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1.
mBio ; 12(4): e0114021, 2021 08 31.
Artigo em Inglês | MEDLINE | ID: mdl-34465019

RESUMO

The recent emergence of multiple variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a significant concern for public health worldwide. New variants have been classified either as variants of concern (VOCs) or variants of interest (VOIs) by the CDC (USA) and WHO. The VOCs include lineages such as B.1.1.7 (20I/501Y.V1 variant), P.1 (20J/501Y.V3 variant), B.1.351 (20H/501Y.V2 variant), and B.1.617.2. In contrast, the VOI category includes B.1.525, B.1.526, P.2, and B.1.427/B.1.429. The WHO provided the alert for last two variants (P.2 and B.1.427/B.1.429) and labeled them for further monitoring. As per the WHO, these variants can be reclassified due to their status at a particular time. At the same time, the CDC (USA) has marked these two variants as VOIs up through today. This article analyzes the evolutionary patterns of all these emerging variants, as well as their geographical distributions and transmission patterns, including the circulating frequency, entropy diversity, and mutational event diversity throughout the genomes of all SARS-CoV-2 lineages. The transmission pattern was observed highest in the B.1.1.7 lineage. Our frequency evaluation found that this lineage achieved 100% frequency in early October 2020. We also critically evaluated the above emerging variants mutational landscape and significant spike protein mutations (E484K, K417T/N, N501Y, and D614G) impacting public health. Finally, the effectiveness of vaccines against newly SARS-CoV-2 variants was also analyzed. IMPORTANCE Irrespective of the aggressive vaccination drive, the newly emerging multiple SARS-CoV-2 variants are causing havoc in several countries. As per the CDC (USA) and WHO, the VOCs include the B.1.1.7, P.1, B.1.351, and B.1.617.2 lineages, while the VOIs include the B.1.525, B.1.526, P.2, and B.1.427/B.1.429 lineages. This study analyzed the evolutionary patterns, geographical distributions and transmission patterns, circulating frequency, entropy diversity, and mutational event diversity throughout the genome of significant SARS-CoV-2 lineages. A higher transmission pattern was observed for the B.1.1.7 variant. The study also evaluated the mutational landscape and important spike protein mutations (E484K, K417T/N, N501Y, and D614G) of all of the above variants. Finally, a survey was performed on the efficacy of vaccines against these variants from the previously published literature. The results presented in this article will help design future countrywide pandemic planning strategies for the emerging variants, next-generation vaccine development using alternative wild-type antigens and significant viral antigens, and immediate planning for ongoing vaccination programs worldwide.


Assuntos
Vacinas contra COVID-19/imunologia , COVID-19/epidemiologia , COVID-19/transmissão , SARS-CoV-2/genética , SARS-CoV-2/imunologia , Glicoproteína da Espícula de Coronavírus/imunologia , Evolução Biológica , COVID-19/imunologia , COVID-19/patologia , Evolução Molecular , Genoma Viral/genética , Humanos , Filogenia , Saúde Pública , Glicoproteína da Espícula de Coronavírus/genética
2.
Braz J Biol ; 83: e247237, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34495154

RESUMO

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.


Assuntos
COVID-19 , Quirópteros , Animais , Simulação por Computador , Genoma Viral/genética , Humanos , Filogenia , SARS-CoV-2
3.
Nat Commun ; 12(1): 4821, 2021 08 10.
Artigo em Inglês | MEDLINE | ID: mdl-34376672

RESUMO

Subclonal genetic heterogeneity and their diverse gene expression impose serious problems in understanding the behavior of cancers and contemplating therapeutic strategies. Here we develop and utilize a capture-based sequencing panel, which covers host hotspot genes and the full-length genome of human T-cell leukemia virus type-1 (HTLV-1), to investigate the clonal architecture of adult T-cell leukemia-lymphoma (ATL). For chronologically collected specimens from patients with ATL or pre-onset individuals, we integrate deep DNA sequencing and single-cell RNA sequencing to detect the somatic mutations and virus directly and characterize the transcriptional readouts in respective subclones. Characteristic genomic and transcriptomic patterns are associated with subclonal expansion and switches during the clinical timeline. Multistep mutations in the T-cell receptor (TCR), STAT3, and NOTCH pathways establish clone-specific transcriptomic abnormalities and further accelerate their proliferative potential to develop highly malignant clones, leading to disease onset and progression. Early detection and characterization of newly expanded subclones through the integrative analytical platform will be valuable for the development of an in-depth understanding of this disease.


