Hepatitis A virus-induced hsa-miR-146a-5p attenuates IFN- β signaling by targeting adaptor protein TRAF6
In this study, we investigated the effects and mechanisms by which HAV-induced miRNAs antagonize IFN-β signaling. A variety of analytical methods, including miRNA microarray, RT-qPCR, dual-luciferase reporter assay, and Western blotting, were performed using HAV-infected cells. The results indicated that HAV infection upregulates the expression of hsa-miR-146a-5p, which in turn partially suppresses the inducti on of IFN-β synthesis, thereby promoting viral replication. Mechanistically, TRAF6 (TNF receptor-associated factor 6), a key adaptor protein in the RIG-I/MDA5-mediated IFN-I signaling pathway, is targeted a...
Source: Archives of Virology - January 18, 2021 Category: Virology Source Type: research

The roles of signaling pathways in SARS-CoV-2 infection; lessons learned from SARS-CoV and MERS-CoV
AbstractThe number of descriptions of emerging viruses has grown at an unprecedented rate since the beginning of the 21st century. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), is the third highly pathogenic coronavirus that has introduced itself into the human population in the current era, after SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Molecular and cellular studies of the pathogenesis of this novel coronavirus are still in the early stages of research; however, based on similarities of SARS-CoV-2 to other coronaviruses, it can...
Source: Archives of Virology - January 18, 2021 Category: Virology Source Type: research

A novel emaravirus comprising five RNA segments is associated with ringspot disease in oak
We report the complete nucleotide sequence of the genome of a novel virus in ringspot-diseased common oak (Quercus robur L.). The newly identified pathogen is associated with leaf symptoms such as mottle, chlorotic spots and ringspots on diseased trees. High-throughput sequencing (HTS, Illumina RNASeq) was used to explore the virome of a ringspot-diseased oak that had chlorotic ringspots of suspected viral origin on leaves for several years. Bioinformatic analysis of the HTS dataset followed by RT-PCR enabled us to determine complete sequences of four RNA genome segments of a novel virus. These sequences showed high simila...
Source: Archives of Virology - January 18, 2021 Category: Virology Source Type: research

Diversity of enteric and non-enteric human adenovirus strains in Brazil, 2006-2011
AbstractDuring 2006-2011, 5035 fecal samples were tested by PCR for human adenovirus (HAdV) and sequenced. HAdV was detected in 198 cases (3.9%), with the highest rate in children ≤ 5 years. Enteric HAdVs were the most prevalent genotypes (78%; 146/187): HAdV-F41 (63.6%; 119/187), HAdV-F40 (12.3%; 23/187), HAdV-A12 (1.6%; 3/187) and HAdV-A31 (0.5%; 1/187). Non-enteric HAdVs were detected in 22% (41/187): HAdV-C1 (8.0%; 15/187), HAdV-C2 (6.9%; 13/187), HAdV-C5 (4.3%; 8/187) , HAdV-D8 (1.3%; 2/187), HAdV-B21 (0.5%; 1/187), HAdV-B3 (0.5%; 1/187) and HAdV-C6 (0.5%; 1/187). This 6-year retrospective study points out a h...
Source: Archives of Virology - January 18, 2021 Category: Virology Source Type: research

Molecular profile of African swine fever virus (ASFV) circulating in Vietnam during 2019-2020 outbreaks
AbstractAfrican swine fever (ASF) is a highly infectious disease of pigs caused by African swine fever virus (ASFV). In order to identify potential genetic variations among ASFV strains circulating in Vietnam, 26 ASFV isolates from organs and blood samples collected from domestic pigs from 23 different provinces of northern, central and southern Vietnam during 2019-2020 ASF outbreaks were genetically characterized. Nucleotide sequences were determined for a portion of the B646L (p72) gene, the complete E183L (p54) gene, the variable region of EP402R (CD2v), the central variable region (CVR) of pB602L, and a tandem repeat s...
Source: Archives of Virology - January 16, 2021 Category: Virology Source Type: research

Complete genome analysis of an active prophage of Vibrio alginolyticus
AbstractAn active prophage,Vibrio phage ValM-yong1, was isolated from pathogenicVibrio alginolyticus by mitomycin C induction. This phage is a member of the familyMyoviridae and contains a head approximately 90 nm in diameter and a retractable tail approximately 250 nm in length. The genome of the phage is 33,851 bp in length with a G+C content of 45.6%. The noteworthy features ofVibrio phage ValM-yong1 are its flower-like head and genomic mosaicism. Here, we focus on presenting the genomic characterization of the virus. (Source: Archives of Virology)
Source: Archives of Virology - January 16, 2021 Category: Virology Source Type: research

