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1.
Rev Soc Bras Med Trop ; 54: e08072020, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34495262

RESUMO

INTRODUCTION: Hepatitis B virus (HBV) infection is a public health problem; therefore, we aimed to report HBV genotypes in Ceará, Brazil. METHODS: A total of 103 HBsAg-positive samples were subjected to HBV genotyping and subgenotyping. RESULTS: The following genetic compositions of samples were found: F-54% (F2-83.33%), A-40% (A1-65%), D-6%, C2-1%, E-1%, and G-1%. CONCLUSIONS: Some genotypes are only prevalent in certain parts of the world; however, the State of Ceará is a hub for migration and has one of the most important liver transplantation centers in Brazil, which can explain the prevalence of the F genotype.


Assuntos
Gastroenterologia , Hepatite B , Brasil/epidemiologia , DNA Viral/genética , Genótipo , Hepatite B/epidemiologia , Antígenos de Superfície da Hepatite B , Vírus da Hepatite B/genética , Humanos , Prevalência
2.
Zhonghua Gan Zang Bing Za Zhi ; 29(8): 771-775, 2021 Aug 20.
Artigo em Chinês | MEDLINE | ID: mdl-34517459

RESUMO

Objective: To analyze the risk factors that may affect the mutations in the reverse transcriptase region in chronic hepatitis B virus-infected patients. Methods: 678 hospitalized cases with chronic HBV infection who underwent HBV RT testing at Tianjin Second People's Hospital from January 1, 2016 to December 31, 2016 were collected retrospectively. Among them, 417 cases were diagnosed with chronic hepatitis B, 219 cases with liver cirrhosis and 42 cases with primary liver cancer. There were 268 cases of non-use of any antiviral therapy, 138 cases of discontinuation of antiviral drugs for 6 months or more, and 272 cases of continuous antiviral therapy. HBV genotyping and RT region mutation sites were detected by direct sequencing. The risk factors that may affect the drug resistant mutation in the HBV RT mutation, including age, genotype, antiviral drug selection and medication time, hepatitis B virus infection, and biochemical markers were analyzed by univariate analysis to screen out independent risk factors. Results: Among 678 HBV-infected cases, 290 cases (42.8%) were detected with RT-region mutation. Among them, the pre-existing drug resistant rate was 6.72%, and the drug resistant mutation rate was 23.19% in treated patients. The drug resistant mutation rate of patients with continuous antiviral therapy was 66.18%. Gene mutations highest rate for 1 ~ 5 years was 27.14% in chronic HBV patients treated with antiviral therapy. Logistic regression analysis of the factors that had led to HBV mutation showed that old age, the selection of nucleoside drugs at the beginning of treatment and medication time were the main factors affecting HBV RT mutations. Conclusion: Abnormal ALT level, HBV genotype, HBV DNA quantitative level are the main factors influencing non-drug resistant mutations. Age over 60 years old, and long-term use of low-barrier nucleoside drugs are high-risk groups for HBV resistant. Therefore, HBV resistant monitoring should be strengthened.


Assuntos
Hepatite B Crônica , Preparações Farmacêuticas , Antivirais/farmacologia , Antivirais/uso terapêutico , DNA Viral/genética , Farmacorresistência Viral/genética , Genótipo , Vírus da Hepatite B/genética , Hepatite B Crônica/tratamento farmacológico , Humanos , Lamivudina/uso terapêutico , Pessoa de Meia-Idade , Mutação , DNA Polimerase Dirigida por RNA/genética , DNA Polimerase Dirigida por RNA/uso terapêutico , Estudos Retrospectivos , Fatores de Risco
3.
Nat Commun ; 12(1): 4710, 2021 08 05.
Artigo em Inglês | MEDLINE | ID: mdl-34354070

