized the genetic lineage of SARS-CoV-2 and report the recombination within the genus and subgenus of coronaviruses. Phylogenetic relationship of thirty nine coronaviruses belonging to its four genera and five subgenera was analyzed by using the Neighbor-joining method using MEGA 6.0. Phylogenetic trees of full length genome, various proteins (spike, envelope, membrane and nucleocapsid) nucleotide sequences were constructed separately. Putative recombination was probed via RDP4. Our analysis describes that the "SARS-CoV-2" although shows great similarity to Bat-SARS-CoVs sequences through whole genome (giving sequence similarity 89%), exhibits conflicting grouping with the Bat-SARS-like coronavirus sequences (MG772933 and MG772934). Furthermore, seven recombination events were observed in SARS-CoV-2 (NC_045512) by RDP4. But not a single recombination event fulfills the high level of certainty. Recombination mostly housed in spike protein genes than rest of the genome indicating breakpoint cluster arises beyond the 95% and 99% breakpoint density intervals. Genetic similarity levels observed among "SARS-CoV-2" and Bat-SARS-CoVs advocated that the latter did not exhibit the specific variant that cause outbreak in humans, proposing a suggestion that "SARS-CoV-2" has originated possibly from bats. These genomic features and their probable association with virus characteristics along with virulence in humans require further consideration.


Resumo O novo coronavírus (nCoV), nomeadamente "SARS-CoV-2", foi considerado responsável pela pandemia atual iniciada em Wuhan (China) desde dezembro de 2019 e foi descrito com ligação epidemiológica à China em cerca de 221 países e territórios até agora. Neste estudo, caracterizamos a linhagem genética do SARS-CoV-2 e relatamos a recombinação dentro do gênero e subgênero dos coronavírus. A relação filogenética de 39 coronavírus pertencentes a seus quatro gêneros e cinco subgêneros foi analisada usando o método de Neighbour-joining usando MEGA 6.0. Árvores filogenéticas do genoma de comprimento total, várias proteínas (espícula, envelope, membrana e nucleocapsídeo), sequências de nucleotídeos foram construídas separadamente. A recombinação putativa foi testada via RDP4. Nossa análise descreve que o "SARS-CoV-2", embora mostre grande semelhança com as sequências de Bat-SARS-CoVs em todo o genoma (dando semelhança de sequência de 89%), exibe agrupamento conflitante com as sequências de coronavírus do tipo Bat-SARS (MG772933 e MG772934) Além disso, sete eventos de recombinação foram observados em SARS-CoV-2 (NC045512) por RDP4. Mas nem um único evento de recombinação preenche o alto nível de certeza. A recombinação está alojada mais em genes de proteína de pico, principalmente, do que no resto do genoma, indicando que o cluster de ponto de interrupção surge além dos intervalos de densidade de ponto de interrupção de 95% e 99%. Os níveis de similaridade genética observados entre "SARS-CoV-2" e Bat-SARS-CoVs defendem que o último não exibe a variante específica que causa surto em humanos, sugerindo que "SARS-CoV-2" tenha se originado possivelmente de morcegos. Essas características genômicas e sua provável associação com as características do vírus, juntamente com a virulência em humanos, requerem uma consideração mais aprofundada.


Assuntos
Humanos , Animais , Quirópteros , COVID-19 , Filogenia , Simulação por Computador , Genoma Viral/genética , SARS-CoV-2
2.
Virol J ; 19(1): 97, 2022 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-35659257

