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1.
Arch Virol ; 169(10): 193, 2024 Sep 06.
Artigo em Inglês | MEDLINE | ID: mdl-39242424

RESUMO

The family Rhabdoviridae includes viruses with a negative-sense RNA genome. This family is divided into four subfamilies, and until recently, the subfamily Betarhabdovirinae, encompassing all plant-associated rhabdoviruses, was further divided into six genera. Here, we report the creation of two new genera within the subfamily Betarhabdovirinae - Alphagymnorhavirus and Betagymnorhavirus - to include recently described gymnosperm-associated viruses. The genus Alphagymnorhavirus includes nine species, while the genus Betagymnorhavirus includes only one species. Phylogenetic analysis indicated that these viruses form two well-supported clades that are clustered with the varicosaviruses, which have bisegmented genomes. In contrast, the 10 viruses included in the newly created genera have the distinctive feature that they have an unsegmented genome encoding five or six proteins. The creation of the genera Alphagymnorhavirus and Betagymnorhavirus has been ratified by the International Committee on Taxonomy of Viruses (ICTV).


Assuntos
Genoma Viral , Filogenia , Doenças das Plantas , Rhabdoviridae , Rhabdoviridae/genética , Rhabdoviridae/classificação , Rhabdoviridae/isolamento & purificação , Genoma Viral/genética , Doenças das Plantas/virologia , Cycadopsida/virologia , RNA Viral/genética
2.
PLoS One ; 19(9): e0310027, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-39241052

RESUMO

HIV-1 CRF08_BC is a significant subtype in China, though its origin and spread remain incompletely understood. Previous studies using partial genomic data have provided insights but lack comprehensive analysis. Here, we investigate the early evolutionary and spatiotemporal dynamics of HIV-1 CRF08_BC in China and Myanmar using near-complete genome sequences. We analyzed 28 near-complete HIV-1 CRF08_BC genomes from China and Myanmar (1997-2013). Phylogenetic, molecular clock, and Bayesian discrete trait analyses were performed to infer the virus's origin, spread, and associated risk groups. Based on Bayesian time-scaled inference with the best-fitting combination of models determined by marginal likelihood estimation (MLE), we inferred the time to the most recent common ancestor (TMRCA) and evolutionary rate of HIV-1 CRF08_BC to be at 3 October 1991 (95% HPD: 22 February1989-27 November 1993) and 2.30 × 10-3 substitutions per site per year (95% HPD: 1.96 × 10-3-2.63 × 10-3), respectively. Our analysis suggests that HIV-1 CRF08_BC originated in Yunnan Province, China, among injecting drug users, and subsequently spread to other regions. This study provides valuable insights into the early dynamics of HIV-1 CRF08_BC through combined genomic and epidemiological data, which may inform effective prevention and mitigation efforts. However, the limited genomic data influenced the extent of our findings, and challenges in collecting accurate risk group information during surveillance were evident.


Assuntos
Teorema de Bayes , Evolução Molecular , Genoma Viral , Infecções por HIV , HIV-1 , Filogenia , HIV-1/genética , HIV-1/classificação , Humanos , Infecções por HIV/transmissão , Infecções por HIV/epidemiologia , Infecções por HIV/virologia , China/epidemiologia , Mianmar/epidemiologia , Masculino
3.
J Med Virol ; 96(9): e29902, 2024 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-39228345

RESUMO

The whole-genome sequence (WGS) analysis of Aichivirus (AiV) identified in Korea was performed in this study. Using Sanger and Nanopore sequencing, the 8228-nucleotide-long genomic sequence of AiV (OQ121963) was determined and confirmed to belong to genotype A. The full-length genome of OQ121963 consisted of a 7296 nt open reading frame (ORF) that encodes a single polyprotein, and 5' UTR (676 nt) and 3' UTR (256 nt) at 5' and 3' ends, respectively. The ORF consisted of leader protein (L), structural protein P1 (VP0, VP1, and VP3), and nonstructural protein P2 (2A, 2B, and 2C) and P3 (3A, 3B, 3C, and 3D). The secondary structure analysis of the 5' UTR identified only stem-loop C (SL-C) and not SL-A and SL-B. The variable region of the AiV genome was analyzed by MegAlign Pro and reconfirmed by SimPlot analysis using 16 AiV whole genomes known to date. Among the entire regions, structural protein region P1 showed the lowest amino acid identity (96.07%) with reference sequence AB040749 (originated in Japan; genotype A), while the highest amino acid identity (98.26%) was confirmed in the 3D region among nonstructural protein region P2 and P3. Moreover, phylogenetic analysis of the WGS of OQ121963 showed the highest homology (96.96%) with JX564249 (originated in Taiwan; genotype A) and lowest homology (90.14%) with DQ028632 (originated in Brazil; genotype B). Therefore, the complete genome characterization of OQ121963 and phylogenetic analysis of the AiV conducted in this study provide useful information allowing to improve diagnostic tools and epidemiological studies of AiVs.


