Genetic and antigenic characterization of influenza A/H5N1 viruses isolated from patients in Indonesia, 2008 –2015
This study provides better insight in genetic diversity of H5N1 viruses during human infection and the presence of human adaptive markers. These findings highlight the importance of evaluating virus genetics for HPAI H5N1 viruses to estimate the risk to human health and the need for increased efforts to monitor the evolution of H5N1 viruses across Indonesia. (Source: Virus Genes)
Source: Virus Genes - June 1, 2020 Category: Genetics & Stem Cells Source Type: research

Phylodynamics of G4P[8] and G2P[4] strains of rotavirus A isolated in Russia in 2017 based on full-genome analyses
Abstract Rotavirus A is a dynamically evolving pathogen causing acute gastroenteritis in children during the first years of life. In the present study, we conducted a phylodynamic analysis based on the complete sequences of 11 segments of rotaviruses with the G4P[8] and G2P[4] genotypes isolated in Russia in 2017. Since rotavirus has a segmented genome, our analysis was performed using the Bayesian approach based on separate samples of nucleotide sequences for each gene of the strains studied. For the strain with the genotype G4P[8], the most likely geographical locations of the nearest common ancestor were Russia (VP7, ...
Source: Virus Genes - May 29, 2020 Category: Genetics & Stem Cells Source Type: research

Molecular characterization of non-polio enteroviruses isolated from children with acute flaccid paralysis in IRAN, 2015 –2018
AbstractIn addition to polioviruses, non-polio enteroviruses (NPEVs) are frequently isolated from patients with acute flaccid paralysis (AFP) worldwide. In polio-free countries, there have been expectations that with disappearing wild poliovirus from the community, the rate of AFP would decrease, but the increasing number of AFP cases proved this notion to be wrong. There are speculations that NPEVs might be the cause of increasing AFP rate. The aim of this study was to investigate frequency, genetic diversity, circulation patterns of NPEVs isolated from AFP cases in Iran from 2015 to 2018. Fifty-three NPEVs were isolated ...
Source: Virus Genes - May 25, 2020 Category: Genetics & Stem Cells Source Type: research

The characteristics and genome analysis of vB_ApiP_XC38, a novel phage infecting Acinetobacter pittii
In this study, a multidrug-resistantA. pittii ABC38 was used as host bacterium to isolate the lytic phage vB_ApiP_XC38. The biological characteristics of vB_ApiP_XC38 were studied and the genome was sequenced and analyzed. vB_ApiP_XC38 belonged toPodoviridae family. The phage had double-stranded genome, which comprised 79,328  bp with 39.58% G+C content displaying very low similarity (
Source: Virus Genes - May 25, 2020 Category: Genetics & Stem Cells Source Type: research

Analysis of viruses present in urine from patients with interstitial cystitis
AbstractThe question of whether some cases of interstitial cystitis may have an infectious etiology has been debated for some time. Previous studies have looked for the presence of certain specific viruses, but generally did not use the types of sensitive and unbiased approaches that are currently available. As part of the MAPP (Multidisciplinary Approach to the Study of Chronic Pelvic Pain) Research Network, we examined urine specimens from interstitial cystitis patients who provided specimens over time and also reported various symptoms at the time of urine collection. We first performed next-generation sequencing to loo...
Source: Virus Genes - May 23, 2020 Category: Genetics & Stem Cells Source Type: research

Genomic diversity and recombination of Seneca Valley viruses emerged in pig herds in Guangdong Province during 2019
AbstractSeneca Valley virus (SVV) is an emerging global picornavirus that causes porcine idiopathic vesicular disease. We characterized the genome and conducted evolutionary and recombination analyses of four newly identified SVV strains which were CH-GDZS-2019, CH-GDMZ-2019, CH-GDHZ01-2019, and CH-GDHZ02-2019. Sequence alignment and phylogenetic analysis showed that strains circulating in swine herds in China were genetically diverse and complex. Recombination analyses indicated that strain CH-GDZS-2019 was derived from strains USA-IA44662-2015-P1 and USA-GBI29-2015, which were both isolated in the USA in 2015, while CH-G...
Source: Virus Genes - May 23, 2020 Category: Genetics & Stem Cells Source Type: research

