Deciphering transmission dynamics and spillover of avian influenza viruses from avian species to swine populations globally
AbstractGenome sequences of eleven avian influenza virus (AIV) subtypes have been reported in swine populations from seven countries until August 2020. To unravel the transmission dynamics and spillover events of AIVs from avian reservoirs to swine, full-length hemagglutinin (HA) sequences of AIV subtypes (n = 11) reported from various avian species and swine were retrieved from the ‘Influenza Research Database’. Phylogenetic analysis identified closely related avian and swine AIV sequences suggesting potential spillover events from multiple domestic and wild avian species, including chicken, d uck, pigeon, goose, ...
Source: Virus Genes - October 8, 2021 Category: Genetics & Stem Cells Source Type: research
Sensitivity of two SARS-CoV-2 variants with spike protein mutations to neutralising antibodies
AbstractSARS-CoV-2 infections elicit a humoral immune response capable of neutralising the virus. However, multiple variants have emerged with mutations in the spike protein amongst others, the key target of neutralising antibodies. We evaluated the neutralising efficacy of 89 serum samples from patients, infected with SARS-CoV-2 in the beginning of 2020, against two virus variants isolated from acutely infected patients and harbouring spike protein mutations. One isolate was assigned to lineage B.1.351 (MUC-IMB-B.1.351) whilst the other (MUC-484) was isolated from an immunocompromised patient, sharing some but not all mut...
Source: Virus Genes - October 4, 2021 Category: Genetics & Stem Cells Source Type: research
Genome characterization of fig umbra-like virus
AbstractThe complete genome of a new umbra-like virus from edible fig (Ficus carica) was identified by high-throughput sequencing. Based on its similarity to umbra-like virus genome sequences available in GenBank, the proposed name of this new virus is “fig umbra-like virus” (FULV). The genome of full-length FULV-1 consists of 3049 nucleotides organized into three open reading frames (ORFs). Pairwise comparisons showed that the complete nucleotide sequence of the virus had the highest identity (71.3%) to citrus yellow vein-associated virus (CY VaV). In addition, phylogenetic trees based on whole-genome nucleotide seque...
Source: Virus Genes - September 15, 2021 Category: Genetics & Stem Cells Source Type: research
Molecular epidemiology of respiratory syncytial virus among children and adults in India 2016 to 2018
This study intended to determine the circulating genotypes of RSV among severe acute respiratory illness (SARI) cases during the period 2016–2018 in India, among hospitalized acute febrile illness cases of age ranging from 1 to 65 years. Throat/nasopharyngeal swab samples were subjected for testing RSV and subgroups by real-time reverse transcriptase polymerase chain reaction (RT-PCR), further sequencing and phylogenetic analysis were performed for the second hypervariable region of the G gene. RSV-A and B subtypes co-circulated during the years 2016, 2017, a nd 2018, with RSV-A as the dominant subtype in 2016, and RSV-...
Source: Virus Genes - September 15, 2021 Category: Genetics & Stem Cells Source Type: research
G1-like PB2 gene improves virus replication and competitive advantage of H9N2 virus
AbstractH9N2 subtype avian influenza virus has dramatically evolved and undergone extensive reassortment since its emergence in early 1990s in China. The genotype S (G57), emerging in 2007 with the substitution of F98-like PB2 and M gene by G1-like ones, has become the overwhelming predominant genotype for the past 11 years since 2010. Here, we found that virus with G1-like PB2 were more efficient in protein expression and in infectious virus production than that with F98-like PB2 gene. By coinfected MDCK cells with the reassortant virus, more survival opportunity for viruses with G1-like PB2 than that of F/98- like was ...
Source: Virus Genes - September 14, 2021 Category: Genetics & Stem Cells Source Type: research
Host proviral and antiviral factors for SARS-CoV-2
AbstractThroughout the viral life cycle, interplays between cellular host factors and virus determine the infectious capacity of the virus. The pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a great threat to human life and health. Extensive studies identified a number of host proviral and antiviral factors for SARS-CoV-2. In this review, we summarize the current understanding of the interplay between SARS-CoV-2 and cellular factors during virus entry and replication. Our review will highlight the future direction of study on the infection and pa...
Source: Virus Genes - September 11, 2021 Category: Genetics & Stem Cells Source Type: research
Correction to: Complete genome sequence of a recombinant isolate of yambean mosaic virus from Canavalia ensiformis
(Source: Virus Genes)
Source: Virus Genes - September 3, 2021 Category: Genetics & Stem Cells Source Type: research
A SARS-CoV-2 mutant from B.1.258 lineage with ∆H69/∆V70 deletion in the Spike protein circulating in Central Europe in the fall 2020
AbstractSARS-CoV-2 mutants carrying the ∆H69/∆V70 deletion in the amino-terminal domain of the Spike protein emerged independently in at least six lineages of the virus (namely, B.1.1.7, B.1.1.298, B.1.160, B.1.177, B.1.258, B.1.375). We analyzed SARS-CoV-2 samples collected from various regions of Slovakia between November and Decemb er 2020 that were presumed to contain B.1.1.7 variant due to drop-out of the Spike gene target in an RT-qPCR test caused by this deletion. Sequencing of these samples revealed that although in some cases the samples were indeed confirmed as B.1.1.7, a substantial fraction of samples conta...
