scholarly journals Next-generation sequencing of southern African Crimean-Congo haemorrhagic fever virus isolates reveals a high frequency of M segment reassortment

2014 ◽  
Vol 142 (9) ◽  
pp. 1952-1962 ◽  
Author(s):  
D. GOEDHALS ◽  
P. A. BESTER ◽  
J. T. PAWESKA ◽  
R. SWANEPOEL ◽  
F. J. BURT
Keyword(s):  
Next Generation Sequencing ◽  
High Frequency ◽  
Complete Genome ◽  
Fever Virus ◽  
Likelihood Method ◽  
Haemorrhagic Fever ◽  
Next Generation ◽  
Genome Sequences ◽  
Crimean Congo Haemorrhagic Fever ◽  
Generation Sequencing

SUMMARYCrimean Congo haemorrhagic fever virus (CCHFV) is a bunyavirus with a single-stranded RNA genome consisting of three segments (S, M, L), coding for the nucleocapsid protein, envelope glycoproteins and RNA polymerase, respectively. To date only five complete genome sequences are available from southern African isolates. Complete genome sequences were generated for 10 southern African CCHFV isolates using next-generation sequencing techniques. The maximum-likelihood method was used to generate tree topologies for 15 southern African plus 26 geographically distinct complete sequences from GenBank. M segment reassortment was identified in 10/15 southern African isolates by incongruencies in grouping compared to the S and L segments. These reassortant M segments cluster with isolates from Asia/Middle East, while the S and L segments cluster with strains from South/West Africa. The CCHFV M segment shows a high level of genetic diversity, while the S and L segments appear to co-evolve. The reason for the high frequency of M segment reassortment is not known. It has previously been suggested that M segment reassortment results in a virus with high fitness but a clear role in increased pathogenicity has yet to be shown.

scholarly journals Complete Genome Sequences, Derived by Next-Generation Sequencing, of JC Polyomavirus Strains Isolated from Vietnamese Renal Transplant Recipients

2020 ◽  
Vol 9 (2) ◽  
Author(s):  
Trang Dinh Van ◽  
Rebecca J. Rockett ◽  
An Phan Hai Ha ◽  
Trung Vu Nguyen ◽  
Dominic E. Dwyer
Keyword(s):  
Next Generation Sequencing ◽  
Renal Transplant ◽  
Complete Genome ◽  
Rolling Circle Amplification ◽  
Renal Transplant Recipients ◽  
Transplant Recipients ◽  
Next Generation ◽  
Genome Sequences ◽  
Jc Polyomavirus ◽  
Generation Sequencing

JC polyomavirus (JCPyV) may cause clinical syndromes such as progressive multifocal leukoencephalopathy in immunocompromised patients. Here, we report seven complete genome sequences of JCPyV genotype 7A, generated directly from urine samples from Vietnamese renal transplant recipients by using rolling-circle amplification and next-generation sequencing.

scholarly journals Evolutionary study of maize dwarf mosaic virus using nearly complete genome sequences acquired by next-generation sequencing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dulanjani Wijayasekara ◽  
Akhtar Ali
Keyword(s):  
Next Generation Sequencing ◽  
Mosaic Virus ◽  
Complete Genome ◽  
Evolutionary Relationship ◽  
Fixation Index ◽  
Maize Dwarf Mosaic Virus ◽  
Next Generation ◽  
Genome Sequences ◽  
The Usa ◽  
Generation Sequencing

AbstractNext-generation sequencing is a robust approach to sequence plant virus genomes in a very short amount of time compared to traditional sequencing methods. Maize dwarf mosaic virus (MDMV) is one of the most important plant viruses worldwide and a significant threat to maize production. In this study, we sequenced 19 MDMV isolates (10 from Johnsongrass and 9 from maize) collected in Oklahoma and Missouri during 2017–2019 using Illumina sequencing and determined the genetic diversity. Sequence reads were assembled and 19 nearly complete genome sequences of MDMV isolates were obtained. Phylogenetic analysis based on complete genomes nucleotide and amino acid sequences revealed two main clusters and a close evolutionary relationship among 19 MDMV isolates. Statistical analysis of individual genes for site-specific selection revealed that all genes are under negative selection. The fixation index (FST) analysis of the MDMV isolates revealed no gene flow between the two main phylogenetic clusters, which emphasizes the divergence of MDMV isolates from the USA. Among the USA MDMV isolates, the mean genetic distance (d) and nucleotide diversity ((π) were highest in the P1 gene coding region. This is the first detailed study on the evolutionary relationship of MDMV isolates based on the nearly complete genome analysis from maize and Johnsongrass.

scholarly journals Next-Generation Sequencing Reveals the First Complete Genome Sequence of Cowpea aphid-borne mosaic virus from Uganda

2018 ◽  
Vol 6 (3) ◽  
Author(s):  
E. K. Mbeyagala ◽  
P. Tukamuhabwa ◽  
J. Bisikwa ◽  
T. Holton ◽  
S. B. Mukasa
Keyword(s):  
Next Generation Sequencing ◽  
Mosaic Virus ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Indian Isolate ◽  
Next Generation ◽  
Genome Sequences ◽  
Cowpea Aphid ◽  
Generation Sequencing