Assuntos
Genoma Viral/genética , Vírus Linfotrópico T Tipo 1 Humano/genética , Leucemia-Linfoma de Células T do Adulto/genética , Análise de Célula Única/métodos , Transcriptoma/genética , Adulto , Linhagem Celular Tumoral , Proliferação de Células/genética , Células Cultivadas , Evolução Clonal/genética , Células Clonais/metabolismo , Células Clonais/patologia , Infecções por HTLV-I/virologia , Vírus Linfotrópico T Tipo 1 Humano/fisiologia , Humanos , Células Jurkat , Leucemia-Linfoma de Células T do Adulto/patologia , Leucemia-Linfoma de Células T do Adulto/virologia , Mutação , RNA-Seq/métodos , Receptor Notch1/genética , Receptores de Antígenos de Linfócitos T/genética , Fator de Transcrição STAT3/genética
4.
Arch Virol ; 166(10): 2881-2885, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34338875

RESUMO

Here, we describe a novel mycovirus, tentatively designated as "Botryosphaeria dothidea mitovirus 3" (BdMV3), isolated from Botryosphaeria dothidea strain FJ, which causes pear ring rot disease in Fujian Province, China. The complete genome nucleotide sequence of BdMV3 is 2538 nt in length and contains a single 2070-nt open reading frame (ORF) encoding a putative RNA-dependent RNA polymerase (RdRp) of 689 amino acids (aa) using the fungal mitochondrial genetic code. BLASTp analysis revealed that the RdRp of BdMV3 shares 28.91%-69.36% sequence identity (query sequence coverage more than 90%) with those of members of the genus Mitovirus, with the highest sequence identity of 69.36% and 68.79% to the corresponding RdRp aa sequences of Rhizoctonia solani mitovirus 10 and Macrophomina phaseolina mitovirus 4, respectively. Phylogenetic analysis based on RdRp aa sequences indicated that BdMV3 is a new member of the genus Mitovirus in the family Mitoviridae.


Assuntos
Ascomicetos/virologia , Genoma Viral/genética , Doenças das Plantas/microbiologia , Pyrus/microbiologia , Vírus de RNA/genética , Sequência de Aminoácidos , China , Micovírus/classificação , Micovírus/genética , Fases de Leitura Aberta/genética , Filogenia , Vírus de RNA/classificação , RNA Viral/genética , RNA Polimerase Dependente de RNA/genética
5.
Arch Virol ; 166(10): 2751-2762, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34341873

RESUMO

Ticks are important vector arthropods that transmit various pathogens to humans and other animals. Tick-borne viruses are of particular concern to public health as these are major agents of emerging and re-emerging infectious diseases. The Phenuiviridae family of tick-borne viruses is one of the most diverse groups and includes important human pathogenic viruses such as severe fever with thrombocytopenia syndrome virus. Phenuivirus-like sequences were detected during the surveillance of tick-borne viruses using RNA virome analysis from a pooled sample of Haemaphysalis formosensis ticks collected in Ehime, Japan. RT-PCR amplification and Sanger sequencing revealed the nearly complete viral genome sequence of all three segments. Comparisons of the viral amino acid sequences among phenuiviruses indicated that the detected virus shared 46%-70% sequence identity with known members of the Kaisodi group in the genus Uukuvirus. Furthermore, phylogenetic analysis of the viral proteins showed that the virus formed a cluster with the Kaisodi group viruses, suggesting that this was a novel virus, which was designated "Toyo virus" (TOYOV). Further investigation of TOYOV is needed, and it will contribute to understanding the natural history and the etiological importance of the Kaisodi group viruses.