Assuntos
Genoma Viral , Genótipo , Kobuvirus , Fases de Leitura Aberta , Filogenia , Sequenciamento Completo do Genoma , Genoma Viral/genética , República da Coreia , Humanos , Kobuvirus/genética , Kobuvirus/classificação , Kobuvirus/isolamento & purificação , Infecções por Picornaviridae/virologia , Infecções por Picornaviridae/epidemiologia , Regiões 5' não Traduzidas/genética , Adulto , RNA Viral/genética , Regiões 3' não Traduzidas/genética
4.
Virulence ; 15(1): 2397512, 2024 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-39282989

RESUMO

Porcine epidemic diarrhea virus (PEDV) causes diarrhea and vomiting in piglets, leading to a mortality rate of 100%. Due to the high frequency of mutation, it is important to monitor the evolution of PEDV and develop potential vaccine candidates. In this study, two PEDV strains (ZJ2022 and ZQ2022) were identified by PCR. These strains were subsequently isolated, and their genome sequences, growth characteristics, and pathogenicity were compared. Phylogenetic and recombination analyses revealed that both strains belonged to GIIa-subgroup, and ZQ2022 was identified as a recombinant strain derived from ZJ2022. Further sequence analysis showed that the ZJ2022 strain had a modified top region of the S1 protein due to a three amino acid insertion (T380_Y380insGGE) in the S1 gene. According to the virus growth curve, ZJ2022 exhibited better cellular adaptation than ZQ2022, with higher viral titers from 8 hpi to 24 hpi. Additionally, ZQ2022 exhibited a high level of pathogenicity, causing severe diarrhea in piglets at 36 hpi and a 100% mortality rate by 96 hpi. In contrast, ZJ2022 showed lower pathogenicity, inducing severe diarrhea in piglets at 60 hpi, with a mortality rate of 60% at 96 hpi and 100% at 120 hpi. In summary, our findings provided evidence of the undergoing mutations in Chinese PEDV strains. Furthermore, the S gene insertion strain ZJ2022 exhibited strong cellular adaptability and low pathogenicity, making it a potential candidate strain for vaccine development.


Assuntos
Animais Recém-Nascidos , Infecções por Coronavirus , Diarreia , Filogenia , Vírus da Diarreia Epidêmica Suína , Doenças dos Suínos , Animais , Vírus da Diarreia Epidêmica Suína/genética , Vírus da Diarreia Epidêmica Suína/patogenicidade , Vírus da Diarreia Epidêmica Suína/isolamento & purificação , Vírus da Diarreia Epidêmica Suína/classificação , Suínos , Doenças dos Suínos/virologia , Infecções por Coronavirus/veterinária , Infecções por Coronavirus/virologia , Virulência , Diarreia/virologia , Diarreia/veterinária , Glicoproteína da Espícula de Coronavírus/genética , Genoma Viral , Mutagênese Insercional , China , Células Vero
5.
Arch Virol ; 169(10): 199, 2024 Sep 16.
Artigo em Inglês | MEDLINE | ID: mdl-39283496

RESUMO

Mycoviruses with an unprecedented genome organization, featuring the RNA-directed RNA polymerase (RdRp) palm domain coding sequence being split into two distinct genome segments, have been found recently in a few fungi and oomycetes of different lineages and have been proposed to be named "splipalmiviruses". One of these, Oidiodendron maius splipalmivirus 1 (OmSPV1), has been detected in the ericoid mycorrhizal fungus Oidiodendron maius, and it has been proposed to be bisegmented. Here, we complete the genome sequence of this virus by describing a third RNA segment, which is 2000 nt long and whose terminal sequences are identical to those of the other two segments of OmSPV1. This segment contains a single open reading frame that codes for a protein with unknown function and has a low level of sequence identity (47%) to the putative protein encoded by the third segment of another splipalmivirus from Magnaporthe oryzae: Magnaporthe oryzae narnavirus virus 1 (MoNV1). Based on these features, we propose the RNA segment to be the third segment of the OmSPV1 genome.