Genetic and antigenic characterization of H5 and H7 avian influenza viruses isolated from migratory waterfowl in Mongolia from 2017 to 2019
AbstractThe circulation of highly pathogenic avian influenza viruses (HPAIVs) of various subtypes (e.g., H5N1, H5N6, H5N8, and H7N9) in poultry remains a global concern for animal and public health. Migratory waterfowls play important roles in the transmission of these viruses across countries. To monitor virus spread by wild birds, active surveillance for avian influenza in migratory waterfowl was conducted in Mongolia from 2015 to 2019. In total, 5000 fecal samples were collected from lakesides in central Mongolia, and 167 influenza A viruses were isolated. Two H5N3, four H7N3, and two H7N7 viruses were characterized in ...
Source: Virus Genes - May 19, 2020 Category: Genetics & Stem Cells Source Type: research

Viruses of endophytic and pathogenic forest fungi
AbstractMycoviruses, just as the fungal endophytes they infect, are ubiquitous biological entities on Earth. Mycoviruses constitute a diverse group of viruses, and metagenomic approaches have —through recent discoveries of been mycoviruses—only recently began to provide evidence of this astonishing diversity. The current review presents (1) various mycoviruses which infect fungal endophytes and forest pathogens, (2) their presumed origins and interactions with fungi, plants and the e nvironment, (3) high-throughput sequencing techniques that can be used to explore the horizontal gene transfer of mycoviruses, an...
Source: Virus Genes - May 9, 2020 Category: Genetics & Stem Cells Source Type: research

Effects of gE/gI deletions on the miRNA expression of PRV-infected PK-15 cells
AbstractPseudorabies virus (PRV) belongs to the Alphaherpesvirinae subfamily of Herpesviridae. PRV-induced pseudorabies is a highly contagious disease that has caused huge economic losses to the global swine industry. The PRV gE/gI gene deletion vaccine strain (Fa ΔgE/gI strain) constructed from the PRV Fa wild-type strain was shown to have a protective effect against infection. However, the interaction between PRV gE/gI genes and host miRNA needs further exploration, and little is known about the regulatory mechanisms of non-coding RNAs during PRV infection . miRNAs play a key regulatory role in viral infection and ...
Source: Virus Genes - May 8, 2020 Category: Genetics & Stem Cells Source Type: research

A potent enzybiotic against methicillin-resistant Staphylococcus aureus
In this study, we cloned, expressed, and purified LysMR-5 fromS. aureus phage MR-5. In silico analysis revealed that LysMR-5 harbors two catalytic and one cell wall-binding domain. Biochemical characterization and LC –MS analysis showed that both catalytic domains were active and had no dependence on divalent ions for their action, Zn2+ exerted a negative effect. The optimal lytic activity of the endolysin was at 37  °C/pH 7.0 and in the presence of ≥ 300 mM concentration of NaCl. Circular dichroism (CD) demonstrated a loss in secondary structure with an increase in temperature confirming the ...
Source: Virus Genes - May 4, 2020 Category: Genetics & Stem Cells Source Type: research

Effect of viral DNA methylation on expression of hepatitis B virus proteins depends on the virus genotype
In conclusion, this study showed that the effect of HBV genomic methylation differs among HBV genotypes, suggesting a potential explanation for the different clinical outcomes of genotypes A, B, and C. (Source: Virus Genes)
Source: Virus Genes - May 2, 2020 Category: Genetics & Stem Cells Source Type: research

Crimean-Congo hemorrhagic fever virus infection triggers the upregulation of the Wnt signaling pathway inhibitor genes
AbstractCrimean-Congo hemorrhagic fever virus (CCHFV) is a highly pathogenic agent. Thus far, vaccines and specific antiviral therapies are not available against the threat of infection. Our knowledge regarding its pathogenesis is indeed limited, and thus, developing effective antiviral therapies is hampered. Several studies have demonstrated that the CCHFV infection has an impact on numerous signal transduction pathways. In parallel, the Wnt signaling pathway components are responsible for different important biological processes including cell fate determination, cell migration and cell polarity. Moreover, its implicatio...
Source: Virus Genes - April 25, 2020 Category: Genetics & Stem Cells Source Type: research

Isolation and characterization of new Puumala orthohantavirus strains from Germany
In conclusion, this is the first isolation of a PUUV strain from Central Europe and the generation of glycoprotein-specific monoclonal antibodies for this PUUV isolate . The obtained virus isolate and GPC-specific antibodies are instrumental tools for future reservoir host studies. (Source: Virus Genes)
Source: Virus Genes - April 23, 2020 Category: Genetics & Stem Cells Source Type: research