RESUMO

Cyanophage S-2L is known to profoundly alter the biophysical properties of its DNA by replacing all adenines (A) with 2-aminoadenines (Z), which still pair with thymines but with a triple hydrogen bond. It was recently demonstrated that a homologue of adenylosuccinate synthetase (PurZ) and a dATP triphosphohydrolase (DatZ) are two important pieces of the metabolism of 2-aminoadenine, participating in the synthesis of ZTGC-DNA. Here, we determine that S-2L PurZ can use either dATP or ATP as a source of energy, thereby also depleting the pool of nucleotides in dATP. Furthermore, we identify a conserved gene (mazZ) located between purZ and datZ genes in S-2L and related phage genomes. We show that it encodes a (d)GTP-specific diphosphohydrolase, thereby providing the substrate of PurZ in the 2-aminoadenine synthesis pathway. High-resolution crystal structures of S-2L PurZ and MazZ with their respective substrates provide a rationale for their specificities. The Z-cluster made of these three genes - datZ, mazZ and purZ - was expressed in E. coli, resulting in a successful incorporation of 2-aminoadenine in the bacterial chromosomal and plasmidic DNA. This work opens the possibility to study synthetic organisms containing ZTGC-DNA.


Assuntos
DNA Bacteriano/genética , Genes Virais , Siphoviridae/genética , 2-Aminopurina/análogos & derivados , 2-Aminopurina/metabolismo , Adenilossuccinato Sintase/química , Adenilossuccinato Sintase/genética , Adenilossuccinato Sintase/metabolismo , Bacteriófagos , Pareamento de Bases , Cristalografia por Raios X , DNA Bacteriano/metabolismo , DNA Viral/genética , DNA Viral/metabolismo , Desoxiadenosinas/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Genoma Viral , Redes e Vias Metabólicas , Modelos Moleculares , Monoéster Fosfórico Hidrolases/química , Monoéster Fosfórico Hidrolases/genética , Monoéster Fosfórico Hidrolases/metabolismo , Podoviridae/classificação , Podoviridae/genética , Conformação Proteica , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Siphoviridae/classificação , Eletricidade Estática , Proteínas Virais/química , Proteínas Virais/genética , Proteínas Virais/metabolismo
4.
Int J Mol Sci ; 22(15)2021 Jul 29.
Artigo em Inglês | MEDLINE | ID: mdl-34360884

RESUMO

Colorectal cancer (CRC) is the third most common cause of cancer-related deaths worldwide. Human papillomaviruses (HPVs) and Epstein-Barr virus (EBV) have been reported to be present in different types of human cancers, including CRCs, where they can play a key role in the onset and/or progression of these cancers. Thus, we herein explored the prevalence of high-risk HPVs and EBV in a cohort of 94 CRC tissue samples and 13 colorectal normal tissues from the Lebanese population using polymerase chain reaction, immunohistochemistry, and tissue microarray methodologies. We found that high-risk HPVs are present in 64%, while EBV is present in 29% of our CRC samples. Additionally, our data showed that high-risk HPV types (16, 18, 35, 58, 51, 45, 52, 31, and 33) are the most frequent in CRC in the Lebanese cohort, respectively. Our data point out that HPVs and EBV are copresent in 28% of the samples. Thus, this study clearly suggests that high-risk HPVs and EBV are present/copresent in CRCs, where they could play an important role in colorectal carcinogenesis. Nevertheless, further investigations using a larger cohort are needed to elucidate the possible cooperation between these oncoviruses in the development of CRC.


Assuntos
Alphapapillomavirus/genética , Neoplasias Colorretais/epidemiologia , Infecções por Vírus Epstein-Barr/epidemiologia , Herpesvirus Humano 4/genética , Infecções por Papillomavirus/epidemiologia , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Estudos de Casos e Controles , Criança , Pré-Escolar , Estudos de Coortes , Neoplasias Colorretais/virologia , DNA Viral/genética , Infecções por Vírus Epstein-Barr/virologia , Feminino , Humanos , Imuno-Histoquímica , Líbano/epidemiologia , Masculino , Pessoa de Meia-Idade , Infecções por Papillomavirus/virologia , Reação em Cadeia da Polimerase , Prevalência , Fatores de Risco , Adulto Jovem
5.
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
6.
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
7.
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
8.
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
9.
Viruses ; 13(7)2021 07 09.
Artigo em Inglês | MEDLINE | ID: mdl-34372533

