Correction to: Complete genome sequencing and characterization of single-stranded DNA Vibrio parahaemolyticus phage from inland saline aquaculture environment
(Source: Virus Genes)
Source: Virus Genes - June 15, 2022 Category: Genetics & Stem Cells Source Type: research
An increase in prevalence of recombinant GII.3[P12] norovirus in sporadic acute diarrhea in children in Nizhny Novgorod, Russia, 2018 –2021
This study shows an increase in the detection rate of recombinant GII.3[P12] norovirus in Nizhny Novgorod, Russia, from 6.8% in 2018 –2019 to 34.9% in 2020–2021. We performed a phylogenetic analysis based on the nucleotide sequences of noroviruses possessing this genotype obtained in this work, as well as presented in the GenBank database. It has been shown that the circulation of GII.3[P12] noroviruses in the study area was the result of several independent introductions, either directly from the Western Pacific region, or through the Asian part of Russia. The polyphyletic origin, the geographical expansion, and the g...
Source: Virus Genes - June 9, 2022 Category: Genetics & Stem Cells Source Type: research
Diversity of mycoviruses in edible fungi
AbstractMycoviruses (fungal viruses) are widespread in all major taxonomic groups of fungi. Although most mycovirus infections are latent, some mycoviruses, such as La France isometric virus, mushroom virus X, and oyster mushroom spherical virus, can cause severe diseases in edible fungi and lead to significant production losses. Recently, deep sequencing has been employed as a powerful research tool to identify new mycoviruses and to enhance our understanding of virus diversity and evolution. An increasing number of novel mycoviruses that can infect edible fungi have been reported, including double-stranded (ds) RNA, posi...
Source: Virus Genes - June 6, 2022 Category: Genetics & Stem Cells Source Type: research
Complete genome sequencing and characterization of single-stranded DNA Vibrio parahaemolyticus phage from inland saline aquaculture environment
AbstractDespite their evolutionary, molecular biology and biotechnological significance, relatively fewer numbers of single-stranded DNA (ssDNA) filamentous phages belonging to the familyInoviridae have been discovered and characterized to date. The present study focused on genome sequencing and characterization of an ssDNAVibrio parahaemolyticus phage V5 previously isolated from an inland saline shrimp culture farm. The complete circular genome of phage V5 consisted of 6658 bp with GC content of 43.7%. During BLASTn analysis, only 36% of phage V5 genome matched with otherVibrio phage genomes in the NCBI database with a ...
Source: Virus Genes - May 30, 2022 Category: Genetics & Stem Cells Source Type: research
Isolation and characterization of the novel bacteriophage vB_SmaS_BUCT626 against Stenotrophomonas maltophilia
In this study, we isolated a novelSiphoviridae bacteriophage vB_SmaS_BUCT626 with lytic activity againstS. maltophilia. Phage vB_SmaS_BUCT626 can lysis 10 of 20S. maltophilia and was relatively stable at a wide range of temperatures (4 –70 °C) and pH values (3.0–13.0) and exhibited good tolerance to chloroform. The genome of phage vB_SmaS_BUCT626 was a 61,662-bp linear double-stranded DNA molecule with a GC content of 56.2%, and contained 100 open-reading frames. It carried no antibiotic resistance, toxin, virulence-related genes, or lysogen-formation gene clusters. Together, these characteristics make phage vB_SmaS_...
Source: Virus Genes - May 28, 2022 Category: Genetics & Stem Cells Source Type: research
Increased virulence of a novel reassortant H1N3 avian influenza virus in mice as a result of adaptive amino acid substitutions
In this study, a novel multiple-gene reassortant H1N3 subtype avian influenza virus (AIV) (A/chicken/Zhejiang/81213/2017, CK81213) was isolated in Eastern China, whose genes were derived from H1 (H1N3), H7 (H7N3 and H7N9), and H10 (H10N3 and H10N8) AIVs. This AIV belongs to the avian Eurasian-lineage and exhibits low pathogenicity. Serial lung-to-lung passages of CK81213 in mice was performed to study the amino acid substitutions potentially related to the adaptation of H1 AIVs in mammals. And the mouse-adapted H1N3 virus showed greater virulence than wild-type H1N3 AIV in mice and the genomic analysis revealed a total of ...
Source: Virus Genes - May 26, 2022 Category: Genetics & Stem Cells Source Type: research
Non-structural proteins of bovine viral diarrhea virus
AbstractBovine viral diarrhea virus (BVDV) belongs to the family Flaviviridae genus pestivirus. The viral genome is a single-stranded, positive-sense RNA that encodes four structural proteins (i.e., C, Erns, E1, and E2) and eight non-structural proteins (NSPs) (i.e., Npro, p7, NS2, NS3, NS4A, NS4B, NS5A, and NS5B). Cattle infected with BVDV exhibit a number of different clinical signs including diarrhea, abortion, and other reproductive disorders which have a serious impact on the cattle industry worldwide. Research on BVDV mainly focuses on its structural protein, however, progress in understanding the functions of the NS...
Source: Virus Genes - May 25, 2022 Category: Genetics & Stem Cells Source Type: research
Phylogenetic analysis of porcine reproductive and respiratory syndrome virus in Vietnam, 2021
This study aimed to investigate the genetic diversity of PRRSV to assist in evaluating the effectiveness of PRRS vaccines. Twenty-eight samples from clinical cases were collected from 19 farms in seven provinces of Vietnam in 2021. Full-length PRRSV ORF5 genes from the 19 samples were amplified, sequenced, and compared to the corresponding sequences of referenced PRRSV strains from Genbank. The genetic analysis showed that 12 isolates were the highly pathogenic PRRSV subtype (HP —PRRSV) lineage 8, sublineage 8.7; six isolates were the classical North American PRRSV subtype (US-PRRSV), NADC-like group, lineage 1, sublinea...