RESUMO

BACKGROUND: The aim of this study was to characterize the genome of a recombinant Enterovirus associated with severe and fatal nosocomial infection; it was typed as Echovirus 11 (E-11) according to the VP1 gene. Enterovirus infection is generally asymptomatic and self-limited, but occasionally it may progress to a more severe clinical manifestation, as in the case described here. Recombination plays a crucial role in the evolution of Enteroviruses (EVs) and has been recognized as the main driving force behind the emergence of epidemic strains associated with severe infection. Therefore, it is of utmost importance to monitor the circulation of recombinant strains for surveillance purposes. METHODS: Enterovirus-RNA was detected in the serum and liver biopsy of patients involved in the nosocomial cluster by commercial One-Step qRT-PCR method and the Enterovirus strains were isolated in vitro. The EVs typing was determined by analyzing the partial-length of the 5'UTR and VP1 sequences with the web-based open-access Enterovirus Genotyping Tool Version 0.1. The amplicons targeting 5'UTR, VP1 and overlapping fragments of the entire genome were sequenced with the Sanger method. Phylogenetic analysis was performed comparing the VP1 and the full-genome sequences of our strains against an appropriate reference set of Enterovirus prototypes of the Picornaviridae genera and species retrieved from the Enterovirus Genotyping Tool. Recombination analysis was performed using RDP4 software. RESULTS: The Neighbor-Joining tree of the VP1 gene revealed that the 4 patients were infected with an identical molecular variant of Echovirus 11 (E-11). While the phylogenetic and the RDP4 analysis of the full-genome sequences provided evidence that it was a chimeric strain between an E-11 and a Coxsackievirus B (CV-B). CONCLUSIONS: The chimeric structure of the E-11 genome might have contributed to the severe infection and epidemic feature of the strain, but further biological characterizations are needed. The evidence reported in this study, highlights the limit of typing techniques based on the VP1 gene, as they fail to identify the emergence of recombinant strains with potentially more pathogenic or epidemic properties, thus providing only partial information on the epidemiology and pathogenesis of Enteroviruses.


Assuntos
Infecção Hospitalar , Infecções por Enterovirus , Enterovirus , Regiões 5' não Traduzidas , Infecção Hospitalar/epidemiologia , Surtos de Doenças , Enterovirus Humano B , Infecções por Enterovirus/epidemiologia , Genoma Viral , Humanos , Filogenia , RNA Viral/química , RNA Viral/genética
3.
Theranostics ; 12(8): 3946-3962, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35664076

RESUMO

Rationale: Viral infections are complex processes based on an intricate network of molecular interactions. The infectious agent hijacks components of the cellular machinery for its profit, circumventing the natural defense mechanisms triggered by the infected cell. The successful completion of the replicative viral cycle within a cell depends on the function of viral components versus the cellular defenses. Non-coding RNAs (ncRNAs) are important cellular modulators, either promoting or preventing the progression of viral infections. Among these ncRNAs, the long non-coding RNA (lncRNA) family is especially relevant due to their intrinsic functional properties and ubiquitous biological roles. Specific lncRNAs have been recently characterized as modulators of the cellular response during infection of human host cells by single stranded RNA viruses. However, the role of host lncRNAs in the infection by human RNA coronaviruses such as SARS-CoV-2 remains uncharacterized. Methods: In the present work, we have performed a transcriptomic study of a cohort of patients with different SARS-CoV-2 viral load and analyzed the involvement of lncRNAs in supporting regulatory networks based on their interaction with RNA-binding proteins (RBPs). Results: Our results revealed the existence of a SARS-CoV-2 infection-dependent pattern of transcriptional up-regulation in which specific lncRNAs are an integral component. To determine the role of these lncRNAs, we performed a functional correlation analysis complemented with the study of the validated interactions between lncRNAs and RBPs. This combination of in silico functional association studies and experimental evidence allowed us to identify a lncRNA signature composed of six elements - NRIR, BISPR, MIR155HG, FMR1-IT1, USP30-AS1, and U62317.2 - associated with the regulation of SARS-CoV-2 infection. Conclusions: We propose a competition mechanism between the viral RNA genome and the regulatory lncRNAs in the sequestering of specific RBPs that modulates the interferon response and the regulation of RNA surveillance by nonsense-mediated decay (NMD).