Assuntos
Vírus de RNA de Sentido Negativo/classificação , Carrapatos/virologia , Sequência de Aminoácidos , Animais , Genoma Viral/genética , Humanos , Japão , Vírus de RNA de Sentido Negativo/genética , Vírus de RNA de Sentido Negativo/isolamento & purificação , Filogenia , RNA Viral/genética , Análise de Sequência de DNA , Proteínas Virais/genética , Viroma/genética
6.
Arch Virol ; 166(10): 2937-2942, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34347169

RESUMO

The genus Gyrovirus was assigned to the family Anelloviridae in 2017 with only one recognized species, Chicken anemia virus. Over the last decade, many diverse viruses related to chicken anemia virus have been identified but not classified. Here, we provide a framework for the classification of new species in the genus Gyrovirus and communicate the establishment of nine new species. We adopted the 'Genus + freeform epithet' binomial system for the naming of these species.


Assuntos
Gyrovirus/classificação , Terminologia como Assunto , Anelloviridae/classificação , Anelloviridae/genética , Animais , Proteínas do Capsídeo/genética , Vírus da Anemia da Galinha/classificação , Vírus da Anemia da Galinha/genética , DNA Viral/genética , Bases de Dados Genéticas , Genoma Viral/genética , Gyrovirus/genética , Humanos , Filogenia , Análise de Sequência de DNA
7.
Arch Virol ; 166(10): 2887-2894, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34347170

RESUMO

The complete genome sequence of the virulent bacteriophage PMBT3, isolated on the proteolytic Pseudomonas grimontii strain MBTL2-21, showed no significant similarity to other known phage genome sequences, making this phage the first reported to infect a strain of P. grimontii. Electron microscopy revealed PMBT3 to be a member of the family Siphoviridae, with notably long and flexible whiskers. The linear, double-stranded genome of 87,196 bp has a mol% G+C content of 60.4 and contains 116 predicted protein-encoding genes. A putative tellurite resistance (terB) gene, originally reported to occur in the genome of a bacterium, was detected in the genome of phage PMBT3.


Assuntos
Pseudomonas/virologia , Animais , Bacteriólise , Composição de Bases , Sequência de Bases , DNA Viral/genética , Genoma Viral/genética , Especificidade de Hospedeiro , Leite/microbiologia , Filogenia , Fagos de Pseudomonas/classificação , Fagos de Pseudomonas/genética , Fagos de Pseudomonas/fisiologia , Fagos de Pseudomonas/ultraestrutura , Siphoviridae/classificação , Siphoviridae/genética , Siphoviridae/fisiologia , Siphoviridae/ultraestrutura , Proteínas Virais/genética , Vírion/ultraestrutura
8.
Arch Virol ; 166(10): 2927-2935, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34350513

RESUMO

The highly diverse virus family Picornaviridae presently comprises 68 approved genera with 158 species plus many unassigned viruses. In order to better match picornavirus taxonomy to the functional and genomic groupings between genera, the establishment of five subfamilies (Caphthovirinae, Kodimesavirinae, Ensavirinae, Paavivirinae and Heptrevirinae) is proposed. The subfamilies are defined by phylogenetic analyses of 3CD (precursor of virus-encoded proteinase and polymerase) and P1 (capsid protein precursor) coding sequences and comprise between 7 and 22 currently approved virus genera. Due to the high within-subfamily and between-subfamily divergences of the picornavirus genera, p-distance estimates are unsuited for the demarcation of subfamilies. Members of the proposed subfamilies typically show some commonalities in their genome organisations, including VP1/2A cleavage mechanisms and possession of leader proteins. Other features, such as internal ribosomal entry site types, are more variable within and between members of genera. Some subfamilies are characterised by homology of proteins 1A, 2A, 2B and 3A encoded by members, which do not belong to the canon of orthologous picornavirus proteins. The proposed addition of a subfamily layer to the taxonomy of picornaviruses provides a valuable additional organisational level to the family that acknowledges the existence of higher-level evolutionary groupings of its component genera.