Source: Virus Genes - May 19, 2022 Category: Genetics & Stem Cells Source Type: research
Characterization of the functional domains of nuclear shuttle protein (NSP) of Indian cassava mosaic virus using green fluorescent protein as reporter
AbstractIndian cassava mosaic virus (ICMV), responsible for the cassava mosaic disease in India, harbours two circular genomic components, DNA-A and DNA-B; the former being responsible for the encapsidation and replication and the latter for intra- and inter-cellular movement of the viral DNA. Two proteins, encoded by DNA-B, the movement protein (MP) and the nuclear shuttle protein (NSP), act in concert on the newly replicated viral DNA to move it from the nucleus to the cell periphery. To map the functional domains of NSP, the intra-cellular localization of its full-length protein and deletion derivatives was studied in t...
Source: Virus Genes - May 14, 2022 Category: Genetics & Stem Cells Source Type: research
Molecular characteristics and pathogenicity of an equid alphaherpesvirus 1 strain isolated in China
AbstractEquid alphaherpesvirus 1 (EHV-1) is prevalent in China, and causes notable economic damage to the equine industry. However, there is no information regarding the molecular characteristics and pathogenicity of the Chinese strains. Therefore, an EHV-1 strain, named YM2019, was isolated from the lung tissue of an aborted horse fetus in Xinjiang, China, and its genome and pathogenicity were analyzed. The full genome of the isolate was 150,267 base pairs in length, with 56.7% G + C content. Genetic and phylogenetic analysis showed that strain YM2019 (GenBank: MT063054) belonged to theORF30 N752 genotype but display...
Source: Virus Genes - May 14, 2022 Category: Genetics & Stem Cells Source Type: research
Muramidase, nuclease, or hypothetical protein genes intervene between paired genes encoding DNA packaging terminase and portal proteins in Wolbachia phages and prophages
AbstractGenomes of the obligate intracellular alpha proteobacteriumWolbachia pipientis often encode prophage-like regions, and in a few cases, purified particles have been recovered. Because the structure of a conserved WO phage genome has been difficult to establish, we examined paired terminase and portal genes inWolbachia phages and prophages, relative to those encoded by the gene transfer agent RcGTA from the free-living alpha proteobacteriumRhodobacter capsulatus. Terminase and portal proteins fromWolbachia have higher similarity to orthologs encoded by RcGTA than to orthologs encoded by bacteriophage lambda. In lambd...
Source: Virus Genes - May 10, 2022 Category: Genetics & Stem Cells Source Type: research
Detection and typing of dengue virus by one-step RT-PCR-based high-resolution melting assay
AbstractDengue is a rapidly spreading arboviral disease that can be transmitted through any of the four types of dengue virus (DENV) serotypes. Previous studies have observed that individuals who have a pre-existing secondary infection due to a different dengue serotype, experience severe forms of this disease. During a DENV outbreak, a time-sensitive preliminary diagnosis of the origin of DENV might be useful in controlling the epidemic. Here, we developed a rapid and accurate one-step TB Green RT-PCR-based high-resolution melting (HRM) assay to identify and serotype DENV using serotyping primers based on the alignment wi...
Source: Virus Genes - May 10, 2022 Category: Genetics & Stem Cells Source Type: research
Characterization of yam mosaic viruses from Brazil reveals a new phylogenetic group and possible incursion from the African continent
AbstractYam (Dioscorea spp.) is an important crop for smallholder farmers in the Northeast region of Brazil. Wherever yam is grown, diseases caused by yam mosaic virus (YMV) are prevalent. In the present study, the diversity of YMV infectingDioscorea cayennensis-rotundata was analyzed. In addition, five species ofDioscorea (D. alata,D. altissima,D. bulbifera,D. subhastata, andD. trifida) commonly found in Brazil were analyzed using ELISA and high-throughput sequencing (HTS). YMV was detected only inD. cayennensis-rotundata, of which 66.7% of the samples tested positive in ELISA. Three YMV genome sequences were assembled fr...
Source: Virus Genes - May 10, 2022 Category: Genetics & Stem Cells Source Type: research
Screening of candidate genes associated with high titer production of oncolytic measles virus based on systems biology approach
In this study, a systems biology approach was considered including collection of gene expression profiles from the Gene Expression Omnibus (GEO) database, obtaining differentially expressed genes (DEGs), performing gene ontology, functional enrichment analyses, and topological analyses on the protein –protein interaction (PPI) network. Then, to validate the in-silico data, total RNA was isolated from five cell lines, and full-length cDNA from template RNA was synthesized. Subsequently, quantitative reverse transcription-PCR (RT-qPCR) was employed. We identified five hub genes, including RAC1, HSP90AA1, DNM1, LTBP1, and F...
Source: Virus Genes - April 27, 2022 Category: Genetics & Stem Cells Source Type: research
An overview of influenza A virus genes, protein functions, and replication cycle highlighting important updates
AbstractThe recent research findings on influenza A virus (IAV) genome biology prompted us to present a comprehensive overview of IAV genes, protein functions, and replication cycle. The eight gene segments of the IAV genome encode 17 proteins, each having unique functions contributing to virus fitness in the host. The polymerase genes are essential determinants of IAV pathogenicity and virulence; however, other viral components also play crucial roles in the IAV replication, transmission, and adaptation. Specific adaptive mutations within polymerase (PB2, PB1, and PA) and glycoprotein —hemagglutinin (HA) and neuraminida...
Source: Virus Genes - April 26, 2022 Category: Genetics & Stem Cells Source Type: research