Assuntos
COVID-19 , RNA Longo não Codificante , COVID-19/genética , Proteína do X Frágil de Retardo Mental , Genoma Viral , Humanos , Imunidade , Proteínas Mitocondriais/metabolismo , RNA Longo não Codificante/genética , RNA Longo não Codificante/metabolismo , RNA não Traduzido/genética , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/metabolismo , SARS-CoV-2/genética , Tioléster Hidrolases/metabolismo
4.
BMC Genomics ; 23(1): 422, 2022 Jun 06.
Artigo em Inglês | MEDLINE | ID: mdl-35668367

RESUMO

BACKGROUND: After an infection, human cells may contain viral genomes in the form of episomes or integrated DNA. Comparing the genomic sequences of different strains of a virus in human cells can often provide useful insights into its behaviour, activity and pathology, and may help develop methods for disease prevention and treatment. To support such comparative analyses, the viral genomes need to be accurately reconstructed from a large number of samples. Previous efforts either rely on customized experimental protocols or require high similarity between the sequenced genomes and a reference, both of which limit the general applicability of these approaches. In this study, we propose a pipeline, named ASPIRE, for reconstructing viral genomes accurately from short reads data of human samples, which are increasingly available from genome projects and personal genomics. ASPIRE contains a basic part that involves de novo assembly, tiling and gap filling, and additional components for iterative refinement, sequence corrections and wrapping. RESULTS: Evaluated by the alignment quality of sequencing reads to the reconstructed genomes, these additional components improve the assembly quality in general, and in some particular samples quite substantially, especially when the sequenced genome is significantly different from the reference. We use ASPIRE to reconstruct the genomes of Epstein Barr Virus (EBV) from the whole-genome sequencing data of 61 nasopharyngeal carcinoma (NPC) samples and provide these sequences as a resource for EBV research. CONCLUSIONS: ASPIRE improves the quality of the reconstructed EBV genomes in published studies and outperforms TRACESPipe in some samples considered.


Assuntos
Infecções por Vírus Epstein-Barr , Herpesvirus Humano 4 , Infecções por Vírus Epstein-Barr/genética , Genoma Viral , Genômica/métodos , Herpesvirus Humano 4/genética , Humanos , Filogenia , Análise de Sequência de DNA/métodos
5.
Curr Microbiol ; 79(7): 213, 2022 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-35672590

RESUMO

PHS21 against Pseudoalteromonas is isolated from Qingdao offshore seawater. The phage was characterized and identified by morphological examination, stability, whole genome sequencing, and bioinformatics analysis. Morphological analysis of PHS21 by transmission electron microscopy shows that belonged to the Siphoviridae family. PHS21 showed strong tolerance with a wide range of temperatures and pH. One-step growth assay indicates that the latent period is about 48 min and the burst size is approximately 218 PFU/cell (plaque forming unit/cell). Its complete genomic sequence is 35,802-bp long with 50 putative open reading frames. Phage PHS21 and PHS3 displayed a very close evolutionary relationship; however, having different DNA packaging proteins indicates that they may have already evolved distinct ways to package DNA in host cells. This study provides the detailed description and genomic characterization of a novel Pseudoalteromonas phage.


Assuntos
Bacteriófagos , Pseudoalteromonas , Siphoviridae , Bacteriófagos/genética , DNA Viral/química , DNA Viral/genética , Genoma Viral , Fases de Leitura Aberta , Filogenia , Pseudoalteromonas/genética , Análise de Sequência de DNA , Siphoviridae/genética
6.
Stud Health Technol Inform ; 290: 729-733, 2022 Jun 06.
Artigo em Inglês | MEDLINE | ID: mdl-35673113

RESUMO

This study leveraged the phylogenetic analysis of more than 10K strains of novel coronavirus (SARS-CoV-2) from 67 countries. Due to the requirement of high-end computational power for phylogenetic analysis, we leverage a fast yet highly accurate alignment-free method to develop the phylogenetic tree out of all the strains of novel coronavirus. K-Means clustering and PCA-based dimension reduction technique were used to identify a representative strain from each location. The resulting phylogenetic tree was able to highlight evolutionary relationships of SARS-CoV-2 genome and, subsequently, linked to the interpretation of facts and figures across the globe for the spread of COVID-19. Our analysis revealed that the geographical boundaries could not be explained by the phylogenetic analysis of novel coronavirus as it placed different countries from Asia, Europe and the USA in very close proximity in the tree. Instead, the commute of people from one country to another is the key to the spread of COVID-19. We believe our study will support the policymakers to contain the spread of COVID-19 globally.