Assuntos
Genoma Viral/genética , Filogenia , Picornaviridae/classificação , Proteases Virais 3C/genética , Sequência de Aminoácidos , Proteínas do Capsídeo/genética , Evolução Molecular , Genômica , Sítios Internos de Entrada Ribossomal/genética , Picornaviridae/genética , Análise de Sequência de DNA
9.
Arch Virol ; 166(10): 2895-2899, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34351521

RESUMO

After the 2005-2009 chikungunya epidemic, intermittent outbreaks were reported in many parts of India. The outbreaks were caused by either locally circulating strains or imported viruses. Virus transmission routes can be traced by complete genome sequencing studies. We investigated two outbreaks in 2014 and 2019 in Kerala, India. Chikungunya virus (CHIKV) was isolated from the samples, and whole genomes were sequenced for a 2014 isolate and a 2019 isolate. Phylogenetic analysis revealed that the isolates formed a separate group with a 2019 isolate from Pune, Maharashtra, and belonged to the East/Central/South African (ECSA) genotype, Indian subcontinent sublineage of the Indian Ocean Lineage (IOL). A novel mutation at amino acid position 76 of the E2 gene was observed in the group. The phylogenetic results suggest that the outbreaks might have been caused by a virus that had been circulating in India since 2014. A detailed study is needed to investigate the evolution of CHIKV in India.


Assuntos
Febre de Chikungunya/epidemiologia , Febre de Chikungunya/virologia , Vírus Chikungunya/genética , Surtos de Doenças , Febre de Chikungunya/transmissão , Vírus Chikungunya/classificação , Vírus Chikungunya/isolamento & purificação , Genoma Viral/genética , Genótipo , Humanos , Índia/epidemiologia , Mutação , Filogenia , RNA Viral/genética , Proteínas do Envelope Viral/genética
10.
Arch Virol ; 166(10): 2841-2846, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34357464

RESUMO

Native Australian soldier flies, Inopus spp. (Diptera: Stratiomyidae), are agricultural pests of economic importance to the sugarcane industry. A screen of the salivary gland transcriptome of Inopus flavus (James) revealed the presence of viral RNA belonging to a potentially novel member of the family Dicistroviridae. The complete genome sequence consists of 9793 nucleotides with two open reading frames. The genome includes two potential internal ribosomal entry sites (IRESs): one within the 5' UTR and the other in the intergenic region (IGR). Virus particles purified from infected larvae and visualised by electron microscopy were found to be icosahedral, non-enveloped, and 30 nm in diameter.


Assuntos
Dicistroviridae/classificação , Dípteros/virologia , Saccharum/parasitologia , Sequência de Aminoácidos , Animais , Austrália , Dicistroviridae/genética , Variação Genética , Genoma Viral/genética , Sítios Internos de Entrada Ribossomal/genética , Larva/virologia , Fases de Leitura Aberta/genética , Filogenia , RNA Viral/genética , Glândulas Salivares/virologia , Vírion/ultraestrutura
11.
Arch Virol ; 166(10): 2901-2904, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34363533

RESUMO

The complete genomic sequence of scorzonera virus A (SCoVA) from a Scorzonera austriaca Willd. plant in South Korea was determined by high-throughput sequencing and confirmed by Sanger sequencing. The SCoVA genome contains 9867 nucleotides, excluding the 3'-terminal poly(A) tail. The SCoVA genome structure is typical of potyviruses and contains a single open reading frame encoding a large putative polyprotein of 3168 amino acids. Pairwise comparison analysis of the complete genome and polyprotein sequences of SCoVA with those of other potyviruses showed that they shared the highest nucleotide and amino acid sequences identity (54.47% and 49.57%, respectively) with those of lettuce mosaic virus (GenBank accession number KJ161185). Phylogenetic analysis of the amino acid sequence of the polyprotein confirmed that SCoVA belongs to the genus Potyvirus. These findings suggest that SCoVA should be considered a novel member of the genus Potyvirus, family Potyviridae.