Assuntos
Micovírus , Genoma Viral , Fases de Leitura Aberta , Filogenia , RNA Viral , Micovírus/genética , Micovírus/classificação , Micovírus/isolamento & purificação , RNA Viral/genética , Vírus de RNA/genética , Vírus de RNA/classificação , Vírus de RNA/isolamento & purificação , Proteínas Virais/genética , Sequência de Bases , Basidiomycota/virologia , Basidiomycota/genética
6.
Front Cell Infect Microbiol ; 14: 1421724, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-39268483

RESUMO

The increase of antibiotic-resistant bacteria has become a global health emergency and the need to explore alternative therapeutic options arises. Phage therapy uses bacteriophages to target specific bacterial strains. Phages are highly specific and can target resistant bacteria. Currently, research in this regard is focused on ensuring reliability and safety to bring this tool into clinical practice. The first step is to conduct comprehensive preclinical research. In this work, we present two novel bacteriophages vB_Kpn_F13 and vB_Kpn_F14 isolated against clinical carbapenem-resistant Klebsiella pneumoniae strains obtained from hospital sewage. Multiple studies in vitro were conducted, such as sequencing, electron microscopy, stability, host range infectivity, planktonic effect and biofilm inhibition in order to discover their ability to be used against carbapenem-resistant K. pneumoniae pathogens causing difficult-to-treat infections.


Assuntos
Bacteriófagos , Biofilmes , Enterobacteriáceas Resistentes a Carbapenêmicos , Carbapenêmicos , Infecções por Klebsiella , Klebsiella pneumoniae , Terapia por Fagos , Klebsiella pneumoniae/virologia , Klebsiella pneumoniae/efeitos dos fármacos , Bacteriófagos/isolamento & purificação , Bacteriófagos/fisiologia , Bacteriófagos/genética , Enterobacteriáceas Resistentes a Carbapenêmicos/isolamento & purificação , Enterobacteriáceas Resistentes a Carbapenêmicos/virologia , Infecções por Klebsiella/microbiologia , Infecções por Klebsiella/terapia , Carbapenêmicos/farmacologia , Biofilmes/crescimento & desenvolvimento , Biofilmes/efeitos dos fármacos , Humanos , Especificidade de Hospedeiro , Esgotos/virologia , Esgotos/microbiologia , Antibacterianos/farmacologia , Genoma Viral , Testes de Sensibilidade Microbiana
7.
J Med Virol ; 96(9): e29912, 2024 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-39279426

RESUMO

The reasons that lead some individuals living with the Human T Lymphotropic Virus 1 (HTLV-1) to develop HAM/TSP are still unclear. To better understand the viral genetic factors that may be associated with the development of HAM/TSP, this study aims to evaluate the impact of HTLV-1 genome mutations on the development of this disease through a systematic review. This review followed the PRISMA guidelines and was registered in the PROSPERO database. The search for articles was performed in PMC, PubMed, Lilacs, SciELO, and Embase databases using the following search descriptors: HTLV-1, HAM/TSP, mutation, polymorphism, genetic variation, and sequenc*. From the 1,929 articles found in the search, 20 were selected according to the pre-defined inclusion and exclusion criteria. A total of 619 HAM/TSP cases were compared with 555 AC controls. The mutations possibly related to the disease progression were detected in hbz (R119Q), tax (A7959V), ORF-I (R88K, P86S, S69G, P45L, L40F, C39R, CR9Y), and gp46 (V247I, N93D, S72G) genetic regions. The data collected and analyzed here indicate that mutations in the HTLV-1 genome could play an important role in the chronic inflammatory state and may be related to the development of HAM/TSP.


Assuntos
Genoma Viral , Infecções por HTLV-I , Vírus Linfotrópico T Tipo 1 Humano , Paraparesia Espástica Tropical , Vírus Linfotrópico T Tipo 1 Humano/genética , Humanos , Paraparesia Espástica Tropical/virologia , Paraparesia Espástica Tropical/genética , Genoma Viral/genética , Infecções por HTLV-I/virologia , Mutação , Variação Genética
8.
Virol J ; 21(1): 211, 2024 Sep 04.
Artigo em Inglês | MEDLINE | ID: mdl-39232804

RESUMO

Leafcutter ants are dominant herbivores in the Neotropics and rely on a fungus (Leucoagaricus gongylophorus) to transform freshly gathered leaves into a source of nourishment rather than consuming the vegetation directly. Here we report two virus-like particles that were isolated from L. gongylophorus and observed using transmission electron microscopy. RNA sequencing identified two +ssRNA mycovirus strains, Leucoagaricus gongylophorus tymo-like virus 1 (LgTlV1) and Leucoagaricus gongylophorus magoulivirus 1 (LgMV1). Genome annotation of LgTlV1 (7401 nt) showed conserved domains for methyltransferase, endopeptidase, viral RNA helicase, and RNA-dependent RNA polymerase (RdRp). The smaller genome of LgMV1 (2636 nt) contains one open reading frame encoding an RdRp. While we hypothesize these mycoviruses function as symbionts in leafcutter farming systems, further study will be needed to test whether they are mutualists, commensals, or parasites.