Source: Virus Genes - August 27, 2021 Category: Genetics & Stem Cells Source Type: research
Distinct interferon response in bat and other mammalian cell lines infected with Pteropine orthoreovirus
We examined the innate immune response against PRV and assessed viral replication in cell lines derived from four bat species (Miniopterus fuliginosus,Pteropus dasymallus,Rhinolophus ferrumequinum, andRousettus leschenaultii), one rodent (Mesocricetous auratus), and human (Homo sapiens). The expression levels of pattern recognition receptors (PRRs) (TLR3,RIG-I, and MDA5) and interferons (IFNB1 andIFNL1) were higher and PRV replication was lower in cell lines derived fromM. fuliginosus,R. ferrumequinum, andR. leschenaultii. Reduction ofIFNB1 expression by the knockdown of PRRs in the cell line derived fromR. ferrumequinum w...
Source: Virus Genes - August 25, 2021 Category: Genetics & Stem Cells Source Type: research
Complete genome sequence of a recombinant isolate of yambean mosaic virus from Canavalia ensiformis
AbstractThe complete genome sequence of a Brazilian isolate of yambean mosaic virus (YBMV) is presented. High-throughput sequencing (Illumina HiSeq) and Sanger sequencing revealed the complete genome sequence of the YBMV-BRA-6 isolate, found inCanavalia ensiformis. The de novo contigs were assembled into a 9612 nucleotides (nt) long scaffold, excluding the 3 ’-terminal poly(A) tail, covering the complete genome. The genomic RNA contains an open reading frame (ORF) typical of members of the genusPotyvirus, familyPotyviridae, encoding a large putative polyprotein of 3078 amino acids (aa) and a small overlapping PIPO ORF. P...
Source: Virus Genes - August 20, 2021 Category: Genetics & Stem Cells Source Type: research
The Citrus yellow mosaic badnavirus ORFI functions as a RNA-silencing suppressor
AbstractCitrus yellow mosaic badnavirus (CMBV) causes mosaic disease in all economically important citrus cultivars of India, with losses reaching up to 70%. CMBV belongs to the genusBadnavirus, familyCaulimoviridae, possessing a circular double-stranded (ds) DNA genome with six open reading frames (ORFs I to VI), whose functions are yet to be deciphered. The RNA-silencing suppressor (RSS) activity has not been assigned to any CMBV ORF as yet. In the present study, it was found that ORFI exhibited RSS activity among all the six CMBV ORFs tested. Studies were done by employing the well-established Agrobacterium-mediated tra...
Source: Virus Genes - August 11, 2021 Category: Genetics & Stem Cells Source Type: research
Development of a dual-labeled, hydrolysis probe-based, real-time quantitative PCR assay for detection of both genotypes of duck circovirus-1 (DuCV-1) and DuCV-2
In this study, we developed a real-time quantitative polymerase chain reaction (qPCR) assay based on a dual-labeled hydrolysis probe to simultaneously detect both duck circovirus (DuCV) 1 and DuCV-2. The reproducibility, sensitivity and specificity of the primer set and probe were evaluated using other duck pathogens. The detection limit was 20 copies per µL. The intra-assay coefficients of variation (CVs) were ≤ 0.73% and the inter-assay CVs were ≤ 1.89%. No cross-reaction occurred with other duck pathogens. In addition, the qPCR assay was successfully applied to the simultaneous detection of DuCV-1 and DuCV-...
Source: Virus Genes - July 26, 2021 Category: Genetics & Stem Cells Source Type: research
Complete genome sequences of infectious spleen and kidney necrosis virus isolated from farmed albino rainbow sharks Epalzeorhynchos frenatum in the United States
This study is the first report of ISKNV in albino rainbow sharks. (Source: Virus Genes)
Source: Virus Genes - July 17, 2021 Category: Genetics & Stem Cells Source Type: research
Phylogenetic and evolutionary analysis of foot-and-mouth disease virus A/ASIA/Sea-97 lineage
AbstractFoot-and-mouth disease virus (FMDV) A/ASIA/Sea-97 is a predominant lineage in Southeast Asia and East Asia. However, Sea-97 lineage has not been well studied since its first outbreak in Thailand in 1997. Thus, we conducted phylogenetic and evolutionary analysis of Sea-97 using 224 VP1 sequences of FMDV A/ASIA during 1960 and 2018. Phylogenetic analysis revealed that Sea-97 lineage can be classified into five groups (G1 –G5). After the emergence of G2 from G1, the genetic diversity of Sea-97 increased sharply, causing divergence into G3, G4 and G5. During this evolutionary process, Sea-97 lineage, which was initia...
Source: Virus Genes - July 14, 2021 Category: Genetics & Stem Cells Source Type: research
A novel one-step amplification refractory mutation system PCR (ARMS-PCR) for differentiation of canine parvovirus-2 variants
AbstractEnteritis caused by CPV-2 antigenic variants (CPV-2a, 2b, and 2c) is frequently reported in dogs worldwide leading to significant morbidity and mortality. Here, we describe about a simple, single-step, ARMS-PCR strategy targeting the mutant 426 amino acid of VP2 to differentiate CPV-2 antigenic types. A total of 150 fecal samples were subjected to ARMS-PCR of which 18 were typed as CPV-2a, 79 were typed as CPV-2b, and 6 were typed as CPV-2c. The ARMS-PCR results were validated by randomly sequencing partialVP2 gene of 14 samples. Phylogenetic analysis of partialVP2 gene sequencing of each of the CPV-2 variants reve...
Source: Virus Genes - July 13, 2021 Category: Genetics & Stem Cells Source Type: research