Assuntos
COVID-19 , SARS-CoV-2 , Ásia , COVID-19/epidemiologia , Genoma Viral/genética , Humanos , Filogenia , SARS-CoV-2/genética
7.
Virol J ; 19(1): 98, 2022 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-35659318

RESUMO

BACKGROUND: Echovirus 9 (E9) is associated with a wide variety of diseases and medical conditions, and the clinical symptoms of sporadic cases caused by E9 often are severe. With a high global prevalence, E9 has caused multiple outbreaks worldwide. However, little is known about the genetic and geographic population dynamics of E9. METHOD: A total of 131 VP1 gene sequences, including15 generated in this study and 116 obtained from GenBank, were used to coestimate time-resolved phylogenies to infer viral evolution and transmission in worldwide. Overlapping fragments representing whole genomes were amplified by reverse transcription polymerase chain reaction (RT-PCR) using specific primers. Then, we reported the genetic characteristics of fifteen E9 strains in the Chinese Mainland. Similarity plots and bootscanning analysis were used to determine recombination patterns of E9. RESULTS: The estimated mean evolutionary rate of global E9 VP1 gene was 4.278 × 10-3 substitutions per site per year (95% confidence interval [CI], 3.822 × 10-3/site/year to 4.710 × 10-3/site/year), and the common ancestor of E9 likely emerged around 1868 (95% CI, 1840 to 1892). The full-length genomic sequences of the fifteen E9 strains showed 76.9-79.6% nucleotide identity and 95.3-95.9% amino acid identity with E9 Barty strain. 11 of 15 E9 whole genome sequence present four recombination patterns, and E9 recombinants have extensive genetic exchanges in the 2C and P3 regions with other Enterovirus B (EV-B) circulated in China. Four of six E9 strains were temperature sensitive, and two were temperature resistant, and a comparative genomics analysis suggested that 411, 865 and 867 amino acid substitution in the P1 region was related to temperature sensitivity. CONCLUSION: This study highlights a persistent transmission network of E9 in worldwide, provides valuable information regarding the molecular epidemiology of E9.


Assuntos
Echovirus 9 , China/epidemiologia , Enterovirus Humano B/genética , Evolução Molecular , Genoma Viral , Filogenia , Recombinação Genética
8.
BMC Genomics ; 23(1): 406, 2022 May 30.
Artigo em Inglês | MEDLINE | ID: mdl-35644636

RESUMO

BACKGROUND: Non-targeted whole genome sequencing is a powerful tool to comprehensively identify constituents of microbial communities in a sample. There is no need to direct the analysis to any identification before sequencing which can decrease the introduction of bias and false negatives results. It also allows the assessment of genetic aberrations in the genome (e.g., single nucleotide variants, deletions, insertions and copy number variants) including in noncoding protein regions. METHODS: The performance of four different random priming amplification methods to recover RNA viral genetic material of SARS-CoV-2 were compared in this study. In method 1 (H-P) the reverse transcriptase (RT) step was performed with random hexamers whereas in methods 2-4 RT incorporating an octamer primer with a known tag. In methods 1 and 2 (K-P) sequencing was applied on material derived from the RT-PCR step, whereas in methods 3 (SISPA) and 4 (S-P) an additional amplification was incorporated before sequencing. RESULTS: The SISPA method was the most effective and efficient method for non-targeted/random priming whole genome sequencing of SARS-CoV-2 that we tested. The SISPA method described in this study allowed for whole genome assembly of SARS-CoV-2 and influenza A(H1N1)pdm09 in mixed samples. We determined the limit of detection and characterization of SARS-CoV-2 virus which was 103 pfu/ml (Ct, 22.4) for whole genome assembly and 101 pfu/ml (Ct, 30) for metagenomics detection. CONCLUSIONS: The SISPA method is predominantly useful for obtaining genome sequences from RNA viruses or investigating complex clinical samples as no prior sequence information is needed. It might be applied to monitor genomic virus changes, virus evolution and can be used for fast metagenomics detection or to assess the general picture of different pathogens within the sample.


