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

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 Characterization of Novel Reoviruses Wad Medani Virus (Orbivirus) and Kundal Virus (Coltivirus) Collected fromHyalomma anatolicumTicks in India during Surveillance for Crimean Congo Hemorrhagic Fever

2019 ◽  
Vol 93 (13) ◽  
Author(s):  
Pragya D. Yadav ◽  
Shannon L. M. Whitmer ◽  
Prasad Sarkale ◽  
Terry Fei Fan Ng ◽  
Cynthia S. Goldsmith ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Common Ancestor ◽  
Hemorrhagic Fever ◽  
Fever Virus ◽  
Hyalomma Anatolicum ◽  
Next Generation ◽  
Crimean Congo Hemorrhagic Fever ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

ABSTRACTIn 2011, ticks were collected from livestock following an outbreak of Crimean Congo hemorrhagic fever (CCHF) in Gujarat state, India. CCHF-negativeHyalomma anatolicumtick pools were passaged for virus isolation, and two virus isolates were obtained, designated Karyana virus (KARYV) and Kundal virus (KUNDV), respectively. Traditional reverse transcription-PCR (RT-PCR) identification of known viruses was unsuccessful, but a next-generation sequencing (NGS) approach identified KARYV and KUNDV as viruses in theReoviridaefamily,OrbivirusandColtivirusgenera, respectively. Viral genomes werede novoassembled, yielding 10 complete segments of KARYV and 12 nearly complete segments of KUNDV. The VP1 gene of KARYV shared a most recent common ancestor with Wad Medani virus (WMV), strain Ar495, and based on nucleotide identity we demonstrate that it is a novel WMV strain. The VP1 segment of KUNDV shares a common ancestor with Colorado tick fever virus, Eyach virus, Tai Forest reovirus, and Tarumizu tick virus from theColtivirusgenus. Based on VP1, VP6, VP7, and VP12 nucleotide and amino acid identities, KUNDV is proposed to be a new species ofColtivirus. Electron microscopy supported the classification of KARYV and KUNDV as reoviruses and identified replication morphology consistent with other orbi- and coltiviruses. The identification of novel tick-borne viruses carried by the CCHF vector is an important step in the characterization of their potential role in human and animal pathogenesis.IMPORTANCETicks and mosquitoes, as wellCulicoides, can transmit viruses in theReoviridaefamily. With the help of next-generation sequencing (NGS), previously unreported reoviruses such as equine encephalosis virus, Wad Medani virus (WMV), Kammavanpettai virus (KVPTV), and, with this report, KARYV and KUNDV have been discovered and characterized in India. The isolation of KUNDV and KARYV fromHyalomma anatolicum, which is a known vector for zoonotic pathogens, such as Crimean Congo hemorrhagic fever virus,Babesia,Theileria, andAnaplasmaspecies, identifies arboviruses with the potential to transmit to humans. Characterization of KUNDV and KARYV isolated fromHyalommaticks is critical for the development of specific serological and molecular assays that can be used to determine the association of these viruses with disease in humans and livestock.

scholarly journals Testing the genomic stability of the Brazilian yellow fever vaccine strain using next-generation sequencing data

2021 ◽  
Vol 11 (4) ◽  
pp. 20200063 ◽  
Author(s):  
Amanda Araújo Serrão de Andrade ◽  
André E. R. Soares ◽  
Luiz Gonzaga Paula de Almeida ◽  
Luciane Prioli Ciapina ◽  
Cristiane Pinheiro Pestana ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Next Generation Sequencing ◽  
Yellow Fever ◽  
Vaccine Strain ◽  
Next Generation Sequencing Data ◽  
Diversity Analysis ◽  
Vaccine Production ◽  
Next Generation ◽  
Genetic Diversity Analysis ◽  
Generation Sequencing

The live attenuated yellow fever (YF) vaccine was developed in the 1930s. Currently, the 17D and 17DD attenuated substrains are used for vaccine production. The 17D strain is used for vaccine production by several countries, while the 17DD strain is used exclusively in Brazil. The cell passages carried out through the seed-lot system of vaccine production influence the presence of quasispecies causing changes in the stability and immunogenicity of attenuated genotypes by increasing attenuation or virulence. Using next-generation sequencing, we carried out genomic characterization and genetic diversity analysis between vaccine lots of the Brazilian YF vaccine, produced by BioManguinhos–Fiocruz, and used during 11 years of vaccination in Brazil. We present 20 assembled and annotated genomes from the Brazilian 17DD vaccine strain, eight single nucleotide polymorphisms and the quasispecies spectrum reconstruction for the 17DD vaccine, through a pipeline here introduced. The V2IDA pipeline provided a relationship between low genetic diversity, maintained through the seed lot system, and the confirmation of genetic stability of lots of the Brazilian vaccine against YF. Our study sets precedents for use of V2IDA in genetic diversity analysis and in silico stability investigation of attenuated viral vaccines, facilitating genetic surveillance during the vaccine production process.

Labordiagnostik bei gastrointestinalen Tumoren

2020 ◽  
Vol 11 (05) ◽  
pp. 232-238
Author(s):  
Marcus Kleber
Keyword(s):  
Next Generation Sequencing ◽  
Kolorektales Karzinom ◽  
Next Generation ◽  
Generation Sequencing

ZUSAMMENFASSUNGDas kolorektale Karzinom (KRK) ist einer der häufigsten malignen Tumoren in Deutschland. Einer frühzeitigen Diagnostik kommt große Bedeutung zu. Goldstandard ist hier die Koloskopie. Die aktuelle S3-Leitlinie Kolorektales Karzinom empfiehlt zum KRK-Screening den fäkalen okkulten Bluttest. Für das Monitoring von Patienten vor und nach Tumorresektion werden die Messung des Carcinoembryonalen Antigens (CEA) und der Mikrosatellitenstabilität empfohlen. Für die Auswahl der korrekten Chemotherapie scheint derzeit eine Überprüfung des Mutationsstatus, mindestens des KRAS-Gens und des BRAF-Gens, sinnvoll zu sein. Eine Reihe an neuartigen Tumormarkern befindet sich momentan in der Entwicklung, hat jedoch noch nicht die Reife für eine mögliche Anwendung in der Routinediagnostik erreicht. Den schnellsten Weg in die breite Anwendung können Next-Generation-Sequencing-basierte genetische Tests finden.

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