Complete genome sequence of a novel foveavirus isolated from Allium sativum L. in China
AbstractThe complete genome sequence of a novel foveavirus identified in garlic (Allium sativum L.) in China was determined using RNA-seq, reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) PCR. The entire genomic RNA (GenBank accession MT981417) is 8748 nucleotides long excluding the 3 ’-terminal poly(A) tail and contains five open reading frames (ORFs). These ORFs encode the viral replicase, a triple gene block, and a coat protein. The virus was tentatively named “garlic yellow stripe associated virus” (GarYSaV). Pairwise comparisons of protein sequences...
Source: Archives of Virology - January 13, 2021 Category: Virology Source Type: research

Human endogenous retrovirus W family envelope protein (HERV-W env) facilitates the production of TNF- α and IL-10 by inhibiting MyD88s in glial cells
In this study, we found that HERV-W env significantly increased the mRNA and protein levels of TNF-α and IL-10 in U251 and A172 cell s. HERV-W env also induced a notable increase in Toll-like receptor 4 (TLR4). Knockdown of TLR4 impaired the expressions of TNF-α and IL-10 induced by HERV-W env. Overexpression of HERV-W env led to the upregulation of MyD88 but caused a decrease in MyD88s. MyD88s overexpression suppressed the expr essions of TNF-α and IL-10 induced by HERV-W env. These findings indicate that HERV-W env upregulates the expressions of IL-10 and TNF-α by inhibiting the producti...
Source: Archives of Virology - January 12, 2021 Category: Virology Source Type: research

First investigation of the prevalence of parvoviruses in slaughterhouse pigs and genomic characterization of ungulate copiparvovirus 2 in Vietnam
AbstractUngulate protoparvovirus 1, also known as porcine parvovirus 1 (PPV1), is considered to be one of the major causes of reproductive failure in pig breeding herds. Other parvoviruses have also been identified in pigs, including ungulate tetraparvovirus 3, or PPV2, ungulate tetraparvovirus 2, or PPV3, and ungulate copiparvovirus 2, or PPV4, but their significance for pigs is unknown. In the present study, the prevalence of PPV1-4 was investigated using a total of 231 lung and serum samples collected from slaughterhouses in 13 provinces throughout Vietnam. The overall prevalence was 54.5% (126/231) for PPV1, 28.0% (65/...
Source: Archives of Virology - January 12, 2021 Category: Virology Source Type: research

Arbovirus serosurvey  ( Orthobunyavirus , Flavivirus , and Alphavirus ) in a draft horse population from Santa Fe, Argentina (2013-2016)
AbstractIn the present study, we serosurveyed the exposure of 222 draft horses to different arboviruses in the city of Santa Fe, Argentina. Plaque reduction neutralization tests confirmed exposure to Fort Sherman virus (FSV), Saint Louis encephalitis virus (SLEV), West Nile virus (WNV), and R ío Negro virus (RNV). Apparently, Western and Eastern equine encephalitis viruses did not circulate in the population tested. The confirmation of five seroconversions for WNV, FSV, and SLEV and the association between prevalence and age are indicative of recent circulation. These results highlight the importance of considering ...
Source: Archives of Virology - January 12, 2021 Category: Virology Source Type: research

Obituary: G ünther M. Keil (1953–2020)
(Source: Archives of Virology)
Source: Archives of Virology - January 11, 2021 Category: Virology Source Type: research

Full genome sequence of a new three-segment gammapartitivirus from the phytopathogenic fungus Alternaria tenuissima on cotton in China
In this study, a new double-stranded RNA (dsRNA) virus, Alternaria tenuissima partitivirus 1 (AttPV1), was isolated fromAlternaria tenuissima strain XJ-BZ-2-6, a phytopathogenic fungus infecting cotton in China. The genome of AttPV1 comprised three dsRNAs of 1,785 nt (dsRNA1), 1,545 nt (dsRNA2), and 1,537 nt (dsRNA3) in length, the nucleotide sequence of which was determined using reverse transcription polymerase chain reaction, random-primed clones, and RNA-ligase-mediated rapid amplification of cDNA ends. dsRNA1 had a single open reading frame encoding a putative 61.54-kDa RNA-dependent RNA polymerase (RdRp). dsRNA2 and ...
Source: Archives of Virology - January 11, 2021 Category: Virology Source Type: research