Assuntos
COVID-19 , Vírus da Influenza A Subtipo H1N1 , Vírus de RNA , Genoma Viral , Humanos , SARS-CoV-2/genética , Sequenciamento Completo do Genoma
9.
F1000Res ; 11: 9, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35707000

RESUMO

Background: SARS-CoV-2 virus is a highly transmissible pathogen that causes COVID-19. The outbreak originated in Wuhan, China in December 2019. A number of nonsynonymous mutations located at different SARS-CoV-2 proteins have been reported by multiple studies. However, there are limited computational studies on the biological impacts of these mutations on the structure and function of the proteins.   Methods: In our study nonsynonymous mutations of the SARS-CoV-2 genome and their frequencies were identified from 30,229 sequences. Subsequently, the effects of the top 10 nonsynonymous mutations of different SARS-CoV-2 proteins were analyzed using bioinformatics tools including co-mutation analysis, prediction of the protein structure stability and flexibility analysis, and prediction of the protein functions.   Results: A total of 231 nonsynonymous mutations were identified from 30,229 SARS-CoV-2 genome sequences. The top 10 nonsynonymous mutations affecting nine amino acid residues were ORF1a nsp5 P108S, ORF1b nsp12 P323L and A423V, S protein N501Y and D614G, ORF3a Q57H, N protein P151L, R203K and G204R. Many nonsynonymous mutations showed a high concurrence ratio, suggesting these mutations may evolve together and interact functionally. Our result showed that ORF1a nsp5 P108S, ORF3a Q57H and N protein P151L mutations may be deleterious to the function of SARS-CoV-2 proteins. In addition, ORF1a nsp5 P108S and S protein D614G may destabilize the protein structures while S protein D614G may have a more open conformation compared to the wild type.   Conclusion: The biological consequences of these nonsynonymous mutations of SARS-CoV-2 proteins should be further validated by in vivo and in vitro experimental studies in the future.


Assuntos
COVID-19 , SARS-CoV-2 , Surtos de Doenças , Genoma Viral , Humanos , SARS-CoV-2/genética , Glicoproteína da Espícula de Coronavírus/química
10.
J Gen Virol ; 103(6)2022 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-35723908

RESUMO

The family Rhabdoviridae comprises viruses with negative-sense (-) RNA genomes of 10-16 kb. Virions are typically enveloped with bullet-shaped or bacilliform morphology but can also be non-enveloped filaments. Rhabdoviruses infect plants or animals, including mammals, birds, reptiles, amphibians or fish, as well as arthropods, which serve as single hosts or act as biological vectors for transmission to animals or plants. Rhabdoviruses include important pathogens of humans, livestock, fish or agricultural crops. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Rhabdoviridae, which is available at ictv.global/report/rhabdoviridae.


Assuntos
Rhabdoviridae , Animais , Aves , Peixes , Genoma Viral , Mamíferos , Répteis , Rhabdoviridae/genética , Vírion , Replicação Viral
11.
Virol J ; 19(1): 103, 2022 Jun 16.
Artigo em Inglês | MEDLINE | ID: mdl-35710544

RESUMO

BACKGROUND: As a new epi-center of COVID-19 in Asia and a densely populated developing country, Indonesia is facing unprecedented challenges in public health. SARS-CoV-2 lineage B.1.466.2 was reported to be an indigenous dominant strain in Indonesia (once second only to the Delta variant). However, it remains unclear how this variant evolved and spread within such an archipelagic nation. METHODS: For statistical description, the spatiotemporal distributions of the B.1.466.2 variant were plotted using the publicly accessible metadata in GISAID. A total of 1302 complete genome sequences of Indonesian B.1.466.2 strains with high coverage were downloaded from the GISAID's EpiCoV database on 28 August 2021. To determine the molecular evolutionary characteristics, we performed a time-scaled phylogenetic analysis using the maximum likelihood algorithm and called the single nucleotide variants taking the Wuhan-Hu-1 sequence as reference. To investigate the spatiotemporal transmission patterns, we estimated two dynamic parameters (effective population size and effective reproduction number) and reconstructed the phylogeography among different islands. RESULTS: As of the end of August 2021, nearly 85% of the global SARS-CoV-2 lineage B.1.466.2 sequences (including the first one) were obtained from Indonesia. This variant was estimated to account for over 50% of Indonesia's daily infections during the period of March-May 2021. The time-scaled phylogeny suggested that SARS-CoV-2 lineage B.1.466.2 circulating in Indonesia might have originated from Java Island in mid-June 2020 and had evolved into two disproportional and distinct sub-lineages. High-frequency non-synonymous mutations were mostly found in the spike and NSP3; the S-D614G/N439K/P681R co-mutations were identified in its larger sub-lineage. The demographic history was inferred to have experienced four phases, with an exponential growth from October 2020 to February 2021. The effective reproduction number was estimated to have reached its peak (11.18) in late December 2020 and dropped to be less than one after early May 2021. The relevant phylogeography showed that Java and Sumatra might successively act as epi-centers and form a stable transmission loop. Additionally, several long-distance transmission links across seas were revealed. CONCLUSIONS: SARS-CoV-2 variants circulating in the tropical archipelago may follow unique patterns of evolution and transmission. Continuous, extensive and targeted genomic surveillance is essential.