Identification of a novel bovine copiparvovirus in pooled fetal bovine serum
AbstractA novel parvovirus was identified as a cell culture contaminant by metagenomic analysis. Droplet digital PCR (ddPCR) was used to determine viral loads in the cell culture supernatant and further analysis, by ddPCR and DNA sequencing, demonstrated that fetal bovine serum (FBS) used during cell culture was the source of the parvovirus contamination. The FBS contained ~  50,000 copies of the novel parvovirus DNA per ml of serum. The viral DNA was resistant to DNAse digestion. Near-full length sequence of the novel parvovirus was determined. Phylogenetic analysis demonstrated that virus belongs to theCopiparvovi...
Source: Virus Genes - April 18, 2020 Category: Genetics & Stem Cells Source Type: research

Variability of E2 protein-coding sequences of bovine viral diarrhea virus in Polish cattle
In this study, and for the first time analysis was made of the E2 glycoprotein coding sequences of 14 Polish BVDV-1 strains which belong to four subtypes: 1b (n = 7), 1f (n = 3), 1s (n = 3), and 1r (n = 1). These sequences showed evidence of strong purifying (negative) selection. However, we also identified positively selected sites. The availability of E2 sequences of Polish BVDV strains for reference, knowledge gained through epitope prediction attempts, and information on protein glycosyl ation sites can afford a better understanding of host–pathogen interact...
Source: Virus Genes - April 16, 2020 Category: Genetics & Stem Cells Source Type: research

Genomic characterization of Changuinola viruses from Panama: evidence for multiple genome segment reassortment
AbstractThe complete coding sequences of five divergent strains of Changuinola virus (CGLV), collected over a 16-year period in Panama, were determined, using viral metagenomics. Each strain had 10 RNA segments that encoded structural and non-structural proteins with amino acid identities ranging from 33 to 99% with sequences of other 15 members of the Changuinola virus (Reoviridae: Orbivirus) species group. Genetic analyses of the five Panamanian virus strains revealed probable reassortment among multiple segments of the viruses. (Source: Virus Genes)
Source: Virus Genes - April 16, 2020 Category: Genetics & Stem Cells Source Type: research

Orientation-dependent toxic effect of human papillomavirus type 33 long control region DNA in Escherichia coli cells
In this study, we report an unexpected difficulty experienced when trying to clone HPV33 long control region (LCR) variants inEscherichia coli. Standard cloning strategies proved to be inappropriate to clone HPV33 LCR variants in the forward orientation into a eukaryotic reporter vector (pGL2-Basic). However, by slight modification of culture conditions (incubation at 25  °C instead of 37 °C), constructs containing the HPV33 LCR variants in the forward orientation were obtained. Transformation experiments performed with different HPV33 LCR constructs indicated that there is a sequence element in the 5&pri...
Source: Virus Genes - April 3, 2020 Category: Genetics & Stem Cells Source Type: research

Comparative analysis of CpG islands in equine infectious anemia virus strains
In this study, we compared the distribution of CpG islands among strains of equine infectious anemia virus (EIAV), a lentivirus in the family Retroviridae and a model for HIV research. We identified CpG islands in 32 full-length EIAV genomic sequences obtained from the GenBank database using MethPrimer. Only one CpG island, from 100 to 120  bp, was identified in the genomes of EIAV strains DV10, DLV3-A, and DLV5-10 from China, V26 and V70 from Japan, and IRE H3, IRE F2, IRE F3, and IRE F4 from Ireland. Importantly, the CpG island was located within theRev gene, which is required for the expression of viral cis-acting ...
Source: Virus Genes - April 1, 2020 Category: Genetics & Stem Cells Source Type: research

A phylogenetic study of new rabies virus strains in different regions of Iran
AbstractRabies is the most critical zoonotic disease in Iran, which imposes many extra costs on health care system in each country. The present study aimed to determine the molecular characteristics of the wild circulating strains of the rabies virus (RABV) collected in Iran during 2015 –2017. Rabies-suspected samples were collected from different regions of Iran and identified for RABV antigen confirmation using fluorescent antibody tests. Polymerase chain reaction (PCR) was performed on positive samples and gene sequencing was done on rabies nucleoprotein and glycoprotein gene s to determine the rabies molecul...
Source: Virus Genes - March 31, 2020 Category: Genetics & Stem Cells Source Type: research