A novel gammapartitivirus from the entomopathogenic fungus Metarhizium brunneum
AbstractHere, we report a novel partitivirus infectingMetarhizium brunneum, which was designated"Metarhizium brunneum partitivirus 2" (MbPV2). The complete genome of MbPV2 consists of two segments, dsRNA1 and dsRNA2, witheach dsRNA possessing a single open reading frame (ORF).dsRNA1 (1,775 bp) encodes a conserved RNA-dependent RNA polymerase (RdRp) with the highest sequence similarity to Plasmopara viticola associated partitivirus 1 (PvAPV1), while dsRNA2 (1,568 bp) encodes a coat protein (CP) with the highest sequence similarity to Colletotrichum partitivirus 1 (CtParV1). Phylogenetic analysis based on RdRp sequ...
Source: Archives of Virology - January 11, 2021 Category: Virology Source Type: research

Construction and characterization of an infectious cDNA clone of enterovirus 71: a rapid method for rescuing infectious virus based on stable cells expressing T7 polymerase
AbstractEnterovirus 71 (EV71) is a causative agent of hand, foot and, mouth disease (HFMD) in young children. It is valuable for virologists to develop a fast method to rescue infectious virus from a viral cDNA clone. Here, we report a method for rapid rescue of infectious EV71 by using cells expressing T7 polymerase. The full-length EV71 genome was amplified in one step by long-distance PCR with a T7 promoter at the 5 ʹ end, and the T7 polymerase gene was cloned into a lentivirus vector for construction of a stable cell line expressing T7 polymerase. The infectious virus was rapidly and efficiently rescued by single tran...
Source: Archives of Virology - January 9, 2021 Category: Virology Source Type: research

Genomic characterization of a nebovirus strain with a novel RdRp genotype in yaks
In this study, we investigated the genomic characteristics of a NeV strain from yaks that has a novel RdRp genotype. The complete genome of this strain (YAK/NRG-A9/19/CH) is 7454 nt in length and shares 68.3%-79.7% nt sequence identity with those of other NeVs. The RNA-dependent RNA polymerase (RdRp) gene of this strain shares 66.5%-78.5% nt sequence identity (74.0%-89.3% aa sequence identity) with the eight available complete NeV RdRp sequences, and a phylogenetic analysis based on these sequences showed that the new strain formed an independent branch, indicating that the RdRp of strain YAK/NRG-A9/19/CH may represent a n...
Source: Archives of Virology - January 9, 2021 Category: Virology Source Type: research

C1QBP inhibits proliferation of porcine circovirus type 2 by restricting nuclear import of the capsid protein
AbstractComplement component 1 Q subcomponent-binding protein (C1QBP) has been shown to interact with the porcine circovirus type 2 (PCV2) Cap protein. Here, using yeast two-hybrid (Y2H) and co-immunoprecipitation assays, as well as laser confocal microscopy, the interaction between C1QBP and Cap was confirmed. Furthermore, overexpression of C1QBP in cells altered the intracellular location of Cap, which was observed using confocal microscopy and verified by detection of Cap in nuclear protein extracts in a Western blot assay. By inhibiting nuclear transport of Cap, overexpression of C1QBP downregulated PCV2 proliferation ...
Source: Archives of Virology - January 9, 2021 Category: Virology Source Type: research

Chemiluminescent-microparticle-immunoassay-based detection and prevalence of human immunodeficiency virus infection in Islamabad, Pakistan
In this study, we determined the prevalence of HIV in Islamabad for the first time using a chemiluminescent microparticle immunoassay (CMIA), which is an advanced serological diagnostic technique. A total of 3659 samples were obtained from the general public in Islamabad, Pakistan, and 85 of them were found to be positive for HIV infection (2.32% prevalence). Of the positive subjects, 78.82% (67/85) were male, 10.6% (9/85) were female, and 10.6% (9/85) were of unidentified gender. The results revealed a significant relationship between age groups and HIV status. The age group of 21- to 30-year-olds was found to have the hi...
Source: Archives of Virology - January 8, 2021 Category: Virology Source Type: research

The emergence, evolution and spread of infectious bronchitis virus genotype GI-23
AbstractAvian infectious bronchitis is a contagious viral disease, caused by avian infectious bronchitis virus (IBV), that leads to severe losses in the poultry industry all over the world. Since the 1950s, IBV has circulated in the Middle East and North Africa, and no tangible evidence has shown any effects of measures taken to control its spread or evolution. Furthermore, new IBV variants are continually discovered. Although several genetic studies on IBV have been conducted, many IBV strains from this region have either been misclassified or remain unclassified. The genotype 23 (GI-23) variant emerged and has prevailed ...
Source: Archives of Virology - January 8, 2021 Category: Virology Source Type: research

hsa-miR-191-5p inhibits replication of human immunodeficiency virus type 1 by downregulating the expression of NUP50
In this study, we used gene chips to analyze miRNA expression profiles in peripheral blood mononuclear cells from ART-naive HIV-1 patients and those receiving ART, as well as from uninfected individuals. We measured differences in miRNA expression by quantitative polymerase chain reaction (qPCR) in an expanded sample. We found significant differences in the expression of has-miR-191-5p among the three groups (P
Source: Archives of Virology - January 8, 2021 Category: Virology Source Type: research