Assuntos
COVID-19 , SARS-CoV-2 , COVID-19/epidemiologia , Evolução Molecular , Genoma Viral , Genômica , Humanos , Indonésia/epidemiologia , Mutação , Filogenia , SARS-CoV-2/genética
12.
Sci Rep ; 12(1): 10297, 2022 Jun 18.
Artigo em Inglês | MEDLINE | ID: mdl-35717436

RESUMO

We classify the main variants of the SARS-CoV-2 virus representing a given biological sequence coded as a symbolic digital sequence and by its evolution by a cellular automata with a properly chosen rule. The spike protein, common to all variants of the SARS-CoV-2 virus, is then by the picture of the cellular automaton evolution yielding a visible representation of important features of the protein. We use information theory Hamming distance between different stages of the evolution of the cellular automaton for seven variants relative to the original Wuhan/China virus. We show that our approach allows to classify and group variants with common ancestors and same mutations. Although being a simpler method, it can be used as an alternative for building phylogenetic trees.


Assuntos
COVID-19 , SARS-CoV-2 , COVID-19/genética , Genoma Viral , Humanos , Mutação , Filogenia , SARS-CoV-2/genética
13.
Sci Data ; 9(1): 336, 2022 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-35701476

RESUMO

Bats are considered reservoirs of many lethal zoonotic viruses and have been implicated in several outbreaks of emerging infectious diseases, such as SARS-CoV, MERS-CoV, and SARS-CoV-2. It is necessary to systematically derive the expression patterns of bat virus receptors and their regulatory features for future research into bat-borne viruses and the prediction and prevention of pandemics. Here, we performed single-nucleus RNA sequencing (snRNA-seq) and single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq) of major organ samples collected from Chinese horseshoe bats (Rhinolophus affinis) and systematically checked the expression pattern of bat-related virus receptors and chromatin accessibility across organs and cell types, providing a valuable dataset for studying the nature of infection among bat-borne viruses.


Assuntos
COVID-19 , Quirópteros , Receptores Virais , SARS-CoV-2 , Animais , Genoma Viral , Humanos , Filogenia , Análise de Célula Única
14.
Front Cell Infect Microbiol ; 12: 829380, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35663472

RESUMO

In 2019, a dengue outbreak occurred with 290 confirmed cases in Wenzhou, a coastal city in southeast China. To identify the origin of the dengue virus (DENV) from this outbreak, viral RNA was extracted from four serum samples and sequenced for whole genome analysis. Then, phylogenetic analysis, gene mutation, secondary structure prediction, selection pressure analysis, and recombination analysis were performed. DENV strains Cam-03 and Cam-11 were isolated from patients traveling from Cambodia, while ZJWZ-18 and ZJWZ-62 strains were isolated from local patients without a record of traveling abroad. The whole genome sequence of all four strains was 10,735 nucleotides long. Phylogenetic tree analysis showed that the four strains belonged to genotype 1 of DENV-1, but the local Wenzhou strains and imported strains clustered in different branches. ZJWZ-18 and ZJWZ-62 were closely related to strain MF033254-Singapore-2016, and Cam-03 and Cam-11 were closely related to strain AB608788-China : Taiwan-1994. A comparison of the coding regions between the local strains and the DENV-1 standard strain (EU848545-Hawaii-1944) showed 82 amino acid mutations between the two strains. A total of 55 amino acid mutations were found between the coding regions of the local and imported strains. The overall secondary structure of the 3' UTR of the local strains had changed: apparent changes in the head and tail position were observed when compared to DENV-1 standard strain. Furthermore, selection pressure analysis and recombination detection using the 4 isolates and 41 reference strains showed two credible positive selection sites and eight credible recombination events, which warrant further studies. This study may enhance the understanding of viral replication, infection, evolution, virulence, and pathogenicity of DENV.