Assuntos
Formigas , Micovírus , Genoma Viral , RNA Viral , Micovírus/genética , Micovírus/classificação , Micovírus/isolamento & purificação , Micovírus/fisiologia , Animais , Formigas/microbiologia , Formigas/virologia , RNA Viral/genética , Filogenia , Fases de Leitura Aberta , Simbiose , RNA Polimerase Dependente de RNA/genética , Microscopia Eletrônica de Transmissão , Vírus de RNA/genética , Vírus de RNA/classificação , Vírus de RNA/isolamento & purificação , Vírus de RNA/fisiologia , Agaricales/virologia , Agaricales/genética
9.
F1000Res ; 13: 380, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-39233781

RESUMO

Bacteria of the genus Aeromonas, especially A. hydrophila and A. veronii are recognized as important fish pathogens that cause significant economic losses in aquaculture. Environmentally friendly bacteriophage-based solutions for the treatment of fish and for the reduction of colonization by pathogenic bacteria in production facilities are currently in high demand. The bacteriophage Gekk3-15 was isolated during a search for novel phage strains potentially suitable for Aeromonas biocontrol applications. Genome sequencing revealed that this virus is a relatively small myovirus with a 64847 bp long dsDNA genome, which is consistent with virion electron microscopy data. Bacteriophage Gekk3-15 is distinct in its nucleotide and encoded aa sequences from all other sequenced bacteriophage genomes, and may represent a new viral taxon at the genus or subfamily level.


Assuntos
Aeromonas , Bacteriófagos , Genoma Viral , Bacteriófagos/genética , Bacteriófagos/isolamento & purificação , Aeromonas/virologia , Aeromonas/genética , Sequenciamento Completo do Genoma/métodos
10.
PLoS Negl Trop Dis ; 18(9): e0012439, 2024 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-39235995

RESUMO

BACKGROUND: Hemorrhagic fever with renal syndrome (HFRS) is a severe public health problem in Jiangxi province, China. Previous studies reported genetic variants of Orthohantavirus hantanense (Hantaan virus, HTNV) in rodents in this area. However, the relationship between HTNV variants and human infection needs to be confirmed. This study aimed to identify the HTNV variants in patients and to understand the clinical characteristics of HFRS caused by these variants. METHODS: Samples were collected from hospitalized suspected cases of HFRS during the acute phase. HFRS cases were confirmed using quantitative real-time RT-PCR. Peripheral blood mononuclear cells (PBMC) from patients with HFRS were inoculated into Vero-E6 cells for viral isolation. The genomic sequences of HTNV from patients were obtained by amplicon-based next-generation sequencing. A retrospective analysis was conducted on the clinical characteristics of the patients. RESULTS: HTNV RNA was detected in 53 of 183 suspected HFRS patients. Thirteen HTNVs were isolated from 32 PBMCs of HFRS cases. Whole genome sequences of 14 HTNVs were obtained, including 13 isolates in cell culture from 13 patients, and one from plasma of the fatal case which was not isolated successfully in cell culture. Genetic analysis revealed that the HTNV sequence from the 14 patients showed significant variations in nucleotide and amino acid to the HTNV strains found in other areas. Fever (100%, 53/53), thrombocytopenia (100%, 53/53), increased serum aspartate aminotransferase (100%, 53/53), and increased lactate dehydrogenase (96.2%, 51/53) were the most common characteristics. Severe acute kidney injury was observed in 13.2% (7/53) of cases. Clinical symptoms, such as pain, petechiae, and gastrointestinal or respiratory symptoms were uncommon. CONCLUSION: The HTNV genetic variants cause human infections in Jiangxi. The clinical symptoms of HFRS caused by the HTNV genetic variant during the acute phase are atypical. In addition to renal dysfunction, attention should be paid to the common liver injuries caused by these genetic variants.


Assuntos
Variação Genética , Febre Hemorrágica com Síndrome Renal , Humanos , Febre Hemorrágica com Síndrome Renal/virologia , Febre Hemorrágica com Síndrome Renal/epidemiologia , China/epidemiologia , Masculino , Feminino , Adulto , Pessoa de Meia-Idade , Chlorocebus aethiops , Animais , Células Vero , Filogenia , RNA Viral/genética , Adulto Jovem , Estudos Retrospectivos , Leucócitos Mononucleares/virologia , Idoso , Genoma Viral , Orthohantavírus/genética , Orthohantavírus/isolamento & purificação , Orthohantavírus/classificação , Adolescente , Vírus Hantaan/genética , Vírus Hantaan/isolamento & purificação , Vírus Hantaan/classificação
11.
Virol J ; 21(1): 210, 2024 Sep 03.
Artigo em Inglês | MEDLINE | ID: mdl-39227954