RESUMO

Approximately 240 million people are chronically infected with hepatitis B virus (HBV), despite four decades of effective HBV vaccination. During chronic infection, HBV forms two distinct templates responsible for viral transcription: (1) episomal covalently closed circular (ccc)DNA and (2) host genome-integrated viral templates. Multiple ubiquitous and liver-specific transcription factors are recruited onto these templates and modulate viral gene transcription. This review details the latest developments in antivirals that inhibit HBV gene transcription or destabilize viral transcripts. Notably, nuclear receptor agonists exhibit potent inhibition of viral gene transcription from cccDNA. Small molecule inhibitors repress HBV X protein-mediated transcription from cccDNA, while small interfering RNAs and single-stranded oligonucleotides result in transcript degradation from both cccDNA and integrated templates. These antivirals mediate their effects by reducing viral transcripts abundance, some leading to a loss of surface antigen expression, and they can potentially be added to the arsenal of drugs with demonstrable anti-HBV activity. Thus, these candidates deserve special attention for future repurposing or further development as anti-HBV therapeutics.


Assuntos
Vírus da Hepatite B/genética , Hepatite B/prevenção & controle , Transcrição Genética/genética , Antivirais/farmacologia , DNA Circular/metabolismo , DNA Viral/genética , Hepatite B/tratamento farmacológico , Hepatite B/genética , Vírus da Hepatite B/patogenicidade , Humanos , Fígado/virologia , RNA Interferente Pequeno/metabolismo , Transcrição Genética/fisiologia , Integração Viral/efeitos dos fármacos , Replicação Viral/efeitos dos fármacos
10.
Viruses ; 13(7)2021 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-34372548

RESUMO

Infections with multiple human papilloma virus (HPV) types have been reported, but their role in cervical carcinogenesis has not been fully elucidated. In this study, 236 cases with multiple HPV infection were examined and compared to 180 cases with single HPV infection. HPV genotyping was performed with cervico-vaginal swab specimens using multiplex (real-time) polymerase chain reaction (PCR). In multiple HPV infection, the most prevalent HPV genotype was HPV 53, followed by HPV 16, 58, 52, and 68. HPV 33, 35, 39, 51, 52, 53, 58, and 68 were high-risk-HPV (HR-HPV) genotypes that were more frequently detected in multiple HPV infection compared to that in single HPV infection. The association between multiple HPV infection and high-grade SIL (HSIL) was significantly stronger compared to that of single HPV infection and HSIL (p = 0.002). Patients with multiple HPV infection displayed persistent and longer duration of the HPV infection compared to patients with single HPV infection. Multiple HPV infections have distinct clinicopathologic characteristics. Since it is associated with persistent HPV infection, HSIL, and different HR-HPV strains in contrast to single HPV infection, the presence of multiple HPV infection should be reported; close follow up is warranted.


Assuntos
Papillomaviridae/patogenicidade , Infecções por Papillomavirus/epidemiologia , Neoplasias do Colo do Útero/epidemiologia , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Alphapapillomavirus/genética , Alphapapillomavirus/patogenicidade , Neoplasia Intraepitelial Cervical/virologia , Colo do Útero/virologia , Coinfecção/epidemiologia , Coinfecção/virologia , DNA Viral/genética , Feminino , Genótipo , Humanos , Pessoa de Meia-Idade , Papillomaviridae/genética , Infecções por Papillomavirus/virologia , República da Coreia/epidemiologia , Neoplasias do Colo do Útero/virologia
11.
Viruses ; 13(7)2021 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-34372550

RESUMO

Persistent hepatitis B virus (HBV) infection remains a serious medical problem worldwide, with an estimated global burden of 257 million carriers. Prophylactic and therapeutic interventions, in the form of a vaccine, immunomodulators, and nucleotide and nucleoside analogs, are available. Vaccination, however, offers no therapeutic benefit to chronic sufferers and has had a limited impact on infection rates. Although immunomodulators and nucleotide and nucleoside analogs have been licensed for treatment of chronic HBV, cure rates remain low. Transcription activator-like effector nucleases (TALENs) designed to bind and cleave viral DNA offer a novel therapeutic approach. Importantly, TALENs can target covalently closed circular DNA (cccDNA) directly with the potential of permanently disabling this important viral replicative intermediate. Potential off-target cleavage by engineered nucleases leading to toxicity presents a limitation of this technology. To address this, in the context of HBV gene therapy, existing TALENs targeting the viral core and surface open reading frames were modified with second- and third-generation FokI nuclease domains. As obligate heterodimers these TALENs prevent target cleavage as a result of FokI homodimerization. Second-generation obligate heterodimeric TALENs were as effective at silencing viral gene expression as first-generation counterparts and demonstrated an improved specificity in a mouse model of HBV replication.