Genetic sequence changes related to the attenuation of avian infectious bronchitis virus strain TW2575/98
AbstractThe attenuated avian infectious bronchitis virus (IBV), derived from a wild strain (TW2575/98w) in chicken embryos after 75 passages, is designed as a commercial vaccine strain (TW2575/98vac) to control the disease in Taiwan. The differences in viral infectivity, replication efficiency, and genome sequences between TW2575/98w and TW2575/98vac were determined and compared. TW2575/98vac caused earlier death of chicken embryos and had higher viral replication efficiency. Thirty amino acid substitutions resulting from 44 mutated nucleotides in the viral genome were found in TW2575/98vac. All of the molecular variations...
Source: Virus Genes - March 30, 2020 Category: Genetics & Stem Cells Source Type: research

Evolutionary and recombination analysis of porcine reproductive and respiratory syndrome isolates in China
AbstractSeven strains of porcine reproductive and respiratory syndrome virus (PRRSV) were isolated from 2014 to 2017 in the Shandong province of China and their genomes were sequenced and analyzed. Results showed that all seven of the isolates belong to PRRSV 2, and are clustered into four lineages (lineage 1, 3, 5 and 8) based on comparisons of the ORF5 gene. Comparative analysis of genomes and specific amino acid sites revealed that three of the strains (SDwh1402, SDwh1602 and SDwh1701) have evolved directly from modified live virus (MLV) JXA1-P80, TJM-F92 and IngelvacPRRS. Further recombination analysis revealed that tw...
Source: Virus Genes - March 20, 2020 Category: Genetics & Stem Cells Source Type: research

Comparison of third-generation sequencing approaches to identify viral pathogens under public health emergency conditions
This study provides a framework for designing the appropriate experiments that are likely to lead to accurate and rapid virus emergency response. (Source: Virus Genes)
Source: Virus Genes - March 19, 2020 Category: Genetics & Stem Cells Source Type: research

Interaction between Translocation-associated membrane protein 1 and σC protein of novel duck reovirus controls virus infectivity
This study confirms the important role TRAM1 during NDRV infection which can help develop new approaches f or NDRV disease prevention and control. (Source: Virus Genes)
Source: Virus Genes - March 16, 2020 Category: Genetics & Stem Cells Source Type: research

Epidemiological survey and genetic evolution of H3N2 subtype influenza viruses from stray dogs in Shanghai, China
In this study, we collected 693 nasal swab samples and 800 blood samples from stray dogs in animal shelters to survey canine influenza epidemiology and characterize the evolution of CIV H3N2 in Shanghai. We tested samples for canine influenza antibodies and canine influenza RNA in January –May, 2019, and the results showed that the positive rate was 17.62% by ELISA, 15.75% by microneutralization (MN) assay, and 18.51% by real time RT-PCR, respectively. We also performed phylogenetic and genomic analysis on six H3N2 CIV isolates. The H3N2 viruses which prevailed in Shanghai originat ed from Beijing and Jiangsu isolate...
Source: Virus Genes - February 27, 2020 Category: Genetics & Stem Cells Source Type: research

Genomic characterization of a novel bat-associated Circovirus detected in European Miniopterus schreibersii bats
We report the detection and full-genome molecular characterization of a novel bat-associated Circovirus identified in faecal samples ofMiniopterus schreibersii bats (Schreiber ’s bent-winged bats) from Sardinia, Italy. Full-genomic sequencing revealed a new putative member ofCircoviridae family, with a genome size of 2063  nt. Sequencing allowed the characterization of the two major ORFs, inversely arranged, encoding replicase and capsid proteins, as well as the finding of a polythymidine tract within the genome, and highlighted phylogenetic relationships of the novel virus. This is the first report of circoviru...
Source: Virus Genes - February 22, 2020 Category: Genetics & Stem Cells Source Type: research

Antivirals in medical biodefense
AbstractThe viruses historically implicated or currently considered as candidates for misuse in bioterrorist events are poxviruses, filoviruses, bunyaviruses, orthomyxoviruses, paramyxoviruses and a number of arboviruses causing encephalitis, including alpha- and flaviviruses. All these viruses are of concern for public health services when they occur in natural outbreaks or emerge in unvaccinated populations. Recent events and intelligence reports point to a growing risk of dangerous biological agents being used for nefarious purposes. Public health responses effective in natural outbreaks of infectious disease may not be...
Source: Virus Genes - February 19, 2020 Category: Genetics & Stem Cells Source Type: research

