The use of next generation sequencing in the diagnosis and typing of respiratory infections

Thorburn, Fiona; Bennett, Susan E.; Modha, Sejal; Murdoch, David R.; Gunson, Rory; Murcia, Pablo R.

doi:10.1016/j.jcv.2015.06.082

Cited by 107 publications

(124 citation statements)

References 19 publications

(19 reference statements)

Supporting

Mentioning

107

Contrasting

Unclassified

Order By: Relevance

“…The literature is very limited regarding such comparisons of threshold sensitivity of qPCR and NGS. Still, a recent study showed that reverse transcription qPCR required less PCR cycle to give a upper threshold signal than NGS (Illumina MiSeq), when targeting viral DNA (23 Ct against 32 Ct in average, respectively, and corresponding to a difference of about 3 Log units) (Thorburn et al, 2015). …”

Section: Discussionmentioning

confidence: 99%

Human-Driven Microbiological Contamination of Benthic and Hyporheic Sediments of an Intermittent Peri-Urban River Assessed from MST and 16S rRNA Genetic Structure Analyses

et al. 2017

View full text Add to dashboard Cite

Rivers are often challenged by fecal contaminations. The barrier effect of sediments against fecal bacteria was investigated through the use of a microbial source tracking (MST) toolbox, and by Next Generation Sequencing (NGS) of V5-V6 16S rRNA gene (rrs) sequences. Non-metric multi-dimensional scaling analysis of V5-V6 16S rRNA gene sequences differentiated bacteriomes according to their compartment of origin i.e., surface water against benthic and hyporheic sediments. Classification of these reads showed the most prevalent operating taxonomic units (OTU) to be allocated to Flavobacterium and Aquabacterium. Relative numbers of Gaiella, Haliangium, and Thermoleophilum OTU matched the observed differentiation of bacteriomes according to river compartments. OTU patterns were found impacted by combined sewer overflows (CSO) through an observed increase in diversity from the sewer to the hyporheic sediments. These changes appeared driven by direct transfers of bacterial contaminants from wastewaters but also by organic inputs favoring previously undetectable bacterial groups among sediments. These NGS datasets appeared more sensitive at tracking community changes than MST markers. The human-specific MST marker HF183 was strictly detected among CSO-impacted surface waters and not river bed sediments. The ruminant-specific DNA marker was more broadly distributed but intense bovine pollution was required to detect transfers from surface water to benthic and hyporheic sediments. Some OTU showed distribution patterns in line with these MST datasets such as those allocated to the Aeromonas, Acinetobacter, and Pseudomonas. Fecal indicators (Escherichia coli and total thermotolerant coliforms) were detected all over the river course but their concentrations were not correlated with MST ones. Overall, MST and NGS datasets suggested a poor colonization of river sediments by bovine and sewer bacterial contaminants. No environmental outbreak of these bacterial contaminants was detected.

show abstract

Section: Discussionmentioning

confidence: 99%

Human-Driven Microbiological Contamination of Benthic and Hyporheic Sediments of an Intermittent Peri-Urban River Assessed from MST and 16S rRNA Genetic Structure Analyses

et al. 2017

View full text Add to dashboard Cite

show abstract

“…During 2002 and 2003, cell culture isolation studies and neutralization tests were used to recover cytopathic isolates and identify HAdVs. In this study, applying next generation sequencing (NGS) in pathogen identification, we sequenced the genomes of the cytopathic isolates which were originally produced in 2002 for further viral identification. The thorough investigation of throat specimens using viral culture, antisera neutralization assays, NGS, and genome‐wide phylogenetic analysis shed light on the origin and evolution of respiratory viruses, circulation of HAdV4 and non‐HAdV4 viruses and the outbreak potential by non‐HAdV pathogens in U.S. military trainees.…”

Section: Introductionmentioning

confidence: 99%

Adenovirus type 4 respiratory infections with a concurrent outbreak of coxsackievirus A21 among United States Army Basic Trainees, a retrospective viral etiology study using next‐generation sequencing