Assuntos
Genoma Viral/genética , Potyvirus/genética , Scorzonera/virologia , Sequência de Aminoácidos , Sequência de Bases , Fases de Leitura Aberta/genética , Filogenia , Poliproteínas/genética , Potyvirus/classificação , Potyvirus/isolamento & purificação , RNA Viral/genética , República da Coreia , Proteínas Virais/genética
12.
Arch Virol ; 166(10): 2789-2801, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34370094

RESUMO

Data mining and metagenomic analysis of 277 open reading frame sequences of bipartite RNA viruses of the genus Nepovirus, family Secoviridae, were performed, documenting how challenging it can be to unequivocally assign a virus to a particular species, especially those in subgroups A and C, based on some of the currently adopted taxonomic demarcation criteria. This work suggests a possible need for their amendment to accommodate pangenome information. In addition, we revealed a host-dependent structure of arabis mosaic virus (ArMV) populations at a cladistic level and confirmed a phylogeographic structure of grapevine fanleaf virus (GFLV) populations. We also identified new putative recombination events in members of subgroups A, B and C. The evolutionary specificity of some capsid regions of ArMV and GFLV that were described previously and biologically validated as determinants of nematode transmission was circumscribed in silico. Furthermore, a C-terminal segment of the RNA-dependent RNA polymerase of members of subgroup A was predicted to be a putative host range determinant based on statistically supported higher π (substitutions per site) values for GFLV and ArMV isolates infecting Vitis spp. compared with non-Vitis-infecting ArMV isolates. This study illustrates how sequence information obtained via high-throughput sequencing can increase our understanding of mechanisms that modulate virus diversity and evolution and create new opportunities for advancing studies on the biology of economically important plant viruses.


Assuntos
Genoma Viral/genética , Especificidade de Hospedeiro/genética , Nepovirus/genética , Evolução Molecular , Variação Genética , Metagenômica , Nepovirus/classificação , Fases de Leitura Aberta/genética , Filogenia , Filogeografia , Plantas/classificação , Plantas/virologia , RNA Viral/genética , Recombinação Genética
13.
Arch Virol ; 166(10): 2853-2857, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34373969

RESUMO

Strains of the HIV-1 circulating recombinant forms (CRFs) 06_cpx and 56_cpx were identified for the first time in Guangzhou, China. The nearly full-length genome (NFLG) sequence was amplified, and the PCR products were sequenced by the Sanger method. The CRF06_cpx and CRF56_cpx strains were identified using the Basic Local Alignment Search Tool (BLAST) and confirmed by neighbour-joining (NJ) phylogenetic analysis. Additionally, these strains were found to contain transmitted drug resistance mutations that have little effect on first-line efavirenz (EFV)-based treatment. Genetic analysis of the detailed sequence data will provide more information on the HIV-1 epidemic in China.


Assuntos
Infecções por HIV/virologia , HIV-1/genética , Adulto , China/epidemiologia , Cidades/epidemiologia , Farmacorresistência Viral/genética , Feminino , Genoma Viral/genética , Genótipo , Infecções por HIV/epidemiologia , HIV-1/classificação , HIV-1/isolamento & purificação , Humanos , Masculino , Mutação , Filogenia , Recombinação Genética , Produtos do Gene pol do Vírus da Imunodeficiência Humana/genética
14.
Arch Virol ; 166(10): 2905-2909, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34383166