RESUMO

BACKGROUND: SARS-CoV-2 is responsible for the ongoing global pandemic, and the continuous emergence of novel variants threatens fragile populations, such as immunocompromised patients. This subgroup of patients seems to be seriously affected by intrahost viral changes, as the pathogens, which are keen to cause replication inefficiency, affect the impaired immune system, preventing efficient clearance of the virus. Therefore, these patients may represent an optimal reservoir for the development of new circulating SARS-CoV-2 variants. The following study aimed to investigate genomic changes in SARS-CoV-2-positive immunocompromised patients over time. METHODS: SARS-CoV-2-positive nasopharyngeal swabs were collected at different time points for each patient (patient A and patient B), extracted and then analyzed through next-generation sequencing (NGS). The resulting sequences were examined to determine mutation frequencies, describing viral evolution over time. CASE PRESENTATION: Patient A was a 53-year-old patient with onco-hematological disease with prolonged infection lasting for 51 days from May 28th to July 18th, 2022. Three confirmed SARS-CoV-2-positive samples were collected on May 28th, June 15th and July 4th. Patient B was 75 years old and had onco-hematological disease with prolonged infection lasting for 146 days. Two confirmed positive SARS-CoV-2 samples were collected at the following time points: May 21st and August 18th. CONCLUSION: Heat map construction provided evidence of gain and/or loss of mutations over time for both patients, suggesting within-host genomic evolution of the virus. In addition, mutation polymorphisms and changes in the SARS-CoV-2 lineage were observed in Patient B. Sequence analysis revealed high mutational pattern variability, reflecting the high complexity of viral replication dynamics in fragile patients.


Assuntos
COVID-19 , Sequenciamento de Nucleotídeos em Larga Escala , Hospedeiro Imunocomprometido , SARS-CoV-2 , Humanos , COVID-19/virologia , SARS-CoV-2/genética , Pessoa de Meia-Idade , Genoma Viral/genética , Masculino , Mutação , Evolução Molecular , Nasofaringe/virologia
12.
Front Public Health ; 12: 1386596, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-39228849

RESUMO

Introduction: SARS-CoV-2 variants are defined by specific genome-wide mutations compared to the Wuhan genome. However, non-clade-defining mutations may also impact protein structure and function, potentially leading to reduced vaccine effectiveness. Our objective is to identify mutations across the entire viral genome rather than focus on individual mutations that may be associated with vaccine failure and to examine the physicochemical properties of the resulting amino acid changes. Materials and methods: Whole-genome consensus sequences of SARS-CoV-2 from COVID-19 patients were retrieved from the GISAID database. Analysis focused on Dataset_1 (7,154 genomes from Italy) and Dataset_2 (8,819 sequences from Spain). Bioinformatic tools identified amino acid changes resulting from codon mutations with frequencies of 10% or higher, and sequences were organized into sets based on identical amino acid combinations. Results: Non-defining mutations in SARS-CoV-2 genomes belonging to clades 21 L (Omicron), 22B/22E (Omicron), 22F/23A (Omicron) and 21J (Delta) were associated with vaccine failure. Four sets of sequences from Dataset_1 were significantly linked to low vaccine coverage: one from clade 21L with mutations L3201F (ORF1a), A27- (S) and G30- (N); two sets shared by clades 22B and 22E with changes A27- (S), I68- (S), R346T (S) and G30- (N); and one set shared by clades 22F and 23A containing changes A27- (S), F486P (S) and G30- (N). Booster doses showed a slight improvement in protection against Omicron clades. Regarding 21J (Delta) two sets of sequences from Dataset_2 exhibited the combination of non-clade mutations P2046L (ORF1a), P2287S (ORF1a), L829I (ORF1b), T95I (S), Y145H (S), R158- (S) and Q9L (N), that was associated with vaccine failure. Discussion: Vaccine coverage associations appear to be influenced by the mutations harbored by marketed vaccines. An analysis of the physicochemical properties of amino acid revealed that primarily hydrophobic and polar amino acid substitutions occurred. Our results suggest that non-defining mutations across the proteome of SARS-CoV-2 variants could affect the extent of protection of the COVID-19 vaccine. In addition, alteration of the physicochemical characteristics of viral amino acids could potentially disrupt protein structure or function or both.