Assuntos
Vírus da Hepatite B/genética , Hepatite B/tratamento farmacológico , Nucleases dos Efetores Semelhantes a Ativadores de Transcrição/genética , Animais , Animais não Endogâmicos , Antivirais/uso terapêutico , Linhagem Celular , Vírus de DNA/genética , DNA Circular , DNA Viral/genética , Desoxirribonucleases de Sítio Específico do Tipo II/genética , Desoxirribonucleases de Sítio Específico do Tipo II/metabolismo , Modelos Animais de Doenças , Endonucleases/genética , Feminino , Terapia Genética/métodos , Células HEK293 , Células Hep G2 , Hepatite B/genética , Hepatite B/imunologia , Hepatite B Crônica/genética , Hepatite B Crônica/virologia , Humanos , Camundongos , Nucleases dos Efetores Semelhantes a Ativadores de Transcrição/uso terapêutico , Replicação Viral/genética
12.
Cell Rep ; 36(7): 109530, 2021 08 17.
Artigo em Inglês | MEDLINE | ID: mdl-34380018

RESUMO

A recent study proposed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hijacks the LINE-1 (L1) retrotransposition machinery to integrate into the DNA of infected cells. If confirmed, this finding could have significant clinical implications. Here, we apply deep (>50×) long-read Oxford Nanopore Technologies (ONT) sequencing to HEK293T cells infected with SARS-CoV-2 and do not find the virus integrated into the genome. By examining ONT data from separate HEK293T cultivars, we completely resolve 78 L1 insertions arising in vitro in the absence of L1 overexpression systems. ONT sequencing applied to hepatitis B virus (HBV)-positive liver cancer tissues located a single HBV insertion. These experiments demonstrate reliable resolution of retrotransposon and exogenous virus insertions by ONT sequencing. That we find no evidence of SARS-CoV-2 integration suggests that such events are, at most, extremely rare in vivo and therefore are unlikely to drive oncogenesis or explain post-recovery detection of the virus.


Assuntos
COVID-19/virologia , DNA Viral/genética , Genoma Humano , SARS-CoV-2/genética , Análise de Sequência de DNA , Integração Viral , Idoso , Animais , COVID-19/diagnóstico , Carcinoma Hepatocelular/virologia , Chlorocebus aethiops , Células HEK293 , Vírus da Hepatite B/genética , Interações Hospedeiro-Patógeno , Humanos , Neoplasias Hepáticas/virologia , Elementos Nucleotídeos Longos e Dispersos , Masculino , Sequenciamento por Nanoporos , Células Vero
13.
Viruses ; 13(7)2021 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-34372577

RESUMO

A novel Enterobacter cloacae phage, EC151, was isolated and characterized. Electron microscopy revealed that EC151 has a siphovirus-like virion morphology. The EC151 nucleotide sequence shows limited similarity to other phage genomes deposited in the NCBI GenBank database. The size of the EC151 genome is 60,753 bp and contains 58 putative genes. Thirty-nine of them encode proteins of predicted function, 18 are defined as hypothetical proteins, and one ORF identifies as the tRNA-Ser-GCT-encoding gene. Six ORFs were predicted to be members of the deazaguanine DNA modification pathway, including the preQ0 transporter. Comparative proteomic phylogenetic analysis revealed that phage EC151 represents a distinct branch within a group of sequences containing clades formed by members of the Seuratvirus, Nonagvirus, and Vidquintavirus genera. In addition, the EC151 genome showed gene synteny typical of the Seuratvirus, Nonagvirus, and Nipunavirus phages. The average genetic distances of EC151/Seuratvirus, EC151/Nonagvirus, and EC151/Vidquintavirus are approximately equal to those between the Seuratvirus, Nonagvirus, and Vidquintavirus genera (~0.7 substitutions per site). Therefore, EC151 may represent a novel genus within the Siphoviridae family. The origin of the deazaguanine DNA modification pathway in the EC151 genome can be traced to Escherichia phages from the Seuratvirus genus.


