Next generation sequencing of southern African Crimean-Congo haemorrhagic fever virus isolates

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.

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Using next generation sequencing to identify yellow fever virus in Uganda

Virology ◽

10.1016/j.virol.2011.08.024 ◽

2012 ◽

Vol 422 (1) ◽

pp. 1-5 ◽

Cited By ~ 34

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

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Comparative analysis of the L, M, and S RNA segments of Crimean-Congo haemorrhagic fever virus isolates from southern Africa

Journal of Medical Virology ◽

10.1002/jmv.24079 ◽

2015 ◽

Vol 87 (5) ◽

pp. 717-724 ◽

Cited By ~ 4

Author(s):

Dominique Goedhals ◽

Phillip A. Bester ◽

Janusz T. Paweska ◽

Robert Swanepoel ◽

Felicity J. Burt

Keyword(s):

Comparative Analysis ◽

Southern Africa ◽

Fever Virus ◽

Haemorrhagic Fever ◽

Crimean Congo Haemorrhagic Fever ◽

Virus Isolates

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Use of Next Generation Sequencing to study two cowpox virus outbreaks

PeerJ ◽

10.7717/peerj.6561 ◽

2019 ◽

Vol 7 ◽

pp. e6561 ◽

Cited By ~ 4

Author(s):

Markus H. Antwerpen ◽

Enrico Georgi ◽

Alexandra Nikolic ◽

Gudrun Zoeller ◽

Peter Wohlsein ◽

...

Keyword(s):

Next Generation Sequencing ◽

Group Method ◽

Common Source ◽

Cowpox Virus ◽

Next Generation ◽

Single Strain ◽

Hemagglutinin Gene ◽

Hospital Acquired ◽

Virus Isolates ◽

Generation Sequencing

BackgroundBetween 2008 and 2011 about 40 cases of human cowpox were reported from Germany and France. Infections had been acquired via close contact to infected, young pet rats. An identical and unique sequence of the hemagglutinin gene was found in various cowpox virus (CPXV) isolates pointing to a common source of infection. In a second CPXV outbreak in cats in a small animal clinic in Germany in 2015, four out of five hospitalized cats showed identical hemagglutinin sequences and thus, a hospital-acquired transmission had been assumed. Next-Generation Sequencing was performed in order to re-investigate the outbreaks, as epidemiological data could not confirm all cases.MethodsHomogenates of lesion material from rats, cats and humans were cultivated in cell culture. The genomes of four virus isolates, nine CPXVs from our strain collections and from DNA of three paraffin-embedded lesion materials were determined by Next Generation Sequencing (NGS). For phylogenetic analyses a MAFFT-alignment was generated. A distance matrix based on concatenated SNPs was calculated and plotted as dendrogram using Unweighted Pair Group Method with Arithmetic mean (UPGMA) for visualization.ResultsAligning of about 200.000 nucleotides of 8 virus isolates associated with the pet rat outbreak revealed complete identity of six genomes, the remainder two genomes differed in as little as 3 SNPs. When comparing this dataset with four already published CPXV genomes also associated with the pet rat outbreak, again a maximum difference of 3 SNPs was found. The outbreak which lasted from 2008 till 2011 was indeed caused by a single strain which has maintained an extremely high level of clonality over 4 years. Aligning genomic sequences from four cases of feline cowpox revealed 3 identical sequences and one sequence which differed in 65 nucleotides. Although identical hemagglutinin sequences had been obtained from four hospitalized cats, genomic sequencing proved that a hospital-acquired transmission had occurred in only three cats.ConclusionAnalyzing the rather short sequence of the hemagglutinin gene is not sufficient to conduct molecular trace back analyses. Instead, whole genome sequencing is the method of choice which can even be applied to paraffin-embedded specimens.

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Generic amplification and next generation sequencing reveal Crimean-Congo hemorrhagic fever virus AP92-like strain and distinct tick phleboviruses in Anatolia, Turkey

Parasites & Vectors ◽

10.1186/s13071-017-2279-1 ◽

2017 ◽

Vol 10 (1) ◽

Cited By ~ 21

Author(s):

Ender Dinçer ◽

Annika Brinkmann ◽

Olcay Hekimoğlu ◽

Sabri Hacıoğlu ◽

Katalin Földes ◽

...

Keyword(s):

Next Generation Sequencing ◽

Hemorrhagic Fever ◽

Fever Virus ◽

Next Generation ◽

Crimean Congo Hemorrhagic Fever ◽

Hemorrhagic Fever Virus ◽

Generation Sequencing

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

Journal of Virology ◽

10.1128/jvi.00106-19 ◽

2019 ◽

Vol 93 (13) ◽

Cited By ~ 2

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.

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Use of Next Generation Sequencing to study two cowpox virus outbreaks

10.1101/444141 ◽

2018 ◽

Author(s):

Markus H. Antwerpen ◽

Enrico Georgi ◽

Alexandra Nikolic ◽

Gudrun Zöller ◽

Peter Wohlsein ◽

...

Keyword(s):

Next Generation Sequencing ◽

Cowpox Virus ◽

Next Generation ◽

Single Strain ◽

Horizon 2020 ◽

Research And Innovation ◽

Hemagglutinin Gene ◽

Hospital Acquired ◽

Virus Isolates ◽

Generation Sequencing

AbstractBackgroundBetween 2008 and 2011 about 40 cases of human cowpox were reported from Germany and France. Infections had been acquired via close contact to infected, young pet rats. Sequencing of the hemagglutinin gene of various cowpox virus (CPXV) isolates resulted in an identical and unique sequence in each case pointing to a common source. In a second CPXV outbreak in cats in a small animal clinic in Germany in 2015, four out of five hospitalized cats showed identical hemagglutinin sequences and thus, a hospital-acquired transmission was assumed.MethodsHomogenates of lesion material from rats, cats and humans were cultivated in cell culture. The genomes of 4 virus isolates, 9 CPXVs from our strain collections and from DNA of 3 paraffin-embedded lesion materials were determined by Next Generation Sequencing (NGS). For phylogenetic analyses a MAFFT-alignment was generated. A distance matrix based on concatenated SNPs was calculated and plotted as dendrogram using Unweighted Pair Group Method with Arithmetic mean (UPGMA) for visualization.ResultsAligning of about 200.000 nucleotides of 8 virus isolates associated with the pet rat outbreak revealed complete identity of six genomes, the remainder two genomes differed in as little as 3 SNPs. When comparing this dataset with four already published CPXV genomes also associated with the pet rat outbreak, again a maximum difference of 3 SNPs was found. The outbreak which lasted from 2008 till 2011 was indeed caused by a single strain which has maintained an extremely high level of clonality over 4 years.Aligning genomic sequences from 4 cases of feline cowpox revealed 3 identical sequences and one sequence which differed in 65 nucleotides. Although identical hemagglutinin sequences had been obtained from four hospitalized cats, genomic sequencing proved that a hospital-acquired transmission had occurred in only three cats.DiscussionAnalyzing the rather short sequence of the hemagglutinin gene is not sufficient to conduct molecular trace back analyses. Instead, whole genome sequencing is the method of choice which can even be applied to paraffin-embedded specimens.Funding StatementThis publication was supported by the European Virus Archive goes Global (EVAg) project that has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No 653316.This study was also supported in part by the European Union’s Horizon 2020 research and innovation program under grant agreement No 643476 (COMPARE).The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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

Genome Announcements ◽

10.1128/genomea.01006-17 ◽

2017 ◽

Vol 5 (37) ◽

Cited By ~ 2

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.

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