A new virus of the family Tombusviridae infecting sugarcane
AbstractMany viral diseases of sugarcane negatively affect yield. A sugarcane accession originating from South Africa exhibiting mosaic symptoms was processed for high-throughput sequencing. Bioinformatic analysis revealed two known sugarcane viruses and a contig of around 2,800 nucleotides resembling umbra-like viruses of the familyTombusviridae. The sequence of the viral contig was confirmed by cloning and Sanger sequencing, and the ends of the virus sequence were determined. Open reading frame analysis revealed the presence of four ORFs. Phylogenetic analysis of the complete virus sequence showed that this virus cluster...
Source: Archives of Virology - January 7, 2021 Category: Virology Source Type: research

Rate of exposure to Mayaro virus (MAYV) in Brazil between 1955 and 2018: a systematic review and meta-analysis
In conclusion, the general rate of exposure to MAYV in Brazil between 1955 and 2018 was considerable, especially in the Legal Amazon, in which 93% of cases were reported. (Source: Archives of Virology)
Source: Archives of Virology - January 7, 2021 Category: Virology Source Type: research

Isolation and molecular characterization of bovine herpesvirus 4 from cattle in mainland China
AbstractBovine herpesvirus 4 (BoHV-4) is one of the most important of the known viral respiratory and reproductive pathogens of both young and adult cattle. However, BoHV-4 has not been isolated or detected in mainland China prior to this study. In 2019, BoHV-4 strain 512 was isolated from cattle in Heilongjiang Province, China, using MDBK cells, and characterized by PCR, nucleotide sequence analysis, and transmission electron microscopy. Two other unknown herpesvirus strains, BL6010 and J4034, which were isolated from cattle in 2009 in China and stored at -70 ℃, were also propagated in MDBK cells and identified as BoHV-...
Source: Archives of Virology - January 7, 2021 Category: Virology Source Type: research

Primary vaccination in foals: a comparison of the serological response to equine influenza and equine herpesvirus vaccines administered concurrently or 2  weeks apart
This study compared concurrent and separate primary vaccination against equid alphaherpesviruses 1 and 4, genusVaricellovirus, subfamilyAlphaherpesvirinae, familyHerpesviridae, and equine influenza A virus, genusAlphainfluenzavirus, familyOrthomyxoviridae. Their vernacular names are equine herpesvirus 1 and 4 (EHV1/4) and equine influenza virus (EIV). Infection with these respiratory pathogens is associated with loss of performance, interruption of training schedules, and on occasion, cancellation of equestrian events. Vaccination is highly recommended, and for some activities it is a mandatory requirement of the relevant ...
Source: Archives of Virology - January 7, 2021 Category: Virology Source Type: research

Ramesh Chandra Sinha (1934 –2020)
(Source: Archives of Virology)
Source: Archives of Virology - January 7, 2021 Category: Virology Source Type: research

Protective cellular and mucosal immune responses following nasal administration of a whole gamma-irradiated influenza A (subtype H1N1) vaccine adjuvanted with interleukin-28B in a mouse model
AbstractThe use of gamma-irradiated influenza A virus ( γ-Flu), retains most of the viral structural antigens, represent a promising option for vaccine development. However, despite the high effectiveness of γ-Flu vaccines, the need to incorporate an adjuvant to improve vaccine-mediated protection seems inevitable. Here, we examined the protective effi cacy of an intranasal gamma-irradiated HIN1 vaccine co-administered with a plasmid encoding mouse interleukin-28B (mIL-28B) as a novel adjuvant in BALB/c mice. Animals were immunized intranasally three times at one-week intervals with γ-Flu, alone or in com...
Source: Archives of Virology - January 6, 2021 Category: Virology Source Type: research

A novel previously undescribed fusarivirus from the phytopathogenic fungus Setosphaeria turcica
AbstractA putative mycovirus belonging to the proposed family “Fusariviridae” was discovered inSetosphaeria turcica by sequencing a double-stranded RNA extracted from this phytopathogenic fungus. The virus was tentatively named “Setosphaeria turcica fusarivirus 1” (StFV1). StFV1 has a genome comprising 6685 nucleotides. The genome contains three open reading frames (ORF). The largest ORF, ORF1, is preceded by an untranslated region (UTR) of 16 nucleotides and separated from ORF2 by an intergenic region of 63 nucleotide s. The smallest ORF, ORF3, overlaps ORF2 by 16 nucleotides and is followed by a 3...
Source: Archives of Virology - January 6, 2021 Category: Virology Source Type: research