Inherited chromosomally integrated HHV-6 possibly modulates human gene expression
AbstractApproximately, 1% of human population possesses a copy of human herpesvirus 6A and 6B (HHV-6A/B) in the genome. This viral element is referred to as inherited chromosomally integrated HHV-6A/B (iciHHV-6A/B) and is encoded in all of their cells. A recent study revealed that iciHHV-6A/B potentially increases the immune responses against HHV-6. However, it remains unclear whether iciHHV-6A/B affects human gene expression. Here, we perform global transcriptome analysis using the datasets obtained from various human tissues. We detected two and four individuals positive for iciHHV-6A and iciHHV-6B, respectively, and rev...
Source: Virus Genes - February 17, 2020 Category: Genetics & Stem Cells Source Type: research

Discovery and molecular characterization of a novel trichovirus infecting sweet cherry
AbstractContigs with the highest sequence similarity (73%) toApricot pseudo-chlorotic leaf spot virus (genusTrichovirus, familyBetaflexiviridae) were identified by high-throughput sequencing from a symptomless sweet cherry accession. The complete genome sequence of this new virus is 7460 nucleotides, excluding the 3 ′ poly(A) tail. Its genome organization is very similar to several trichoviruses infecting fruit trees, with three open reading frames encoding putative replicase, movement protein and coat protein (CP). The virus shares amino acid sequence identities of 60–73% at replicase and 53–76% at CP wi...
Source: Virus Genes - February 17, 2020 Category: Genetics & Stem Cells Source Type: research

Molecular evolution of GII.P17-GII.17 norovirus associated with sporadic acute gastroenteritis cases during 2013 –2018 in Zhoushan Islands, China
In this study, we investigated the molecular characteristics and spatio-temporal dynamics of GII.P17-GII.17 norovirus in Zhoushan Islands during 2013 –2018. We collected 1849 samples from sporadic acute gastroenteritis patients between January 2013 and August 2018 in Zhoushan Islands, China. Among the 1849 samples, 134 (7.24%) samples were positive for human norovirus (HuNoV). The complete sequence of GII.17 VP1 gene was amplified from 31 HuNoV -positive samples and sequenced. A phylogenetic tree was constructed based on the full-length sequence of the VP1 gene. Phylogenetic analysis revealed that the GII.17 genotype...
Source: Virus Genes - February 17, 2020 Category: Genetics & Stem Cells Source Type: research

Approaches to optimize therapeutic bacteriophage and bacteriophage-derived products to combat bacterial infections
This article presents a short overview of the clinical phage application including their use in military medicine and discusses the genotypic and phenotypic properties of a potential “ideal” therapeutic phage. We describe current efforts to engineer phage for their improved usability in pathogen treatment. In addition, phage can be applied for pathogen detection, selective drug delivery, vaccine development, or food and surface decontamination. Instead of viable phage, (engi neered) phage-derived enzymes, such as polysaccharide depolymerases or peptidoglycan-degrading enzymes, are considered as promising therap...
Source: Virus Genes - February 8, 2020 Category: Genetics & Stem Cells Source Type: research

Molecular identification of novel and genetically diverse adenoviruses in Passeriform birds
AbstractKnowledge about adenoviruses in birds of the order Passeriformes is very scarce. Based on molecular characterizations, only two siadenoviruses, great tit adenovirus 1 and Gouldian finch adenovirus, have been described so far occurring in great tits and Gouldian finches, respectively. Assuming a broader occurrence of adenoviruses, various passeriform birds including pet, zoo, and wild birds were examined using a broad-range PCR targeting a fragment of the adenovirus DNA polymerase gene. Adenoviruses were detected in 25 individual birds belonging to 13 species and seven zoological families (Ploceidae, Fringillidae, E...
Source: Virus Genes - February 7, 2020 Category: Genetics & Stem Cells Source Type: research

Development of a colloidal gold-based immunochromatographic strip test using two monoclonal antibodies to detect H7N9 avian influenza virus
AbstractH7N9 low pathogenic avian influenza viruses (AIVs) emerged in China in 2013 and mutated into highly pathogenic strains in 2017, causing disease in infected birds and humans. Thus, the development of rapid, specific, and sensitive detection methods is urgently required. Herein, two specific monoclonal antibodies against H7N9 AIV were produced to develop a colloidal gold-based immunochromatographic test strip to detect H7N9 AIV. High specificity, repeatability, and sensitivity were achieved, with a detection limit of two hemagglutinin units or 102.55 50% tissue culture infective dose. This assay may represent a power...
Source: Virus Genes - February 7, 2020 Category: Genetics & Stem Cells Source Type: research