Assuntos
Vacinas contra COVID-19 , COVID-19 , Mutação , Proteoma , SARS-CoV-2 , Humanos , SARS-CoV-2/genética , SARS-CoV-2/imunologia , COVID-19/prevenção & controle , Vacinas contra COVID-19/genética , Vacinas contra COVID-19/imunologia , Genoma Viral/genética , Eficácia de Vacinas , Espanha , Itália
13.
Nat Commun ; 15(1): 7702, 2024 Sep 04.
Artigo em Inglês | MEDLINE | ID: mdl-39231967

RESUMO

The human gut virome, which is mainly composed of bacteriophages, also includes viruses infecting archaea, yet their role remains poorly understood due to lack of isolates. Here, we characterize a temperate archaeal virus (MSTV1) infecting Methanobrevibacter smithii, the dominant methanogenic archaeon of the human gut. The MSTV1 genome is integrated in the host chromosome as a provirus which is sporadically induced, resulting in virion release. Using cryo-electron tomography, we capture several intracellular virion assembly intermediates and confirm that only a small fraction of the host population actively produces virions in vitro. Similar low frequency of induction is observed in a mouse colonization model, using mice harboring a stable consortium of 12 bacterial species (OMM12). Transcriptomic analysis suggests a regulatory lysogeny-lysis switch involving an interplay between viral proteins to maintain virus-host equilibrium, ensuring host survival and viral persistence. Thus, our study sheds light on archaeal virus-host interactions and highlights similarities with bacteriophages in establishing stable coexistence with their hosts in the gut.


Assuntos
Vírus de Archaea , Microbioma Gastrointestinal , Methanobrevibacter , Animais , Humanos , Methanobrevibacter/genética , Methanobrevibacter/metabolismo , Camundongos , Vírus de Archaea/genética , Vírus de Archaea/fisiologia , Vírus de Archaea/ultraestrutura , Genoma Viral/genética , Vírion/ultraestrutura , Lisogenia , Feminino
14.
PLoS Genet ; 20(9): e1011384, 2024 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-39231196

RESUMO

Lytic bacteriophages hold substantial promise in medical and biotechnological applications. Therefore a comprehensive understanding of phage infection mechanisms is crucial. CRISPR-Cas systems offer a way to explore these mechanisms via site-specific phage mutagenesis. However, phages can resist Cas-mediated cleavage through extensive DNA modifications like cytosine glycosylation, hindering mutagenesis efficiency. Our study utilizes the eukaryotic enzyme NgTET to temporarily reduce phage DNA modifications, facilitating Cas nuclease cleavage and enhancing mutagenesis efficiency. This approach enables precise DNA targeting and seamless point mutation integration, exemplified by deactivating specific ADP-ribosyltransferases crucial for phage infection. Furthermore, by temporally removing DNA modifications, we elucidated the effects of these modifications on T4 phage infections without necessitating gene deletions. Our results present a strategy enabling the investigation of phage epigenome functions and streamlining the engineering of phages with cytosine DNA modifications. The described temporal modulation of the phage epigenome is valuable for synthetic biology and fundamental research to comprehend phage infection mechanisms through the generation of mutants.


Assuntos
Bacteriófagos , Sistemas CRISPR-Cas , DNA Viral , Epigenoma , DNA Viral/genética , Bacteriófagos/genética , Engenharia Genética/métodos , Bacteriófago T4/genética , Mutagênese Sítio-Dirigida/métodos , Escherichia coli/genética , Escherichia coli/virologia , Genoma Viral
15.
Prog Mol Biol Transl Sci ; 208: 43-58, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-39266187

RESUMO

Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system possess a broad range of applications for genetic modification, diagnosis and treatment of infectious as well as non-infectious disease. The CRISPR-Cas system is found in bacteria and archaea that possess the Cas protein and guide RNA (gRNA). Cas9 and gRNA forms a complex to target and cleave the desired gene, providing defense against viral infections. Human immunodeficiency virus (HIV), hepatitis B virus (HBV), herpesviruses, human papillomavirus (HPV), and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) cause major life threatening diseases which cannot cure completely by drugs. This chapter describes the present strategy of CRISPR-Cas systems for altering the genomes of viruses, mostly human ones, in order to control infections.


Assuntos
Sistemas CRISPR-Cas , Edição de Genes , Humanos , Sistemas CRISPR-Cas/genética , Viroses/genética , Viroses/terapia , Viroses/virologia , Vírus/genética , Genoma Viral/genética
16.
Sci Rep ; 14(1): 21281, 2024 09 11.
Artigo em Inglês | MEDLINE | ID: mdl-39261582

