scholarly journals Molecular Characterization of Novel Cucurbit Aphid Borne Yellows Virus Strains Infecting Squash and Watermelon in India

2022 ◽  
Author(s):  
Nagendran Krishnan ◽  
Shweta Kumari ◽  
Koshlendra Kumar Pandey ◽  
Sudhakar Pandey ◽  
Tusar Kanti Behera ◽  
...  
Keyword(s):  
Asian American ◽  
Recombinant Strain ◽  
Sequence Similarity ◽  
Uttar Pradesh ◽  
Amino Acid Sequences ◽  
Full Length ◽  
Rt Pcr ◽  
Genome Sequences ◽  
Species Demarcation Threshold ◽  
Full Length Genome

Abstract The pathogen responsible for yellowing and downward rolling of leaves of squash and watermelon plants from Uttar Pradesh state, India, was identified as probably strains of Cucurbit aphid-borne yellows virus (CABYV) through RT-PCR using universal Polerovirus primers followed by sequencing. The full-length genome sequences of an isolate from squash (POL-SQ - 5650 nt) and one from watermelon (POL-WM - 5647nt) were determined by sequencing the products from RT-PCR with six sets of primers with overlapping products. Sequence comparison and phylogenetic analysis showed that these isolates had closest identity with a recombinant strain obtained between CABYV and Melon aphid-borne yellows virus (MABYV) reported from Taiwan infecting Luffa aegyptiaca (CABYV-R-TW82) rather than other Asian, American, or European isolates. The deduced amino acid sequences of the P0, P1 and P1-P2 proteins showed >10% variation, whereas the P3, P4 and P3-P5 proteins showed <10% variation when compared to the corresponding proteins of other strains of CABYV worldwide. Thus, according to the Polerovirus species demarcation threshold, these new sequences should be regarded as representing strains of a novel previously undescribed Polerovirus species. However, based on their sequence similarity and phylogenetic grouping with the recombinant strain from Taiwan we suggest these sequences represent recombinant strains of CABYV. These are the first full-length genome sequences for CABYV strains from India and this study adds watermelon as host for CABYV in India.

scholarly journals Full-Length Genome Sequences of Recombinant and Nonrecombinant Sympatric Strains of Rice yellow mottle virus from Western Kenya

2018 ◽  
Vol 6 (8) ◽  
Author(s):  
Antony Kigaru Adego ◽  
Nils Poulicard ◽  
Agnès Pinel-Galzi ◽  
Benard Mukoye ◽  
Denis Fargette ◽  
...  
Keyword(s):  
Full Length ◽  
Mottle Virus ◽  
Rice Yellow Mottle Virus ◽  
Genome Sequences ◽  
Western Kenya ◽  
Yellow Mottle ◽  
Full Length Genome

ABSTRACT Five isolates of Rice yellow mottle virus from western Kenya were fully sequenced. One isolate of strain S4lv had been collected in 1966. Two isolates belonged to the emerging strain S4ug recently described in Uganda. Two isolates collected in 2012 are putative recombinants between the S4lv and S4ug strains.

scholarly journals Natural infection of Atlantic salmon (Salmo salar L.) with salmonid alphavirus 3 generates numerous viral deletion mutants

2013 ◽  
Vol 94 (9) ◽  
pp. 1945-1954 ◽  
Author(s):  
Elin Petterson ◽  
Marit Stormoen ◽  
Øystein Evensen ◽  
Aase B. Mikalsen ◽  
Øyvind Haugland
Keyword(s):  
Atlantic Salmon ◽  
Salmo Salar ◽  
Natural Infection ◽  
Sequence Divergence ◽  
Heart Tissue ◽  
Full Length ◽  
Deletion Mutants ◽  
Genome Sequences ◽  
Pancreas Disease ◽  
Full Length Genome

Salmon pancreas disease virus (SPDV) also referred to as salmonid alphavirus (SAV) is a virus causing pancreas disease in Atlantic salmon (Salmo salar L.) and rainbow trout (Oncorhynchus mykiss). Although the virus causes an economically important disease, relatively few full-length genome sequences of SAV strains are currently available. Here, we report full-length genome sequences of nine SAV3 strains from sites farming Atlantic salmon geographically spread along the Norwegian coastline. The virus genomes were sequenced directly from infected heart tissue, to avoid culture selection bias. Sequence analysis confirmed a high level of sequence identity within SAV3 strains, with a mean nucleotide diversity of 0.11 %. Sequence divergence was highest in 6K and E2, while lowest in the capsid protein and the non-structural proteins (nsP4 and nsP2). This study reports for the first time that numerous defective viruses containing genome deletions are generated during natural infection with SAV. Deletions occurred in all virus strains and were not distributed randomly throughout the genome but instead tended to aggregate in certain areas. We suggest imprecise homologous recombination as an explanation for generation of defective viruses with genome deletions. The presence of such viruses, provides a possible explanation for the difficulties in isolating SAV in cell culture. Primary virus isolation was successfully achieved for only two of eight strains, despite extensive attempts using three different cell lines. Both SAV isolates were easily propagated further and concomitant viral deletion mutants present in clinically infected heart tissue were maintained following serial passage in CHH-1 cells.

