Urinary genome detection and tracking of Hantaan virus from hemorrhagic fever with renal syndrome patients using multiplex PCR-based next-generation sequencing

Background Hantavirus infection occurs through the inhalation of aerosolized excreta, including urine, feces, and saliva of infected rodents. The presence of Hantaan virus (HTNV) RNA or infectious particles in urine specimens of patient with hemorrhagic fever with renal syndrome (HFRS) remains to be investigated. Methodology/Principal findings We collected four urine and serum specimens of Republic of Korea Army (ROKA) patients with HFRS. We performed multiplex PCR-based next-generation sequencing (NGS) to obtain the genome sequences of clinical HTNV in urine specimens containing ultra-low amounts of viral genomes. The epidemiological and phylogenetic analyses of HTNV demonstrated geographically homogenous clustering with those in Apodemus agrarius captured in highly endemic areas, indicating that phylogeographic tracing of HTNV genomes reveals the potential infection sites of patients with HFRS. Genetic exchange analyses showed a genetic configuration compatible with HTNV L segment exchange in nature. Conclusion/Significance Our results suggest that whole or partial genome sequences of HTNV from the urine enabled to track the putative infection sites of patients with HFRS by phylogeographically linking to the zoonotic HTNV from the reservoir host captured at endemic regions. This report raises awareness among physicians for the presence of HTNV in the urine of patients with HFRS.

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Phylogeographic analysis of hemorrhagic fever with renal syndrome patients using multiplex PCR-based next generation sequencing

Scientific Reports ◽

10.1038/srep26017 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 13

Author(s):

Won-Keun Kim ◽

Jeong-Ah Kim ◽

Dong Hyun Song ◽

Daesang Lee ◽

Yong Chul Kim ◽

...

Keyword(s):

Next Generation Sequencing ◽

Multiplex Pcr ◽

Hemorrhagic Fever ◽

Next Generation ◽

Phylogeographic Analysis ◽

Generation Sequencing

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Genotyping and Molecular Diagnosis of Hepatitis A Virus in Human Clinical Samples Using Multiplex PCR-Based Next-Generation Sequencing

Microorganisms ◽

10.3390/microorganisms10010100 ◽

2022 ◽

Vol 10 (1) ◽

pp. 100

Author(s):

Geum-Young Lee ◽

Won-Keun Kim ◽

Seungchan Cho ◽

Kyungmin Park ◽

Jongwoo Kim ◽

...

Keyword(s):

Next Generation Sequencing ◽

Multiplex Pcr ◽

Molecular Diagnosis ◽

Hepatitis A ◽

Hepatitis A Virus ◽

Severe Illness ◽

Whole Genome ◽

Next Generation ◽

Genome Sequences ◽

Generation Sequencing

Hepatitis A virus (HAV) is a serious threat to public health worldwide. We used multiplex polymerase chain reaction (PCR)-based next-generation sequencing (NGS) to derive information on viral genetic diversity and conduct precise phylogenetic analysis. Four HAV genome sequences were obtained using multiplex PCR-based NGS. HAV whole-genome sequence of one sample was obtained by conventional Sanger sequencing. The HAV strains demonstrated a geographic cluster with sub-genotype IA strains in the Republic of Korea. The phylogenetic pattern of HAV viral protein (VP) 3 region showed no phylogenetic conflict between the whole-genome and partial-genome sequences. The VP3 region in serum and stool samples showed sensitive detection of HAV with differences of quantification that did not exceed <10 copies/μL than the consensus VP4 region using quantitative PCR (qPCR). In conclusion, multiplex PCR-based NGS was implemented to define HAV genotypes using nearly whole-genome sequences obtained directly from hepatitis A patients. The VP3 region might be a potential candidate for tracking the genotypic origin of emerging HAV outbreaks. VP3-specific qPCR was developed for the molecular diagnosis of HAV infection. This study may be useful to predict for the disease management and subsequent development of hepatitis A infection at high risk of severe illness.

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Anchored multiplex PCR enables detection of internal tandem duplications in FLT3 by next-generation sequencing

10.26226/morressier.578f37ffd462b8028d88fe2e ◽

2016 ◽

Author(s):

Marc Roland Bessette

Keyword(s):

Next Generation Sequencing ◽

Multiplex Pcr ◽

Next Generation ◽

Generation Sequencing ◽

Tandem Duplications

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Comparison of three human papillomavirus DNA detection methods: Next generation sequencing, multiplex-PCR and nested-PCR followed by Sanger based sequencing

Journal of Medical Virology ◽

10.1002/jmv.24413 ◽

2015 ◽

Vol 88 (5) ◽

pp. 888-894 ◽

Cited By ~ 14

Author(s):

Allex Jardim da Fonseca ◽

Renata Silva Galvão ◽

Angelica Espinosa Miranda ◽

Luiz Carlos de Lima Ferreira ◽

Zigui Chen

Keyword(s):

Human Papillomavirus ◽

Next Generation Sequencing ◽

Multiplex Pcr ◽

Nested Pcr ◽

Dna Detection ◽

Detection Methods ◽

Next Generation ◽

Papillomavirus Dna ◽

Generation Sequencing

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

Epidemiology and Infection ◽

10.1017/s0950268814000818 ◽

2014 ◽

Vol 142 (9) ◽

pp. 1952-1962 ◽

Cited By ~ 15

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.

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