ABSTRACT We present here the first complete genome sequence of Cowpea aphid-borne mosaic virus (CABMV) isolated from cowpea in Uganda and compare it with five CABMV complete genome sequences from Brazil (2), India (2), and Zimbabwe (1). It most resembled the genomes of two Brazilian isolates (MG-Avr and BR1) and one Indian isolate (RR3).

scholarly journals Near-Complete Genome Sequences of Vesicular Stomatitis Virus Indiana Laboratory Strains HR and T1026R1 and Plaque Isolates 22-20 and 22-25

2019 ◽  
Vol 8 (14) ◽  
Author(s):  
Thomas M. Russell ◽  
Evan E. Santo ◽  
Lisa Golebiewski ◽  
Nathan S. Haseley ◽  
Maureen C. Ferran
Keyword(s):  
Next Generation Sequencing ◽  
Vesicular Stomatitis Virus ◽  
Complete Genome ◽  
Next Generation ◽  
M Gene ◽  
Genome Sequences ◽  
Heat Resistant ◽  
Vesicular Stomatitis ◽  
Generation Sequencing

We report four near-complete genome sequences of vesicular stomatitis virus (VSV) Indiana obtained with Sanger and Illumina next-generation sequencing, namely, laboratory strains HR (heat resistant) and T1026R1 and isolates 22-20 and 22-25. Previously, only the M gene of these viruses had been sequenced, and these sequences were not deposited in GenBank.

scholarly journals Complete Genome Sequences of Two Vesicular Stomatitis Virus Isolates Collected in Mexico

2017 ◽  
Vol 5 (37) ◽  
Author(s):  
Lauro Velazquez-Salinas ◽  
Pavel Isa ◽  
Steven J. Pauszek ◽  
Luis L. Rodriguez
Keyword(s):  
New Jersey ◽  
Next Generation Sequencing ◽  
Vesicular Stomatitis Virus ◽  
Complete Genome ◽  
Full Genome ◽  
Next Generation ◽  
Genome Sequences ◽  
Vesicular Stomatitis ◽  
Virus Isolates ◽  
Generation Sequencing

ABSTRACT We report two full-genome sequences of vesicular stomatitis New Jersey virus (VSNJV) obtained by Illumina next-generation sequencing of RNA isolated from epithelial suspensions of cattle naturally infected in Mexico. These genomes represent the first full-genome sequences of vesicular stomatitis New Jersey viruses circulating in Mexico deposited in the GenBank database.

scholarly journals Complete Genome Sequences of Six Measles Virus Strains

2018 ◽  
Vol 6 (13) ◽  
Author(s):  
My V. T. Phan ◽  
Claudia M. E. Schapendonk ◽  
Bas B. Oude Munnink ◽  
Marion P. G. Koopmans ◽  
Rik L. de Swart ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Complete Genome ◽  
Measles Virus ◽  
Genetic Characterization ◽  
Critical Component ◽  
Wild Type ◽  
Genome Sequences ◽  
Virus Strains ◽  
Generation Sequencing

ABSTRACT Genetic characterization of wild-type measles virus (MV) strains is a critical component of measles surveillance and molecular epidemiology. We have obtained complete genome sequences of six MV strains belonging to different genotypes, using random-primed next generation sequencing.

scholarly journals Using next generation sequencing to identify yellow fever virus in Uganda

Virology ◽  
2012 ◽  
Vol 422 (1) ◽  
pp. 1-5 ◽  
Author(s):  
Laura K. McMullan ◽  
Mike Frace ◽  
Scott A. Sammons ◽  
Trevor Shoemaker ◽  
Stephen Balinandi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Yellow Fever ◽  
Yellow Fever Virus ◽  
Fever Virus ◽  
Next Generation ◽  
Generation Sequencing

Screening of an Indian cohort with breast and/or ovarian cancer by a next-generation sequencing-based panel to detect a high frequency of mutations.

2015 ◽  
Vol 33 (15_suppl) ◽  
pp. e12505-e12505
Author(s):  
Ashraf U Mannan ◽  
Jaya Singh ◽  
Rupali Gadkari ◽  
Ravikiran Lakshmikeshava ◽  
Payal Manek ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Next Generation Sequencing ◽  
High Frequency ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Complete Genome Sequence of a Novel Human Gammapapillomavirus Isolated from Skin

2017 ◽  
Vol 5 (34) ◽  
Author(s):  
Rosario N. Brancaccio ◽  
Alexis Robitaille ◽  
Sankhadeep Dutta ◽  
Dana E. Rollison ◽  
Nicole Fischer ◽  
...  
Keyword(s):  
Human Papillomavirus ◽  
Next Generation Sequencing ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Open Reading Frame ◽  
Next Generation ◽  
Degenerate Pcr ◽  
Reading Frame ◽  
Generation Sequencing

ABSTRACT A novel human papillomavirus (HPV ICB1) was fully characterized from a skin swab by using a sensitive degenerate PCR protocol combined with next-generation sequencing. The L1 open reading frame of HPV ICB1 shares 70.54% nucleotide homology with its closest relative, HPV164, and thus constitutes a novel human gammapapillomavirus.

Sign in / Sign up

Export Citation Format

Share Document