Assuntos
Bacteriófagos/genética , Enterobacter cloacae/genética , Enterobacter cloacae/virologia , DNA Viral/genética , Enterobacter cloacae/metabolismo , Genoma Viral/genética , Genômica , Especificidade de Hospedeiro , Filogenia , Proteômica , Siphoviridae/genética , Proteínas Virais/genética , Vírion/metabolismo
14.
Viruses ; 13(7)2021 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-34372586

RESUMO

Hepatitis B (HBV) and delta (HDV) viruses are endemic in the Amazon region, but vaccine coverage against HBV is still limited. People who use illicit drugs (PWUDs) represent a high-risk group due to common risk behavior and socioeconomic factors that facilitate the acquisition and transmission of pathogens. The present study assessed the presence of HBV and HBV-HDV co-infection, identified viral sub-genotypes, and verified the occurrence of mutations in coding regions for HBsAg and part of the polymerase in HBV-infected PWUDs in municipalities of the Brazilian states of Amapá and Pará, in the Amazon region. In total, 1074 PWUDs provided blood samples and personal data in 30 municipalities of the Brazilian Amazon. HBV and HDV were detected by enzyme-linked immunosorbent assay and polymerase chain reaction. Viral genotypes were identified by nucleotide sequencing followed by phylogenetic analysis, whereas viral mutations were analyzed by specialized software. High rates of serological (32.2%) and molecular (7.2%) markers for HBV were detected, including cases of occult HBV infection (2.5%). Sub-genotypes A1, A2, D4, and F2a were most frequently found. Escape mutations due to vaccine and antiviral resistance were identified. Among PWUDs with HBV DNA, serological (19.5%) and molecular (11.7%) HDV markers were detected, such as HDV genotypes 1 and 3. These are worrying findings, presenting clear implications for urgent prevention and treatment needs for the carriers of these viruses.


Assuntos
Hepatite B/genética , Hepatite D/genética , Transtornos Relacionados ao Uso de Substâncias/virologia , Adulto , Brasil/epidemiologia , Coinfecção , Estudos Transversais , DNA Viral/genética , Usuários de Drogas , Ensaio de Imunoadsorção Enzimática/métodos , Feminino , Genótipo , Hepatite B/diagnóstico , Antígenos de Superfície da Hepatite B/análise , Antígenos de Superfície da Hepatite B/sangue , Vírus da Hepatite B/genética , Vírus da Hepatite B/patogenicidade , Hepatite D/diagnóstico , Vírus Delta da Hepatite/genética , Vírus Delta da Hepatite/patogenicidade , Humanos , Drogas Ilícitas , Masculino , Pessoa de Meia-Idade , Epidemiologia Molecular/métodos , Filogenia , RNA Viral/genética , Análise de Sequência de DNA/métodos
15.
Arch Virol ; 166(9): 2505-2520, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34236511

RESUMO

In this study, a novel Escherichia coli-specific bacteriophage, vB_EcoM_IME392, was isolated from chicken farm sewage in Qingdao, China. The genome of IME392 was found by next-generation sequencing to be 116,460 base pairs in length with a G+C content of 45.4% (GenBank accession number MH719082). BLASTn results revealed that only 2% of the genome sequence of IME392 shows sequence similarity to known phage sequences in the GenBank database, which indicates that IME392 is a novel bacteriophage. Transmission electron microscopy showed that IME392 belongs to the family Myoviridae. The host range, the multiplicity of infection, and a one-step growth curve were also determined.