RESUMO

Golden trumpet (Allamanda cathartica) plants were observed to exhibit mottling and distortion symptoms on leaves. The genome of an associated begomovirus (Al-K1) was amplified by rolling-circle amplification, cloned, and sequenced. The viral genome consisted of two circular ssDNA molecules, and the organization of the ORFs was similar to those of DNA-A and DNA-B components of bipartite begomoviruses. The size of DNA-A (KC202818) and DNA-B (MG969497) of the begomovirus was 2772 and 2690 nucleotides, respectively. Sequence analysis revealed that the DNA-A and DNA-B components shared the highest sequence identity with duranta leaf curl virus (MN537564, 87.8%) and cotton leaf curl Alabad virus (MH760452, 81.0%), respectively. Interestingly, the Al-K1 isolate shared significantly less nucleotide sequence identity with allamanda leaf curl virus (EF602306, 71.6%), the only monopartite begomovirus reported previously in golden trumpet from China. Al-K1 shared less than 91% sequence identity with other begomoviruses, and hence, according to the latest ICTV guidelines for species demarcation of begomoviruses, Al-K1 is proposed to be a member of a new species, and we propose the name "allamanda leaf mottle distortion virus" (AllLMoDV-[IN-Al_K1-12]) for this virus. AllLMoDV was detected in various golden trumpet samples from different locations by PCR with specific primers based on the genome sequence determined in this study. Our study provides evidence of the occurrence of a new bipartite begomovirus in a perennial ornamental plant in India.


Assuntos
Apocynaceae/virologia , Begomovirus/genética , Doenças das Plantas/virologia , Sequência de Bases , Begomovirus/classificação , DNA Viral/genética , Genoma Viral/genética , Índia , Fases de Leitura Aberta/genética , Filogenia , Folhas de Planta/virologia , Análise de Sequência de DNA , Especificidade da Espécie
15.
Arch Virol ; 166(10): 2943-2953, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34383165

RESUMO

Anelloviruses are small negative-sense single-stranded DNA viruses with genomes ranging in size from 1.6 to 3.9 kb. The family Anelloviridae comprised 14 genera before the present changes. However, in the last five years, a large number of diverse anelloviruses have been identified in various organisms. Here, we undertake a global analysis of mammalian anelloviruses whose full genome sequences have been determined and have an intact open reading frame 1 (ORF1). We established new criteria for the classification of anelloviruses, and, based on our analyses, we establish new genera and species to accommodate the unclassified anelloviruses. We also note that based on the updated species demarcation criteria, some previously assigned species (n = 10) merge with other species. Given the rate at which virus sequence data are accumulating, and with the identification of diverse anelloviruses, we acknowledge that the taxonomy will have to be dynamic and continuously evolve to accommodate new members.


Assuntos
Anelloviridae/classificação , Mamíferos/virologia , Anelloviridae/genética , Animais , Sequência de Bases , DNA Viral/genética , Bases de Dados Genéticas , Genoma Viral/genética , Fases de Leitura Aberta/genética , Filogenia , Terminologia como Assunto
16.
PLoS One ; 16(8): e0255691, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34351998

RESUMO

Accurate and timely diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is clinically essential, and is required also to monitor confirmed cases aiming to prevent further spread. Positive real-time PCR results at late time points following initial diagnosis may be clinically misleading as this methodology cannot account for the infection capabilities and the existence of whole genome sequences. In this study, 47 serial respiratory samples were tested by Allplex-nCoV test (Seegene), a triplex of three assays targeting the SARS-CoV-2 RdRP, E and N genes and subsequently assessed by next generation sequencing (NGS). COVID19 patients were tested at an early stage of the disease, when all these viral gene targets were positive, and at an advanced stage, when only the N gene target was positive in the Allplex-nCoV test. The corresponding NGS results showed the presence of complete viral genome copies at both early and advanced stages of the disease, although the total number of mapped sequences was lower in samples from advanced disease stages. We conclude that reduced viral transmission at this late disease stage may result from the low quantities of complete viral sequences and not solely from transcription favoring the N gene.