Marek ’s disease virus in vaccinated poultry flocks in Turkey: its first isolation with molecular characterization
In this study, 16 dead commercial chickens from flocks with suspected MD were necropsied immediately after death. Pathological findings were compatible with MD, and gallid alphaherpesvirus 2 was identified in PCR of spleen samples. Virus isolation was performed in primary cell culture, and partial sequencing of themeq gene of the isolate revealed>99% nucleotide sequence identity to virulent and very virulent plus strains from a number of European countries, placing it in the same subclade of clade III as two virulent Italian strains and a very virulent plus Polish strain as well as virulent strains of geese and ducks. T...
Source: Archives of Virology - January 6, 2021 Category: Virology Source Type: research

A novel mycovirus infecting Aspergillus nidulans that is closely related to viruses in a new genus of the family Partitiviridae
AbstractThe bisegmented genome of a novel double-stranded (ds) RNA mycovirus, named “Aspergillus nidulans partitivirus 1” (AnPV1), isolated from the fungusAspergillus nidulans strain HJ5-47, was sequenced and analyzed. AnPV1 contains two segments, AnPV1-1 and AnPV1-2. AnPV1-1 has 1837 bp with an open reading frame (ORF) that potentially encodes a putative RNA-dependent RNA polymerase (RdRp) of 572 amino acids (aa). AnPV1-2 has 1583 bp with an ORF encoding a putative capsid protein (CP) of 488 aa. Phylogenetic analyses indicated that AnPV1 and related viruses clustered in a group that could represent a new uncla...
Source: Archives of Virology - January 6, 2021 Category: Virology Source Type: research

Gene expression and in vitro replication of bovine gammaherpesvirus type 4
AbstractIn vitro cell cultures are widely used models for dissecting cellular and molecular mechanisms that lead to certain physiological conditions and diseases. The pathogenesis of BoHV-4 in the bovine reproductive tract has been studied by conducting tests on primary cultures. However, many questions remain to be answered about the role of BoHV-4 in endometrial cells. The aim of this study was to compare the replication and gene expression of BoHV-4 in cell lines and bovine reproductive tract primary cells as anin vitro model for the study of this virus. We demonstrated that BoHV-4 strains differ in theirin vitro growth...
Source: Archives of Virology - January 5, 2021 Category: Virology Source Type: research

Downregulation of miR-296-3p by highly pathogenic porcine reproductive and respiratory syndrome virus activates the IRF1/TNF- α signaling axis in porcine alveolar macrophages
In this study, we used a highly pathogenic PRRSV-2 (speciesBetaarterivirus suid 2) strain to show that PRRSV infection robustly downregulates the expression of miR-296-3p in porcine alveolar macrophages (PAMs). Furthermore, we demonstrated that overexpression of miR-296-3p increases the replication of highly pathogenic (HP)-PRRSV in PAMs. Notably, the overexpression of miR-296-3p inhibited the induction of TNF- α, even with increased viral replication, compared with that in the HP-PRRSV-infected control group. We also demonstrated that miR-296-3p targets IRF1-facilitated viral infection and modulates the expression o...
Source: Archives of Virology - January 4, 2021 Category: Virology Source Type: research

Revisiting Orthotospovirus phylogeny using full-genome data and testing the contribution of selection, recombination and segment reassortment in the origin of members of new species
In this study, we examined 67 complete genome sequences from members of 22 species. Our study confirms the existence of four phylogroups (A to D), grouped in two major clades (A-B and C-D) within the genus. We found strong evidence that within-segment recombination events and reassortment of segments during mixed infections have been involved in the origin of new orthotospoviruses. Also, selection pressures were analyzed for each gene, and evidence of positive selection was found in all genes. (Source: Archives of Virology)
Source: Archives of Virology - January 4, 2021 Category: Virology Source Type: research

Swine virome on rural backyard farms in Mexico: communities with different abundances of animal viruses and phages
AbstractDomestic swine have been introduced by humans into a wide diversity of environments and have been bred in different production systems. This has resulted in an increased risk for the occurrence and spread of diseases. Although viromes of swine in intensive farms have been described, little is known about the virus communities in backyard production systems around the world. The aim of this study was to describe the viral diversity of 23 healthy domestic swine maintained in rural backyards in Morelos, Mexico, through collection and analysis of nasal and rectal samples. Next-generation sequencing was used to identify...
Source: Archives of Virology - January 4, 2021 Category: Virology Source Type: research