scholarly journals The full-length genome sequences of nine HCV genotype 4 variants representing a new subtype 4s and eight unclassified lineages

Virology ◽  
2015 ◽  
Vol 482 ◽  
pp. 111-116 ◽  
Author(s):  
Ling Lu ◽  
Yan Xu ◽  
Jie Yuan ◽  
Chunhua Li ◽  
Donald G. Murphy
Keyword(s):  
Full Length ◽  
Genome Sequences ◽  
Genotype 4 ◽  
Hcv Genotype ◽  
Full Length Genome

scholarly journals The Analysis of Near Full-Length Genome Sequences of HIV Type 1 Subtype A Viruses from Russia Supports the Monophyly of Major Intrasubtype Clusters

2012 ◽  
Vol 28 (10) ◽  
pp. 1340-1343 ◽  
Author(s):  
Aurora Fernández-García ◽  
Ana Revilla ◽  
Elena Vázquez-de Parga ◽  
Anna Vinogradova ◽  
Aza Rakhmanova ◽  
...  
Keyword(s):  
Full Length ◽  
Genome Sequences ◽  
Hiv Type 1 ◽  
Subtype A ◽  
Full Length Genome

scholarly journals The Cryptococcus neoformans GeneDHA1 Encodes an Antigen That Elicits a Delayed-Type Hypersensitivity Reaction in Immune Mice

2000 ◽  
Vol 68 (11) ◽  
pp. 6196-6201 ◽  
Author(s):  
M. Alejandra Mandel ◽  
Greg G. Grace ◽  
Kris I. Orsborn ◽  
Fredda Schafer ◽  
Juneann W. Murphy ◽  
...  
Keyword(s):  
Amino Acid ◽  
Cryptococcus Neoformans ◽  
Culture Filtrate ◽  
Genomic Library ◽  
Amino Acid Sequences ◽  
Full Length ◽  
Delayed Type Hypersensitivity ◽  
Pcr Analysis ◽  
Rt Pcr ◽  
Fruiting Body Formation

ABSTRACT When mice are vaccinated with a culture filtrate fromCryptococcus neoformans (CneF), they mount a protective cell-mediated immune response as detected by dermal delayed-type hypersensitivity (DTH) to CneF. We have identified a gene (DHA1) whose product accounts at least in part for the DTH reactivity. Using an acapsular mutant (Cap-67) of C. neoformans strain B3501, we prepared a culture filtrate (CneF-Cap67) similar to that used for preparing the commonly used skin test antigen made with C. neoformans 184A (CneF-184A). CneF-Cap67 elicited DTH in mice immunized with CneF-184A. Deglycosylation of CneF-Cap67 did not diminish its DTH activity. Furthermore, size separation by either chromatography or differential centrifugation identified the major DTH activity of CneF-Cap67 to be present in fractions that contained proteins of approximately 19 to 20 kDa. Using N-terminal and internal amino acid sequences derived from the 20-kDa band, oligonucleotide primers were designed, two of which produced a 776-bp amplimer by reverse transcription-PCR (RT-PCR) using RNA from Cap-67 to prepare cDNA for the template. The amplimer was used as a probe to isolate clones containing the full-lengthDHA1 gene from a phage genomic library prepared from strain B3501. The full-length cDNA was obtained by 5′ rapid amplification of cDNA ends and RT-PCR. Analysis of DHA1 revealed a similarity between the deduced open reading frame and that of a developmentally regulated gene from Lentinus edodes(shiitake mushroom) associated with fruiting-body formation. Also, the gene product contained several amino acid sequences identical to those determined biochemically from the purified 20-kDa peptide encoded byDHA1. Recombinant DHA1 protein expressed inEscherichia coli was shown to elicit DTH reactions similar to those elicited by CneF-Cap67 in mice immunized against C. neoformans. Thus, DHA1 is the first gene to be cloned from C. neoformans whose product has been shown to possess immunologic activity.

Near-Full-Length Genome Sequences of a Novel HIV-1 Circulating Recombinant Form, CRF01_AE/B′/C (CRF78_cpx), in Yunnan, China

2016 ◽  
Vol 32 (6) ◽  
pp. 601-606 ◽  
Author(s):  
Yindi Song ◽  
Yue Feng ◽  
Zhijiang Miao ◽  
Binghui Wang ◽  
Ming Yang ◽  
...  
Keyword(s):  
Full Length ◽  
Recombinant Form ◽  
Genome Sequences ◽  
Full Length Genome ◽  
Hiv 1
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