Genetic variants in Argentinean isolates of Spodoptera frugiperda Multiple Nucleopolyhedrovirus
AbstractThe fall armyworm,Spodoptera frugiperda (JE Smith) is a key pest in the Americas. Control strategies are mainly carried out by use of chemical insecticides and transgenic crops expressingBacillus thuringiensis toxins. In the last years, resistance ofS. frugiperda populations to transgenic corn was reported in different Latin American countries. The baculovirusSpodoptera frugiperda Multiple Nucleopolyhedrovirus (SfMNPV) is a pathogenic agent for the fall armyworm and a potential alternative for its control in integrated pest management strategies. In this work, we analyze some characteristics of two baculovirus isol...
Source: Virus Genes - February 6, 2020 Category: Genetics & Stem Cells Source Type: research

Genetic characterization of bovine ephemeral fever virus in southern China, 2013 –2017
AbstractBovine ephemeral fever virus (BEFV) can cause bovine ephemeral fever and is an economically important arbovirus of cattle. To expand the knowledge of the molecular epidemiology of BEFV in southern China, the complete surface glycoprotein G gene of BEFV was sequenced from samples collected in five restricted outbreaks from 2013 to 2017, namely 2013ZH, 2014HM, 2015GX, 11082-2016, and qy2017. It was noted that both 2014HM and 11082-2016 were detected in cattle regularly vaccinated with inactivated vaccine. Phylogenetic analysis demonstrated that all five strains grouped into cluster I. However, qy2017 was closer to th...
Source: Virus Genes - February 6, 2020 Category: Genetics & Stem Cells Source Type: research

Peculiarities in the designations of hepatitis B virus genes, their products, and their antigenic specificities: a potential source of misunderstandings
AbstractThe nomenclature of the hepatitis B virus (HBV) genes and their products has developed stepwise, occasionally in an erratic way, creating many misunderstandings, especially among those who do not know the structure of HBV and its genome in detail. One of the most frequent misunderstandings, even presented in leading journals, is the designation of HBV “e”-antigen asenvelope orearly antigen. Another problem area are the so-called “pre” regions in the HBV genome present upstream of both the core and the surface genes of HBV, inadvertently suggesting that they may be a part of correspondingprec...
Source: Virus Genes - February 6, 2020 Category: Genetics & Stem Cells Source Type: research

Detection, genetic, and codon usage bias analyses of the VP2 gene of mink bocavirus
This study provides evidence that MiBoV1 has a low prevalence in Jilin and Hebei provinces in China. Moreover, it contributes information regarding the expansion of the limited mink bocavirus sequence and determines the codon usage bias of the VP2 gene for the first time. Epidemiological surveillance is necessary to understand the importance and evolution of MiBoV1. (Source: Virus Genes)
Source: Virus Genes - February 4, 2020 Category: Genetics & Stem Cells Source Type: research

Human polyomavirus modulation of the host DNA damage response
Abstract The human DNA damage response (DDR) is a complex signaling network constituting many factors responsible for the preservation of genomic integrity. Human polyomaviruses (HPyVs) are able to harness the DDR machinery during their infectious cycle by expressing an array of tumor (T) antigens. These molecular interactions between human polyomavirus T antigens and the DDR create conditions that promote viral replication at the expense of host genomic stability to cause disease as well as carcinogenesis in the cases of the Merkel cell polyomavirus and BK polyomavirus. This review focuses on the six HPyVs with disease ...
Source: Virus Genes - January 29, 2020 Category: Genetics & Stem Cells Source Type: research

The ea22 gene of lambdoid phages:  preserved prolysogenic function despite of high sequence diversity
In this study, we provided evidence thatea22, the largest gene of this region, favors the lysogenic pathway over the lytic pathway in contrast to other characterizedexo-xis region genes includingea8.5,orf61, orf60a, andorf63. Our assays also suggest some functional analogies between Ea22 and the phage integrase protein (Int). While it is unsurprising that Ea22 operates similarly in both λ and Stx phages, we have observed some distinctions that may arise from considerable sequence dissimilarity at the carboxy termini of each protein. (Source: Virus Genes)
Source: Virus Genes - January 22, 2020 Category: Genetics & Stem Cells Source Type: research