Assuntos
Colífagos/genética , Escherichia coli/virologia , Myoviridae/genética , Sequenciamento Completo do Genoma , Composição de Bases , Sequência de Bases , China , Mapeamento Cromossômico , Colífagos/classificação , DNA Viral/genética , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala , Especificidade de Hospedeiro , Concentração de Íons de Hidrogênio , Myoviridae/classificação , Filogenia , Proteômica , Esgotos/virologia , Temperatura
16.
Arch Virol ; 166(9): 2623-2625, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34244860

RESUMO

Here, using viral metagenomics combined with conventional PCR, the complete genome sequence of a novel anellovirus (named anel-ch-zj and GenBank no. MT157223) from nasopharynx secretion specimens from hospitalized neonates was determined, and the deduced amino acid sequence of its ODF1 protein was found to be only 33.19%-39.33% identical to those of related anelloviruses with sequences available in the GenBank database, suggesting that it represents a putative new genus within the family Anelloviridae. PCR screening of 135 samples (including 45 nasopharynx secretion, 45 blood, and 45 fecal specimens collected from 45 individual hospitalized neonates) indicated that two nasopharynx secretion, two blood, and four fecal samples were positive for anel-ch-zj. Further PCR screening of 50 blood samples, 115 fecal samples, and 396 nasopharynx secretions collected from hospitalized children 1-5 years old did not yield any positive results. Whether this novel anellovirus detected in neonates is associated with specific diseases needs future investigation.


Assuntos
Anelloviridae/classificação , Anelloviridae/isolamento & purificação , Criança Hospitalizada , Filogenia , Anelloviridae/genética , DNA Viral/genética , Fezes/virologia , Humanos , Recém-Nascido , Metagenômica , Nasofaringe/virologia , Reação em Cadeia da Polimerase , Sequenciamento Completo do Genoma
17.
Cell Physiol Biochem ; 55(S2): 71-88, 2021 Jul 10.
Artigo em Inglês | MEDLINE | ID: mdl-34242500

RESUMO

Psychological stress is an important factor involved in disease manifestations of human papillomavirus (HPV) infection, and it can participate in HPV-associated carcinogenesis. The impact or effect which stress can have (exert) depends on a person's genetic pool, experiences and behaviors. Due to inconsistencies in some study results, this issue remains a subject of research. Concerning the course of HPV manifestations, it has been observed that a higher number of life stressors in at least the previous 6 months, the absence of social support and the types of personal coping mechanisms employed, all influence HPV progression. In women with cervical dysplasia, a connection between greater stress experiences and dysregulation of specific immune responses has been observed. Once HPV enters a cell via the α6 integrin there are three possible sequences: latent infection, subclinical infection, and clinically manifest disease. HPV proliferation in differentiated epithelial cells induces morphologically cytopathic changes (koilocytosis, epidermal thickening, hyperplasia, hyperkeratosis). Oncogenic transformation requires the integration of the virus genome into the host genome. In doing so, DNA in the E1 region of E2 breaks down, leading to transcription disorders of E6 and E7. For the formation of irreversible malignancy, the following sequence is necessary: initial expression of E6 and E7 genes followed by suppression of apoptosis and the stabile expression of E6 and E7 proteins that protect transformed cells from apoptosis. A successful immune response is characterized by a strong, local cell-mediated immune response. Several factors are important for the regression of HPV manifestation/infection, among which is psychological stress which can prolong the duration and severity of HPV disease. Stress hormones may reactivate latent tumor viruses, stimulate viral oncogene expression, and inhibit antiviral host responses. In the regression of HPV infection, increased activity of Th1 cells was observed. However, during psychosocial stress, a decrease in the Th1 type of immune response is seen, and there is a shift towards a Th2 response. Understanding perceived stress and biological changes in stress, as well as the evaluation of immune parameters, gives researchers a better picture of how stress influences HPV infections and how to improve disease management and outcomes.