RESUMO

Tomato brown rugose fruit virus (ToBRFV) poses a significant threat to tomato production worldwide, prompting extensive research into its genetic diversity, evolutionary dynamics, and adaptive strategies. In this study, we conducted a comprehensive analysis of ToBRFV at the codon level, focusing on codon usage bias, selection pressures, and evolutionary patterns across multiple genes. Our analysis revealed distinct patterns of codon usage bias and selection pressures within the ToBRFV genome, with varying levels of genetic diversity and evolutionary constraints among different genes. We observed a transition/transversion bias of 2.07 across the entire ToBRFV genome, with the movement protein (MP) gene exhibiting the highest transition/transversion bias and SNP density, suggesting potential evolutionary pressures or a higher mutation rate in this gene. Furthermore, our study identified episodic positive selection primarily in the MP gene, highlighting specific codons subject to adaptive changes in response to host immune pressures or environmental factors. Comparative analysis of codon usage bias in the coat protein (CP) and RNA-dependent RNA polymerase (RdRp) genes revealed gene-specific patterns reflecting functional constraints and adaptation to the host's translational machinery. Our findings provide valuable insights into the molecular mechanisms driving ToBRFV evolution and adaptation, with implications for understanding viral pathogenesis, host-virus interactions, and the development of control strategies. Future research directions include further elucidating the functional significance of codon usage biases, exploring the role of episodic positive selection in viral adaptation, and leveraging these insights to inform the development of effective antiviral strategies and crop protection measures.


Assuntos
Uso do Códon , Evolução Molecular , Genoma Viral , Solanum lycopersicum , Solanum lycopersicum/virologia , Solanum lycopersicum/genética , Seleção Genética , Adaptação Fisiológica/genética , Doenças das Plantas/virologia , Doenças das Plantas/genética , Códon/genética , Variação Genética
17.
Int J Mol Sci ; 25(17)2024 Aug 27.
Artigo em Inglês | MEDLINE | ID: mdl-39273250

RESUMO

Tuberculosis (TB), caused by Mycobacterium tuberculosis, is an infectious disease that seriously affects human life and health. Despite centuries of efforts to control it, in recent years, the emergence of multidrug-resistant bacterial pathogens of M. tuberculosis due to various factors has exacerbated the disease, posing a serious threat to global health. Therefore, a new method to control M. tuberculosis is urgently needed. Phages, viruses that specifically infect bacteria, have emerged as potential biocontrol agents for bacterial pathogens due to their host specificity. In this study, a mycobacterium phage, Henu3, was isolated from soil around a hospital. The particle morphology, biological characteristics, genomics and phylogeny of Henu3 were characterized. Additionally, to explore the balance between phage resistance and stress response, phage Henu3-resistant strains 0G10 and 2E1 were screened by sequence passage and bidirectional validation methods, which significantly improved the sensitivity of phage to antibiotics (cefotaxime and kanamycin). By whole-genome re-sequencing of strains 0G10 and 2E1, 12 genes involved in cell-wall synthesis, transporter-encoded genes, two-component regulatory proteins and transcriptional regulatory factor-encoded genes were found to have mutations. These results suggest that phage Henu3 has the potential to control M. tuberculosis pathogens, and phage Henu3 has the potential to be a new potential solution for the treatment of M. tuberculosis infection.


Assuntos
Mycobacterium tuberculosis , Mycobacterium tuberculosis/virologia , Mycobacterium tuberculosis/genética , Filogenia , Genoma Viral , Bacteriófagos/genética , Bacteriófagos/fisiologia , Humanos , Micobacteriófagos/genética , Micobacteriófagos/fisiologia , Sequenciamento Completo do Genoma , Aptidão Genética
18.
Int J Mol Sci ; 25(17)2024 Sep 04.
Artigo em Inglês | MEDLINE | ID: mdl-39273543

RESUMO

The rise of carbapenem-resistant Klebsiella pneumoniae (CRKP) presents a significant global challenge in clinical and healthcare settings, severely limiting treatment options. This study aimed to utilize a bacteriophage as an alternative therapy against carbapenem-resistant K. pneumoniae. A novel lytic N4-like Klebsiella phage, vB_kpnP_KPYAP-1 (KPYAP-1), was isolated from sewage. It demonstrated efficacy against the K62 serotype polysaccharide capsule of blaOXA-48-producing K. pneumoniae. KPYAP-1 forms small, clear plaques, has a latent period of 20 min, and reaches a growth plateau at 35 min, with a burst size of 473 plaque-forming units (PFUs) per infected cell. Phylogenetic analysis places KPYAP-1 in the Schitoviridae family, Enquatrovirinae subfamily, and Kaypoctavirus genus. KPYAP-1 employs an N4-like direct terminal repeat mechanism for genome packaging and encodes a large virion-encapsulated RNA polymerase. It lacks integrase or repressor genes, antibiotic resistance genes, bacterial virulence factors, and toxins, ensuring its safety for therapeutic use. Comparative genome analysis revealed that the KPYAP-1 genome is most similar to the KP8 genome, yet differs in tail fiber protein, indicating variations in host recognition. In a zebrafish infection model, KPYAP-1 significantly improved the survival rate of infected fish by 92% at a multiplicity of infection (MOI) of 10, demonstrating its potential for in vivo treatment. These results highlight KPYAP-1 as a promising candidate for developing phage-based therapies targeting carbapenemase-producing K. pneumoniae.