Development of a reverse transcription loop-mediated isothermal amplification assay (RT-LAMP) that detects enteroviruses by targeting the highly conserved 5 ′-UTR region
In this study, we developed a rapid, simple, sensitive, and specific isothermal reverse transcription assay (RT-Loop -Mediated Amplification, RT-LAMP) for the detection ofEV-A, B, C, and D species of enteroviruses, by targeting the highly conserved 5 ′UTR region. The assay was designed and validated based on reference sequences of the four species and on clinical and environmental isolates. The limit of detection of the assay is 0.75 CCID50/assay forEnterovirus A, B, andD and 0.075 CCID50/assay forEnterovirus C. LAMP allows immediate diagnosis in just 30 –50 min, instead of a minimum of 120 min needed...
Source: Virus Genes - January 18, 2020 Category: Genetics & Stem Cells Source Type: research

Phylogenetic analysis of rabies viruses isolated from cattle in southern Brazil
AbstractBats and dogs are the main reservoirs of rabies virus (RABV) in Latin America and are responsible for the maintenance of different cycles of infection. In the two neighbour and most southern Brazilian states of Rio Grande do Sul (RS) and Santa Catarina (SC), rabies in dogs has been successfully controlled for more than 30  years. However, rabies associated to the rural cycle remains endemic, with a significant, though oscillating—annual incidence of rabies in cattle. Despite the plethora of studies on genetic analyses of Brazilian RABV, isolates from southern Brazil have only scarcely been investigated. ...
Source: Virus Genes - January 18, 2020 Category: Genetics & Stem Cells Source Type: research

Human immunodeficiency virus type-1 Tat protein induces secretory leukocyte protease inhibitor expression in African green monkey but not human cells
AbstractAfrican monkeys are resistant to HIV-1 infection due to intrinsic restriction mechanisms found in their cells. However, although they can be infected by monkey-adapted modified HIV-1 particles that are designed to overcome known restriction factors, virus numbers drop to undetectable levels in immunocompetent animals. These results indicate the possibility of the presence of yet unidentified factor(s) that restrict HIV-1 in old-world monkey (OWM) cells after integration of the viral genome into the host cell chromosome. In the light of these findings, we hypothesized that OWMs might have evolved resistance mechanis...
Source: Virus Genes - January 10, 2020 Category: Genetics & Stem Cells Source Type: research

Screening pigs for xenotransplantation in China: investigation of porcine endogenous retrovirus in Diannan small-eared pigs
AbstractPorcine endogenous retrovirus (PERV), which integrates as a provirus into the genome of pig cells, is an important biosafety issue in xenotransplantation. Screening and analyzing the presence and expression of PERV will provide essential parameters for assessing the biosafety of donor sources. In the present study, we investigated the prevalence of PERV in Diannan small-eared pigs, a unique closed colony that is distributed in southern Yunnan Province in southwestern China. PCR was performed to amplifyenv-A, env-B, env-C, pol, gag, and mtDNA in peripheral blood samples. The results revealed that PERVenv-A, env-B, p...
Source: Virus Genes - January 8, 2020 Category: Genetics & Stem Cells Source Type: research

Characterization of a distinct variant of hop stunt viroid and a new apscaviroid detected in grapevines
AbstractUsing next-generation sequencing, we detected a novel variant of hop stunt viroid (HSVd) in grapevine ‘Chenin blanc’ (Vitis vinifera L.) and a new viroid species in ‘Nachubearmarie’ (Vitis labrusca L.  × V. vinifera). The HSVd variant termed HSVd-CB has 296 nucleotides with up to 82% sequence identity with other HSVd variants such as HSVd-AP1 (Genbank accession EF523826). Many nucleotide changes, deletions, and insertions were sporadically found in HSVd-CB relative to HSVd-AP1 in the pathogenic and variable domains. Although several variations were also found in the centr...
Source: Virus Genes - January 8, 2020 Category: Genetics & Stem Cells Source Type: research

Whole-genome sequencing and comparative transcriptome analysis of Bombyx mori nucleopolyhedrovirus La strain
AbstractThe Bombyx mori nucleopolyhedrovirus (BmNPV) La is a variant BmNPV strain isolated in Laos. La has different features from BmNPV type strain T3 in virulence, production of the polyhedrin protein, and the formation of multicapsid occlusion-derived viruses. Here, the whole-genome sequence of La was compared to the sequences of nine BmNPV and two Bombyx mandarina nucleopolyhedrovirus strains. The complete La genome consisted of 127,618 base pairs with a G  + C content of 40.3% and contained putative 136 open reading frames encoding more than 60 amino acids. The La genome lacked thebro-b gene and had the ...
Source: Virus Genes - January 7, 2020 Category: Genetics & Stem Cells Source Type: research