Assuntos
Vírus da Dengue , Dengue , Aminoácidos , China/epidemiologia , Dengue/epidemiologia , Surtos de Doenças , Genoma Viral , Genótipo , Humanos , Filogenia
15.
Sci Rep ; 12(1): 9863, 2022 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-35701436

RESUMO

The unmapped readspace of whole genome sequencing data tends to be large but is often ignored. We posit that it contains valuable signals of both human infection and contamination. Using unmapped and poorly aligned reads from whole genome sequences (WGS) of over 1000 families and nearly 5000 individuals, we present insights into common viral, bacterial, and computational contamination that plague whole genome sequencing studies. We present several notable results: (1) In addition to known contaminants such as Epstein-Barr virus and phiX, sequences from whole blood and lymphocyte cell lines contain many other contaminants, likely originating from storage, prep, and sequencing pipelines. (2) Sequencing plate and biological sample source of a sample strongly influence contamination profile. And, (3) Y-chromosome fragments not on the human reference genome commonly mismap to bacterial reference genomes. Both experiment-derived and computational contamination is prominent in next-generation sequencing data. Such contamination can compromise results from WGS as well as metagenomics studies, and standard protocols for identifying and removing contamination should be developed to ensure the fidelity of sequencing-based studies.


Assuntos
Bacteriófagos , Infecções por Vírus Epstein-Barr , Biologia Computacional , Genoma Bacteriano , Genoma Humano , Genoma Viral , Herpesvirus Humano 4/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Sequenciamento Completo do Genoma
16.
Curr Microbiol ; 79(8): 221, 2022 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-35704129

RESUMO

Vibrio parahaemolyticus is a bacterial pathogen in marine aquaculture systems and a major cause of food-borne illnesses worldwide. In the present study, Vibrio phage KIT05 was isolated from water collected from a shrimp farm in the Mekong Delta, Vietnam. It was characterized based on its morphology, growth curve, lytic properties, and genome sequence. Under the electron microscope, KIT05 particles had an icosahedral head with a diameter of 62.3 nm and a short tail of 24.1 nm. The one-step growth curve of KIT05 showed that its latency time was approximately 40 min and burst size was 18 plaque-forming units/cell. The genome of KIT05 comprises 50,628 bp with a GC content of 41.63%. It contains 60 open reading frames that are encoded within both strands and four tRNAs. The presence of direct terminal repeats of 130 bp at both ends of the KIT05 DNA was determined. According to phage morphology, genomic organization, and phylogeny analysis, Vibrio phage KIT05 was classified into the family Podoviridae. The genome annotation revealed that KIT05 had no virulent or lysogenic genes. This study may help identify a novel candidate for developing biocontrol agents for Vibrio parahaemolyticus.


Assuntos
Bacteriófagos , Podoviridae , Vibrio parahaemolyticus , Bacteriófagos/genética , Genoma Viral , Genômica , Filogenia , Podoviridae/genética , Vibrio parahaemolyticus/genética
17.
PLoS Pathog ; 18(6): e1010589, 2022 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-35666744