Assuntos
Bacteriófagos , Infecções por Klebsiella , Klebsiella pneumoniae , Peixe-Zebra , Klebsiella pneumoniae/virologia , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/genética , Animais , Bacteriófagos/genética , Bacteriófagos/fisiologia , Bacteriófagos/isolamento & purificação , Infecções por Klebsiella/terapia , Infecções por Klebsiella/microbiologia , Filogenia , Genoma Viral , Carbapenêmicos/farmacologia , Enterobacteriáceas Resistentes a Carbapenêmicos/genética , Enterobacteriáceas Resistentes a Carbapenêmicos/efeitos dos fármacos , Antibacterianos/farmacologia , Terapia por Fagos
19.
Microb Pathog ; 195: 106908, 2024 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-39218377

RESUMO

Outbreaks of the foot-and-mouth disease (FMD) have major economic impact on the global livestock industry by affecting the animal health and product safety. L-protease, a non-structural protein of FMDV, is a papain-like cysteine proteinase involved in viral protein processing as well as cleavage of host proteins for promoting the virus growth. FMDV synthesizes two forms of leader proteinase, Lpro (Labpro and Lbpro), where the deletion of Labpro is lethal and Lbpro deletion is reported to be attenuated. Defective replicons have been used by trans-complementing the deleted gene to produce one time replicating virus; thus, the bio-safety procedure can be compromised in the production units. Attempts are made to rescue of ΔLbproFMDV Asia1 virus by co-expressing the Lbpro protein carried in pcDNA plasmid. Mutant FMDV cDNA, pAsia-ΔLbpro, was constructed by PCR mediated mutagenesis using inverse primers. Transfection of BHK-21 cells with in-vitro transcribed RNA from the constructs failed to produce an infective mutant FMDV. Genetic trans-complementation of the Lbpro, which was done by co-transfecting the pcDNALbpro plasmid DNA along with the pAsia-ΔLbpro RNA in BHK-21 cells also failed to produce viable virus. Expression experiments of reporter genes and indirect immune-fluorescence confirmed the production of the viral proteins in wild type FMDV pAsiaWT; however, it was absent in the pAsia-ΔLbpro indicating that the leaderless virus was unable to produce infectious progeny and infect the cells. Failure to produce virus either by Lbpro deleted mutant clone or by genetic complementation suggests little chance of reversion of the disabled virus with large deletions of FMDV genome.


Assuntos
Vírus da Febre Aftosa , Vírus da Febre Aftosa/genética , Animais , Linhagem Celular , Genoma Viral/genética , Replicação Viral , Febre Aftosa/virologia , Cricetinae , Plasmídeos/genética , Cisteína Endopeptidases/genética , Cisteína Endopeptidases/metabolismo , Proteínas Virais/genética , Proteínas Virais/metabolismo , Deleção de Genes , Endopeptidases
20.
Bioinformatics ; 40(9)2024 Sep 02.
Artigo em Inglês | MEDLINE | ID: mdl-39226177

RESUMO

MOTIVATION: Tracking SARS-CoV-2 variants through genomic sequencing has been an important part of the global response to the pandemic and remains a useful tool for surveillance of the virus. As well as whole-genome sequencing of clinical samples, this surveillance effort has been aided by amplicon sequencing of wastewater samples, which proved effective in real case studies. Because of its relevance to public healthcare decisions, testing and benchmarking wastewater sequencing analysis methods is also crucial, which necessitates a simulator. Although metagenomic simulators exist, none is fit for the purpose of simulating the metagenomes produced through amplicon sequencing of wastewater. RESULTS: Our new simulation tool, SWAMPy (Simulating SARS-CoV-2 Wastewater Amplicon Metagenomes with Python), is intended to provide realistic simulated SARS-CoV-2 wastewater sequencing datasets with which other programs that rely on this type of data can be evaluated and improved. Our tool is suitable for simulating Illumina short-read RT-PCR amplified metagenomes. AVAILABILITY AND IMPLEMENTATION: The code for this project is available at https://github.com/goldman-gp-ebi/SWAMPy. It can be installed on any Unix-based operating system and is available under the GPL-v3 license.


Assuntos
COVID-19 , Metagenoma , SARS-CoV-2 , Águas Residuárias , Águas Residuárias/virologia , SARS-CoV-2/genética , SARS-CoV-2/isolamento & purificação , COVID-19/virologia , COVID-19/diagnóstico , Metagenômica/métodos , Software , Humanos , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala/métodos
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