Rose virus R, a cytorhabdovirus infecting rose
AbstractRNA was extracted from ‘Hugh Dickson’ rose leaves displaying virus-like symptoms in Maryland, USA. Using high-throughput sequencing, we identified a new virus, tentatively named “rose virus R”. This virus has a negative-sense, single-stranded RNA genome and exhibits genomic features of a rhabdovirus, including a g enome organization of 3’–N–P–P3–M–G–P6–L–5’ and a gene junction region consensus sequence 3’-AUUUAUUUUGACUCUA-5’. Rose virus R is phylogenetically related to cytorhabdoviruses, and the nucleotide and amino acid...
Source: Archives of Virology - January 4, 2021 Category: Virology Source Type: research

Detection and genetic characteristics of porcine bocavirus in central China
AbstractTo investigate the epidemic profile and genetic diversity of porcine bocavirus (PBoV), 281 clinical samples, including 236  intestinal tissue samples and 45 fecal samples were collected from diarrheic piglets on 37 different pig farms in central China, and two SYBR Green I–based quantitative PCR assays were developed to detect PBoV1/2 and PBoV3/4/5, respectively. One hundred forty-eight (52.67%) of the 281 clinical s amples were positive for PBoV1/2, 117 (41.63%) were positive for PBoV3/4/5, 55 (19.57%) were positive for both PBoV1/2 and PBoV3/4/5, and 86.49% (32/37) of the pig farms were positive for PB...
Source: Archives of Virology - January 4, 2021 Category: Virology Source Type: research

Characterization of bacteriophage T7-Ah reveals its lytic activity against a subset of both mesophilic and psychrophilic Aeromonas salmonicida strains
This study sheds light on the surprising diversity of lifestyles of the bacterial strains sensitive to phage T7-Ah and opens the door to the potential use of this phage againstA.  salmonicida infections in aquaculture. (Source: Archives of Virology)
Source: Archives of Virology - January 4, 2021 Category: Virology Source Type: research

Focus on hepatitis C virus genotype distribution in Tunisia prior to elimination: a 16-year retrospective study
AbstractWith the introduction of direct-acting antiviral treatment (DAA), Tunisia has committed to achieving the international goal of eliminating viral hepatitis. Because the specific DAA prescribed depends on viral genotype, viral genotyping remains of great importance. The aim of the present study was to outline the trends in the distribution of HCV genotypes from 2002 to 2017 in the Tunisian general population in order to guide authorities towards the most appropriate therapeutic strategies for preventing HCV infection. A total of 2532 blood samples were collected over a 16-year period and from all regions of Tunisia. ...
Source: Archives of Virology - January 4, 2021 Category: Virology Source Type: research

Viral meningitis: an overview
AbstractMeningitis is a serious condition that affects the central nervous system. It is an inflammation of the meninges, which is the membrane that surrounds both the brain and the spinal cord. Meningitis can be caused by bacterial, viral, or fungal infections. Many viruses, such as enteroviruses, herpesviruses, and influenza viruses, can cause this neurological disorder. However, enteroviruses have been found to be the underlying cause of most viral meningitis cases worldwide. With few exceptions, the clinical manifestations and symptoms associated with viral meningitis are similar for the different causative agents, whi...
Source: Archives of Virology - January 3, 2021 Category: Virology Source Type: research

Composition, codon usage pattern, protein properties, and influencing factors in the genomes of members of the family Anelloviridae
AbstractThe present study was carried out on 62 genome sequences of members of the familyAnelloviridae, as there have been no reports of genome analysis of these DNA viruses using a bioinformatics approach. The genes were found to be rich in AC content with low codon usage bias (CUB). Relative synonymous codon usage (RSCU) values identified the preferred codons for each amino acid in the family. The codon AGA was overrepresented, while the codons TCG, TTG, CGG, CGT, ACG, GCG and GAT were underrepresented in all of the genomes. A significant correlation was found between the effective number of codons (ENC) and base constra...
Source: Archives of Virology - January 3, 2021 Category: Virology Source Type: research

Insights into the origin and diversification of bovine viral diarrhea virus 1 subtypes
In this study, we performed phylogenetic and evolutionary analysis on bovine viral diarrhea virus 1 (BVDV-1) sequences to investigate the origin and temporal diversification of different BVDV-1 subtypes. Dated phylogenies using the complete polyprotein sequence were reconstructed, and the time of the most recent common ancestor (tMRCA) was estimated. The results demonstrated that BVDV-1 subtypes clustered into two phylogenetic clades, where the predominant subtypes worldwide grouped together. In the temporal analysis, the tMRCA of BVDV-1 was 1336, and the diversification into different subtypes appears to have occurred aro...
Source: Archives of Virology - January 3, 2021 Category: Virology Source Type: research