Assuntos
COVID-19/genética , SARS-CoV-2/genética , Sequenciamento Completo do Genoma/métodos , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , COVID-19/diagnóstico , Feminino , Genoma Viral/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Masculino , Pessoa de Meia-Idade , RNA Viral/genética , Reação em Cadeia da Polimerase em Tempo Real/métodos , SARS-CoV-2/patogenicidade
17.
Front Public Health ; 9: 685315, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34395364

RESUMO

Background: The ongoing coronavirus disease 2019 (COVID-19) pandemic has posed an unprecedented challenge to public health in Southeast Asia, a tropical region with limited resources. This study aimed to investigate the evolutionary dynamics and spatiotemporal patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the region. Materials and Methods: A total of 1491 complete SARS-CoV-2 genome sequences from 10 Southeast Asian countries were downloaded from the Global Initiative on Sharing Avian Influenza Data (GISAID) database on November 17, 2020. The evolutionary relationships were assessed using maximum likelihood (ML) and time-scaled Bayesian phylogenetic analyses, and the phylogenetic clustering was tested using principal component analysis (PCA). The spatial patterns of SARS-CoV-2 spread within Southeast Asia were inferred using the Bayesian stochastic search variable selection (BSSVS) model. The effective population size (Ne) trajectory was inferred using the Bayesian Skygrid model. Results: Four major clades (including one potentially endemic) were identified based on the maximum clade credibility (MCC) tree. Similar clustering was yielded by PCA; the first three PCs explained 46.9% of the total genomic variations among the samples. The time to the most recent common ancestor (tMRCA) and the evolutionary rate of SARS-CoV-2 circulating in Southeast Asia were estimated to be November 28, 2019 (September 7, 2019 to January 4, 2020) and 1.446 × 10-3 (1.292 × 10-3 to 1.613 × 10-3) substitutions per site per year, respectively. Singapore and Thailand were the two most probable root positions, with posterior probabilities of 0.549 and 0.413, respectively. There were high-support transmission links (Bayes factors exceeding 1,000) in Singapore, Malaysia, and Indonesia; Malaysia involved the highest number (7) of inferred transmission links within the region. A twice-accelerated viral population expansion, followed by a temporary setback, was inferred during the early stages of the pandemic in Southeast Asia. Conclusions: With available genomic data, we illustrate the phylogeography and phylodynamics of SARS-CoV-2 circulating in Southeast Asia. Continuous genomic surveillance and enhanced strategic collaboration should be listed as priorities to curb the pandemic, especially for regional communities dominated by developing countries.


Assuntos
COVID-19 , SARS-CoV-2 , Ásia Sudeste/epidemiologia , Teorema de Bayes , Genoma Viral/genética , Humanos , Filogenia
18.
Arch Virol ; 166(10): 2869-2873, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34292373

RESUMO

Eriophyid mites are commonly found on the leaf surface of different plant species. In the present study, a novel virus associated with an eriophyid mite species was detected using high-throughput sequencing (HTS) of total RNA from fruit tree leaves, primarily growing under greenhouse conditions. The complete genome sequence was characterized using rapid amplification of cDNA ends followed by Sanger sequencing, revealing a genome of 8885 nucleotides in length. The single positive-stranded RNA genome was predicted to encode typical conserved domains of members of the genus Iflavirus in the family Iflaviridae. Phylogenetic analysis showed this virus to be closely related to the unclassified iflavirus tomato matilda associated virus (TMaV), with a maximum amino acid sequence identity of 59% in the RNA-dependent RNA polymerase domain. This low identity value justifies the recognition of the novel virus as a potential novel iflavirus. In addition to a lack of graft-transmissibility evidence, RT-PCR and HTS detection of this virus in the putative host plants were not consistent through different years and growing seasons, raising the possibility that rather than a plant virus, this was a virus infecting an organism associated with fruit tree leaves. Identification of Tetra pinnatifidae HTS-derived contigs in all fruit tree samples carrying the novel virus suggested this mite as the most likely host of the new virus (p-value < 1e-11), which is tentatively named "eriophyid mite-associated virus" (EMaV). This study highlights the importance of a careful biological study before assigning a new virus to a particular plant host when using metagenomics data.