RESUMO

Non-coding regions of viral RNA (vRNA) genomes are critically important in the regulation of gene expression. In particular, pseudoknot (PK) structures, which are present in a wide range of RNA molecules, have a variety of roles. The 5' untranslated region (5' UTR) of foot-and-mouth disease virus (FMDV) vRNA is considerably longer than in other viruses from the picornavirus family and consists of a number of distinctive structural motifs that includes multiple (2, 3 or 4 depending on the virus strain) putative PKs linked in tandem. The role(s) of the PKs in the FMDV infection are not fully understood. Here, using bioinformatics, sub-genomic replicons and recombinant viruses we have investigated the structural conservation and importance of the PKs in the FMDV lifecycle. Our results show that despite the conservation of two or more PKs across all FMDVs, a replicon lacking PKs was replication competent, albeit at reduced levels. Furthermore, in competition experiments, GFP FMDV replicons with less than two (0 or 1) PK structures were outcompeted by a mCherry FMDV wt replicon that had 4 PKs, whereas GFP replicons with 2 or 4 PKs were not. This apparent replicative advantage offered by the additional PKs correlates with the maintenance of at least two PKs in the genomes of FMDV field isolates. Despite a replicon lacking any PKs retaining the ability to replicate, viruses completely lacking PK were not viable and at least one PK was essential for recovery of infections virus, suggesting a role for the PKs in virion assembly. Thus, our study points to roles for the PKs in both vRNA replication and virion assembly, thereby improving understanding the molecular biology of FMDV replication and the wider roles of PK in RNA functions.


Assuntos
Vírus da Febre Aftosa , Febre Aftosa , Regiões 5' não Traduzidas , Animais , Vírus de DNA , Febre Aftosa/genética , Vírus da Febre Aftosa/genética , Genoma Viral , RNA Viral/química , Replicação Viral/genética
18.
PLoS Pathog ; 18(6): e1010578, 2022 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-35653410

RESUMO

Human bocavirus 1 (HBoV1), a member of the genus Bocaparvovirus of the family Parvoviridae, causes acute respiratory tract infections in young children. Well-differentiated pseudostratified human airway epithelium cultured at an air-liquid interface (HAE-ALI) is an ideal in vitro culture model to study HBoV1 infection. Unique to other parvoviruses, bocaparvoviruses express a small nonstructured protein NP1 of ~25 kDa from an open reading frame (ORF) in the center of the viral genome. NP1 plays an important role in viral DNA replication and pre-mRNA processing. In this study, we performed an affinity purification assay to identify HBoV1 NP1-inteacting proteins. We identified that Ku70 and RPA70 directly interact with the NP1 at a high binding affinity, characterized with an equilibrium dissociation constant (KD) of 95 nM and 122 nM, respectively. Furthermore, we mapped the key NP1-interacting domains of Ku70 at aa266-439 and of RPA70 at aa181-422. Following a dominant negative strategy, we revealed that the interactions of Ku70 and RPA70 with NP1 play a significant role in HBoV1 DNA replication not only in an in vitro viral DNA replication assay but also in HBoV1-infected HAE-ALI cultures. Collectively, our study revealed a novel mechanism by which HBoV1 NP1 enhances viral DNA replication through its direct interactions with Ku70 and RPA70.


Assuntos
Bocavirus Humano , Infecções por Parvoviridae , Criança , Pré-Escolar , Replicação do DNA , DNA Viral/genética , DNA Viral/metabolismo , Genoma Viral , Bocavirus Humano/genética , Bocavirus Humano/metabolismo , Humanos , Replicação Viral/genética
20.
PLoS Genet ; 18(5): e1010179, 2022 05.
Artigo em Inglês | MEDLINE | ID: mdl-35500034

RESUMO

Like many viruses, Hepatitis C Virus (HCV) has a high mutation rate, which helps the virus adapt quickly, but mutations come with fitness costs. Fitness costs can be studied by different approaches, such as experimental or frequency-based approaches. The frequency-based approach is particularly useful to estimate in vivo fitness costs, but this approach works best with deep sequencing data from many hosts are. In this study, we applied the frequency-based approach to a large dataset of 195 patients and estimated the fitness costs of mutations at 7957 sites along the HCV genome. We used beta regression and random forest models to better understand how different factors influenced fitness costs. Our results revealed that costs of nonsynonymous mutations were three times higher than those of synonymous mutations, and mutations at nucleotides A or T had higher costs than those at C or G. Genome location had a modest effect, with lower costs for mutations in HVR1 and higher costs for mutations in Core and NS5B. Resistance mutations were, on average, costlier than other mutations. Our results show that in vivo fitness costs of mutations can be site and virus specific, reinforcing the utility of constructing in vivo fitness cost maps of viral genomes.


Assuntos
Hepacivirus , Hepatite C , Genoma Viral/genética , Hepacivirus/genética , Hepatite C/genética , Humanos , Mutação , Taxa de Mutação
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA
...