Hang

Vento

Norby

et al. 2017

Journal of Medical Virology

View full text Add to dashboard Cite

Human adenoviruses (HAdV), in particular types 4 and 7, frequently cause acute respiratory disease (ARD) during basic military training. HAdV4 and HAdV7 vaccines reduced the ARD risk in U.S. military. It is important to identify other respiratory pathogens and assess their potential impact on military readiness. In 2002, during a period when the HAdV vaccines were not available, throat swabs were taken from trainees (n = 184) with respiratory infections at Fort Jackson, South Carolina. Viral etiology was investigated initially with viral culture and neutralization assay and recently in this study by sequencing the viral isolates. Viral culture and neutralization assays identified 90 HAdV4 isolates and 27 additional cultures that showed viral cytopathic effects (CPE), including some with picornavirus-like CPE. Next-generation sequencing confirmed these results and determined viral genotypes, including 77 HAdV4, 4 HAdV3, 1 HAdV2, 17 coxsackievirus A21 (CAV21), and 1 enterovirus D68. Two samples were positive for both HAdV4 and CAV21. The identified genotypes are phylogenetically close to but distinct from those found during other years or in other military/non-military sites. HAdV4 is the predominant respiratory pathogen in unvaccinated military trainee. HAdV4 has temporal and demographic variability. CAV21 is a significant respiratory pathogen and needs to be evaluated for its current significance in military basic trainees.

show abstract

“…11,12 Using the NGS technology, the whole-genome sequencing of viruses, such as Schmallenberg virus, Dengue virus, enterovirus, and respiratory syncytial virus, has been completed. [13][14][15] This approach is cost effective and highly efficient for the recovery of viral genome sequences, taking advantage of the detection and characterization of viral genomes and viral metagenomics. 16,17 Sequence-independent, single-primer amplification (SISPA) is a methodology to synthesize and enrich viral genomes using random hexamer and SISPA sequences (5′-GCCGGAGCTCTGCAGATATC-3′).…”

Section: Introductionmentioning

confidence: 99%

Sequence-Independent, Single-Primer Amplification Next-Generation Sequencing of Hantaan Virus Cell Culture–Based Isolates

Song

Kim

et al. 2017

The American Society of Tropical Medicine and Hygiene

View full text Add to dashboard Cite

Abstract. Hantaan virus (HTNV), identified in the striped field mouse (Apodemus agrarius), belongs to the genus Hantavirus of the family Bunyaviridae and contains tripartite RNA genomes, small (S), medium (M), and large (L) segments. HTNV is a major causative for hemorrhagic fever with renal syndrome (HFRS) with fatality rates ranging from 1% to 15% in the Republic of Korea (ROK) and China. Defining of HTNV whole-genome sequences and isolation of the infectious particle play a critical role in the characterization and preventive and therapeutic strategies of hantavirus outbreaks. Next-generation sequencing (NGS) provides an advanced tool for massive genomic sequencing of viruses. However, the isolation of viral infectious particles is a huge obstacle to investigate and develop anti-virals for hantaviruses. Here, we report 12 HTNV isolates from lung tissues of the striped field mouse in the highly HFRS-endemic areas. Sequence-independent, single-primer amplification (SISPA) NGS was attempted to recover the genomic sequences of HTNV isolates. The nucleotide sequence of HTNV S, M, and L segments were covered up to 99.4-100%, 97.5-100%, and 95.6-99.8%, respectively, based on the full length of the prototype HTNV 76-118. The whole-genome sequencing of HTNV isolates was accomplished by additional reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification cDNA ends (RACE) PCR. In conclusion, this study will lead to the attempt and usage of SISPA NGS technologies to delineate the whole-genome sequence of hantaviruses, providing a new era of viral genomics for the surveillance, trace, and disease risk management of HFRS incidents.

show abstract

The use of next generation sequencing in the diagnosis and typing of respiratory infections

Cited by 107 publications

References 19 publications

Human-Driven Microbiological Contamination of Benthic and Hyporheic Sediments of an Intermittent Peri-Urban River Assessed from MST and 16S rRNA Genetic Structure Analyses

Human-Driven Microbiological Contamination of Benthic and Hyporheic Sediments of an Intermittent Peri-Urban River Assessed from MST and 16S rRNA Genetic Structure Analyses

Adenovirus type 4 respiratory infections with a concurrent outbreak of coxsackievirus A21 among United States Army Basic Trainees, a retrospective viral etiology study using next‐generation sequencing

Sequence-Independent, Single-Primer Amplification Next-Generation Sequencing of Hantaan Virus Cell Culture–Based Isolates

Contact Info

Product

Resources

About