Assuntos
Frutas/parasitologia , Ácaros/virologia , Vírus de RNA de Cadeia Positiva/classificação , Árvores/parasitologia , Sequência de Aminoácidos , Animais , Frutas/virologia , Genoma Viral/genética , Metagenômica , Filogenia , Extratos Vegetais , Folhas de Planta/parasitologia , Folhas de Planta/virologia , Vírus de RNA de Cadeia Positiva/genética , RNA Viral/genética , RNA Polimerase Dependente de RNA , Árvores/virologia
19.
Arch Virol ; 166(10): 2865-2868, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34292374

RESUMO

A putative new virus with sequence similarity to members of the genus Cavemovirus in the family Caulimoviridae was identified in wild chicory (Cichorium intybus) by next-generation sequencing (NGS). The putative new virus was tentatively named "chicory mosaic cavemovirus" (ChiMV), and its genome was determined to be 7,775 nucleotides (nt) long with the typical genome organization of cavemoviruses. ORF1 encodes a putative coat protein/movement polyprotein (1,278 aa), ORF2 encodes a putative replicase (650 aa), and ORF3 encodes a putative transactivator factor (384 aa). The first two putative proteins have 46.2% and 68.7% amino acid sequence identity to the CP/MP protein (YP_004347414) and replicase (YP_004347415), respectively, of sweet potato collusive virus (SPCV). ORF3 encodes a protein with 38.5% amino acid sequence identity to the putative transactivator factor (NP_056849) of cassava vein mosaic virus (CsVMV). The new putative viral genome and those of three cavemoviruses (epiphyllum virus 4 [EpV-4], SPCV, and CsVMV) differ by 24-27% in the nt sequence of the replicase gene, which exceeds the species demarcation cutoff (>20%) for the family.


Assuntos
Caulimoviridae/genética , Chicória/virologia , Sequência de Aminoácidos , Caulimoviridae/classificação , Genoma Viral/genética , Fases de Leitura Aberta/genética , Filogenia , Doenças das Plantas/virologia , Folhas de Planta/virologia , RNA Viral/genética , Especificidade da Espécie , Proteínas Virais/genética
20.
Arch Virol ; 166(10): 2875-2879, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34297223

RESUMO

Wheat plants showing yellowing and mosaic in leaves and stunting were collected from wheat fields in Henan Province, China. Analysis of these plants by transmission electron microscopy showed that they contained two types of filamentous virus-like particles with a length of 200-500 nm and 1000-1300 nm, respectively. RNA-seq revealed a coinfection with wheat yellow mosaic virus (WYMV) and an unknown wheat-infecting virus. The genome of the unknown virus is 8,410 nucleotides long, excluding its 3' poly(A) tail. It has six open reading frames (ORFs). ORF1 encodes a putative viral replication-associated protein (Rep), and ORFs 2, 3, and 4 encode the triple gene block (TGB) proteins. ORFs 5 and 6 encode the capsid protein (CP) and a protein with unknown function, respectively. Phylogenetic analysis showed that this novel virus is evolutionarily related to members of the subfamily Quinvirinae, family Betaflexiviridae. It is, however, distinct from the viruses in the currently established genera. Based on the species and genus demarcation criteria set by the International Committee on Taxonomy of Viruses (ICTV), we tentatively name this novel virus "wheat yellow stunt-associated betaflexivirus" (WYSaBV), and we propose it to be a member of a new genus in the family Betaflexiviridae.


Assuntos
Flexiviridae/genética , Triticum/virologia , China , Flexiviridae/classificação , Flexiviridae/patogenicidade , Flexiviridae/ultraestrutura , Genoma Viral/genética , Fases de Leitura Aberta/genética , Filogenia , Doenças das Plantas/virologia , Folhas de Planta/virologia , RNA Viral/genética , Especificidade da Espécie , Proteínas Virais/genética , Vírion/ultraestrutura
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