Isolation and characterization of the novel Pseudomonas stutzeri bacteriophage 8P
AbstractBacteriophage 8P was isolated with aPseudomonas stutzeri strain isolated from an oil reservoir as its host bacterium. The phage genome comprises 63,753 base pairs with a G+C content of 64.35. The phage encodes 63 predicted proteins, and 27 of them were functionally assigned. No tRNA genes were found. Comparative genomics analysis showed that 8P displayed some relatedness to F116-like phages (78% identity, 20% query coverage). The genome has very low sequence similarity to the other phage genomes in the GenBank database and Viral Sequence Database. Based on whole-genome analysis and transmission electron microscopy ...
Source: Archives of Virology - January 3, 2021 Category: Virology Source Type: research

Enterococcus phage Nonaheksakonda infecting clinical isolates of Enterococcus faecalis represents a new lineage in the family Siphoviridae
AbstractEnterococcus phage Nonaheksakonda was isolated from wastewater, using a vancomycin-resistant strain of the opportunistic pathogenEnterococcus faecalis (VRE) as a host. Nonaheksakonda is a lytic phage infectingE. faecalis V583 and clinical isolates with at least four different multi-locus sequence types (MLSTs). The genome is a 41.9-kb double-stranded DNA molecule (34.6% GC) with 74 coding sequences. Comparative analysis revealed only one close relative, Enterococcus phage heks. All other phages had low protein similarity and shared less than 54% nucleotide sequence identity with phage Nonaheksakonda. The most simil...
Source: Archives of Virology - January 3, 2021 Category: Virology Source Type: research

Molecular evolution and pathogenicity of chicken anemia virus isolates in China
AbstractChicken infectious anemia (CIA), caused by chicken anemia virus (CAV), is an important immunosuppressive disease that seriously threatens the global poultry industry. Here, we isolated and identified 30 new CAV strains from CAV-positive flocks. TheVP1 genes of these strains were sequenced and analyzed at the nucleotide and amino acid levels and were found to have very similar nucleotide sequences (>  97% identity); however, they showed 93.9–100.0% sequence identity to theVP1 genes of 55 reference strains. Furthermore, alignment of the deduced amino acid sequences revealed some unique mutations. Phylog...
Source: Archives of Virology - January 3, 2021 Category: Virology Source Type: research

Porcine circovirus genotypes and their copathogens in pigs with respiratory disease in southern provinces of Vietnam
This study was conducted to investigate the genetic diversity of porcine circovirus type 2 (PCV2) and its coinfecting pathogens in pigs with respiratory disease in Vietnam. Samples from 127 clinical cases were obtained from different southern provinces of Vietnam from January 2018 to January 2020 for PCR and sequence analysis. The infection rate of PCV2 was 78.8%, and the major pathogens found in coinfections with PCV2 were porcine reproductive and respiratory syndrome virus,Mycoplasma hyopneumoniae, andHaemophilus parasuis. Forty-three PCV2-positive clinical samples were selected for amplification and sequencing of the OR...
Source: Archives of Virology - January 3, 2021 Category: Virology Source Type: research

Molecular survey of selected viral pathogens in wild leopard cats ( Prionailurus bengalensis ) in Taiwan with an emphasis on the spatial and temporal dynamics of carnivore protoparvovirus 1
AbstractThe leopard cat (Prionailurus bengalensis) was listed as an endangered species under the Wildlife Conservation Act in Taiwan in 2009. However, no study has evaluated the possible direct or indirect effects of pathogens on the Taiwanese leopard cat population. Here, we targeted viral pathogens, including carnivore protoparvovirus 1 (genusProtoparvovirus), feline leukemia virus (FeLV), feline immunodeficiency virus (FIV), coronaviruses (CoVs), and canine distemper virus (CDV), through molecular screening. The spatial and temporal dynamics of the target pathogens were evaluated. Through sequencing and phylogenetic ana...
Source: Archives of Virology - January 3, 2021 Category: Virology Source Type: research