Assuntos
Papillomaviridae/fisiologia , Infecções por Papillomavirus/psicologia , Estresse Psicológico , Carcinogênese , DNA Viral/genética , DNA Viral/metabolismo , Células Epiteliais/citologia , Células Epiteliais/virologia , Humanos , Sistema Nervoso/metabolismo , Sistema Nervoso/virologia , Papillomaviridae/genética , Infecções por Papillomavirus/imunologia , Infecções por Papillomavirus/patologia , Sistema Hipófise-Suprarrenal/metabolismo , Sistema Hipófise-Suprarrenal/virologia
18.
Arch Virol ; 166(10): 2835-2839, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34319454

RESUMO

The bovine adenovirus 7 (BAdV-7) isolate SD18-74 was recovered from lung tissue of calves in South Dakota. The 30,043-nucleotide (nt) genome has the typical organization of Atadenovirus genus members. The sequence shares over 99% nt sequence identity with two Japanese BAdV-7 sequences, followed by 74.9% nt sequence identity with the ovine adenovirus 7 strain OAV287, a member of the species Ovine atadenovirus D. SD18-74 was amplified in both bovine and ovine primary nasal turbinate cells, demonstrating greater fitness in bovine cells. The genomic and biological characteristics of BAdV-7 SD18-74 support the inclusion of the members of the BAdV-7 group in a new species in the genus Atadenovirus.


Assuntos
Infecções por Adenoviridae/veterinária , Atadenovirus/classificação , Atadenovirus/genética , Bovinos/virologia , Infecções por Adenoviridae/virologia , Animais , Atadenovirus/isolamento & purificação , Atadenovirus/fisiologia , Doenças dos Bovinos/virologia , Linhagem Celular , DNA Viral/genética , Genoma Viral/genética , Ovinos , Estados Unidos , Replicação Viral
19.
Biophys J ; 120(16): 3292-3302, 2021 08 17.
Artigo em Inglês | MEDLINE | ID: mdl-34265262

RESUMO

Bacteriophages densely pack their long double-stranded DNA genome inside a protein capsid. The conformation of the viral genome inside the capsid is consistent with a hexagonal liquid crystalline structure. Experiments have confirmed that the details of the hexagonal packing depend on the electrochemistry of the capsid and its environment. In this work, we propose a biophysical model that quantifies the relationship between DNA configurations inside bacteriophage capsids and the types and concentrations of ions present in a biological system. We introduce an expression for the free energy that combines the electrostatic energy with contributions from bending of individual segments of DNA and Lennard-Jones-type interactions between these segments. The equilibrium points of this energy solve a partial differential equation that defines the distributions of DNA and the ions inside the capsid. We develop a computational approach that allows us to simulate much larger systems than what is possible using the existing molecular-level methods. In particular, we are able to estimate bending and repulsion between the DNA segments as well as the full electrochemistry of the solution, both inside and outside of the capsid. The numerical results show good agreement with existing experiments and with molecular dynamics simulations for small capsids.


Assuntos
Bacteriófagos , Capsídeo , Bacteriófagos/genética , DNA Viral/genética , Íons , Conformação de Ácido Nucleico
20.
Comput Math Methods Med ; 2021: 1835056, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34306171

RESUMO

In a general computational context for biomedical data analysis, DNA sequence classification is a crucial challenge. Several machine learning techniques have used to complete this task in recent years successfully. Identification and classification of viruses are essential to avoid an outbreak like COVID-19. Regardless, the feature selection process remains the most challenging aspect of the issue. The most commonly used representations worsen the case of high dimensionality, and sequences lack explicit features. It also helps in detecting the effect of viruses and drug design. In recent days, deep learning (DL) models can automatically extract the features from the input. In this work, we employed CNN, CNN-LSTM, and CNN-Bidirectional LSTM architectures using Label and K-mer encoding for DNA sequence classification. The models are evaluated on different classification metrics. From the experimental results, the CNN and CNN-Bidirectional LSTM with K-mer encoding offers high accuracy with 93.16% and 93.13%, respectively, on testing data.


Assuntos
COVID-19/virologia , Sequenciamento de Nucleotídeos em Larga Escala/estatística & dados numéricos , Redes Neurais de Computação , SARS-CoV-2/genética , Análise de Sequência de DNA/estatística & dados numéricos , Sequência de Bases , Biologia Computacional , DNA Viral/classificação , DNA Viral/genética , Bases de Dados de Ácidos Nucleicos/estatística & dados numéricos , Aprendizado Profundo , Humanos , Pandemias , SARS-CoV-2/classificação
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