Genomic and biological characterization of a pandemic norovirus variant GII.4 Sydney 2012
In this study, we isolated a GII.4 NoV strain (designated 2015HN08) from a kid presenting with acute gastroenteritis and determined its near-complete genome sequence. We then performed sequence analysis by comparing this strain with the prototypical GII.4 strain. Virus-like particles (VLPs) derived from the major capsid protein (VP1) were expressed by using a recombinant-baculovirus expression system, and monoclonal antibodies (mAbs) were produced to compare changes in antigenic or histo-blood group antigens (HBGAs) binding sites with the previously characterized GII.4 NoV strain (JZ403). The genome of 2015HN08 was 7559 nu...
Source: Virus Genes - January 7, 2020 Category: Genetics & Stem Cells Source Type: research

Identification and characterisation of common glow-worm RNA viruses
AbstractThe common glow-worms (Lampyris noctiluca) are best known for emission of green light by their larvae and sexually active adult females. However, both their DNA and RNA viruses remain unknown. Glow-worms are virologically interesting, as they are non-social and do not feed as adults, and hence their viral transmission may be limited. We identified viral sequences from 11 different virus taxa by the RNA-sequencing of two Finnish populations of adult glow-worms. The viruses represent nine different virus families and have negative, positive, or double-stranded RNA genomes. We also found a complete retroviral genome. ...
Source: Virus Genes - January 3, 2020 Category: Genetics & Stem Cells Source Type: research

Integration of hepatitis B virus DNA into p21-activated kinase 3 (PAK3) gene in HepG2.2.15 cells
This study may provide a novel insight into the elucidation of etiology of HBV integration. (Source: Virus Genes)
Source: Virus Genes - January 2, 2020 Category: Genetics & Stem Cells Source Type: research

Changes in the G N /G C of the M segment show positive selection and recombination of one aggressive isolate and two mild isolates of tomato spotted wilt virus
AbstractWe isolated and compared three tomato spotted wilt virus (TSWV) isolates from lettuce (TSWV-Let), pepper (TSWV-Pep), and tomato (TSWV-Tom) from central Mexico to determine their ability to infect a set of eighteen differential plant species from seven families. TWSV-Let was an aggressive isolate with the ability to infect up to 52% of the differential plants, including maize, under greenhouse conditions. The nucleotide (nt) sequences of the three isolates are more than 90% similar in the M and S RNA segments. In the M segment of the TSWV-Let isolate, we detected nt changes in their intergenic region (IGR) and, in t...
Source: Virus Genes - January 2, 2020 Category: Genetics & Stem Cells Source Type: research

Single amino acid substitutions in the coat protein and RNA-dependent RNA polymerase alleviated the virulence of Cucumber green mottle mosaic virus and conferred cross protection against severe infection
The objective of this paper was to screen attenuated mutants of CGMMV and evaluate their potential in cross protection. An infectious cDNA clone of CGMMV, pCGMMV, was obtained by cloning intron-containing CGMMV genome to modified pCambia0390 vector with theCauliflower mosaic virus 35S promoter. Five pCGMMV-derived mutants were obtained via site-directed mutagenesis and inoculated toNicotiana benthamiana plants for symptom observation. The attenuated CGMMV mutants were evaluated for their efficiency in cross protection. The intron-containing clone pCGMMV induced similar disease symptoms and accumulated similar titres of vir...
Source: Virus Genes - January 1, 2020 Category: Genetics & Stem Cells Source Type: research

Cytokines and chemokines involved in the defense reaction against HIV-1 and hepatitis B virus: isn ’t it time to use a standardized nomenclature of the involved mediators?
AbstractDiscovery of new mediators of immune cell activation and interaction facilitated elucidation of the various ways of defense against infectious agents and happened some 40  years ago. Each involved group of researchers named the mediators according to their scope of investigation; often the same molecules were published at the same time with different names. To avoid confusion resulting from using different names for the same mediators and to prevent a Babylonian con fusion, standardization was implemented—as in the field of metrics, music, or science including virology. For cytokines and chemokines a sta...
Source: Virus Genes - December 17, 2019 Category: Genetics & Stem Cells Source Type: research