Viral communities associated with porcine diarrhoeal disease and genetic characterization of a bufavirus in Tibetan pigs in China
AbstractTo investigate the viral communities in diarrhoeal faeces of Tibetan pigs, 146 diarrhoeic samples were collected from 16 pigs farms on the Tibetan plateau. Nineteen viruses belonging to eleven viral taxonomic families were identified in a pooled library. Metagenomics analysis revealed that the viruses were mainly small linear and circular DNA viruses. Furthermore, sequences of 10 NS1 genes and two complete genomes of PBuVs were obtained by PCR amplification. Sequence comparisons and phylogenetic analysis showed that the PBuVs from Tibetan pigs displayed more abundant genetic diversity than those from domestic pigs....
Source: Archives of Virology - January 3, 2021 Category: Virology Source Type: research

Characterization of vB_VpaP_MGD2, a newly isolated bacteriophage with biocontrol potential against multidrug-resistant Vibrio parahaemolyticus
AbstractVibrio parahaemolyticus is a major foodborne pathogen and is also pathogenic to shrimp. Due to the emergence of multidrug-resistantV. parahaemolyticus strains, bacteriophages have shown promise as antimicrobial agents that could be used for controlling antibiotic-resistant strains. Here, aV. parahaemolyticus phage, vB_VpaP_MGD2, was isolated from a clam (Meretrix meretrix) and further characterized to evaluate its potential capability for biocontrol. Podophage vB_VpaP_MGD2 had a wide host range and was able to lyse 27 antibiotic-resistantV. parahaemolyticus strains. A one-step growth curve showed that vB_VpaP_MGD2 ...
Source: Archives of Virology - January 3, 2021 Category: Virology Source Type: research

The complete genomic sequence of the novel myovirus RP13 infecting Ralstonia solanacearum , the causative agent of bacterial wilt
AbstractA novel lytic bacteriophage,Ralstonia phage RP13, was isolated from tomato fields in Pang Nga, Thailand. Electron microscopic observation showed it to have the features of a myovirus with a novel triangulation number (T = 21,dextro). The RP13 DNA appeared to be heavily modified. By applying RNA sequencing and RNA-sequence-mediated DNA sequencing, the whole genome of RP31 was determined to be 170,942 bp in length with a mean G+C content of 39.2%. A total of 277 ORFs were identified as structural, functional, or hypothetical genes in addition to four tRNA genes. Phylogenetic analysis suggested that RP13 is not closel...
Source: Archives of Virology - January 2, 2021 Category: Virology Source Type: research

Complete genome sequence of pleioblastus mosaic virus, a distinct member of the genus Potyvirus
AbstractPleioblastus mosaic virus (PleMV) is a tentative member of the genusPotyvirus in the familyPotyviridae and was discovered in bamboo with mosaic symptoms in Tokyo, Japan. Since no information on the genome sequence of PleMV has been reported, its taxonomic position has long been uncertain. Here, we report the first complete genome sequences of two distinct PleMV isolates. Excluding the 3 ′-terminal poly(A) tail, their genomic RNA sequences consist of 9,634 and 9,643 nucleotides (nt); both contain a large open reading frame (ORF) encoding a polyprotein and a small ORF termedPIPO. The large ORFs of the two isola...
Source: Archives of Virology - January 1, 2021 Category: Virology Source Type: research

Genomic characteristics and pathogenicity of a new recombinant strain of porcine reproductive and respiratory syndrome virus
In this study, we report a recombinant PRRSV (SD-YL1712) isolated from a pig farm. The genome of SD-YL1712 is 15,014 nucleotides in length, and its nucleotide and amino acid sequence conservation is higher than that of PRRSV strain JXA1 except within the NSP2 region. The NSP2 region of SDYL1712 shares the highest nucleotide (85.9%) and amino acid (84.1%) sequence identity with PRRSV strain NADC30. SD-YL1712 was found to contain a characteristic 131-amino-acid deletion in the NSP2 region. Two recombination breakpoints were detected at nt 2134 and nt 3958 within the NSP2 region, which revealed that SD-YL1712 originated from ...
Source: Archives of Virology - January 1, 2021 Category: Virology Source Type: research

Full genome sequence of bovine alphaherpesvirus 2 (BoHV-2)
We present the complete genome sequence of bovine alphaherpesvirus 2 (BoHV-2), a member of the familyHerpesviridae, subfamilyAlphaherpesvirinae, genusSimplexvirus. BoHV-2 is the causative agent of bovine ulcerative mammillitis (bovine herpes mammillitis) and pseudo-lumpy skin disease. The genomic architecture of BoHV-2 is typical of most simplexvirus genomes and congruent with that of human alphaherpesvirus 1 (HHV-1). The genome comprises a total of 131,245 base pairs and has an overall G+C content of 64.9 mol%. A total of 75 open reading frames are predicted. The gene repertoire of BoHV-2 is analogous to that of HHV-1, al...
Source: Archives of Virology - December 14, 2020 Category: Virology Source Type: research