Viral genome sequencing by random priming methods

Djikeng, Appolinaire; Halpin, Rebecca; Kuzmickas, Ryan; DePasse, Jay V.; Feldblyum, Jeremy I.; Sengamalay, Naomi; Afonso, Claudio L.; Zhang, Xinsheng; Anderson, Norman G.; Ghedin, Elodie; Spiro, David

doi:10.1186/1471-2164-9-5

Cited by 295 publications

(287 citation statements)

References 18 publications

Supporting

Mentioning

284

Contrasting

Unclassified

Order By: Relevance

“…The influenza A virus genomic RNA segments were simultaneously amplified from 3 l of purified RNA by using a multisegment reverse transcription-PCR (M-RT-PCR) strategy (30,31). Influenza virus M-RT-PCR products were randomly amplified and prepared for nextgeneration sequencing by using a sequence-independent single-primer amplification (SISPA) method (32). Two aliquots were then submitted for sequencing with 454 GS FLXϩ (one plate) and Illumina HiSeq (one lane) sequencing technologies.…”

Section: Methodsmentioning

confidence: 99%

Spread and Persistence of Influenza A Viruses in Waterfowl Hosts in the North American Mississippi Migratory Flyway

Fries

Nolting

Bowman

et al. 2015

J Virol

View full text Add to dashboard Cite

While geographic distance often restricts the spread of pathogens via hosts, this barrier may be compromised when host species are mobile. Migratory waterfowl in the order Anseriformes are important reservoir hosts for diverse populations of avian-origin influenza A viruses (AIVs) and are assumed to spread AIVs during their annual continental-scale migrations. However, support for this hypothesis is limited, and it is rarely tested using data from comprehensive surveillance efforts incorporating both the temporal and spatial aspects of host migratory patterns. We conducted intensive AIV surveillance of waterfowl using the North American Mississippi Migratory Flyway (MMF) over three autumn migratory seasons. Viral isolates (n ‫؍‬ 297) from multiple host species were sequenced and analyzed for patterns of gene dispersal between northern staging and southern wintering locations. Using a phylogenetic and nucleotide identity framework, we observed a larger amount of gene dispersal within this flyway rather than between the other three longitudinally identified North American flyways. Across seasons, we observed patterns of regional persistence of diversity for each genomic segment, along with limited survival of dispersed AIV gene lineages. Reassortment increased with both time and distance, resulting in transient AIV constellations. This study shows that within the MMF, AIV gene flow favors spread along the migratory corridor within a season, and also that intensive surveillance during bird migration is important for identifying virus dispersal on time scales relevant to pandemic responsiveness. In addition, this study indicates that comprehensive monitoring programs to capture AIV diversity are critical for providing insight into AIV evolution and ecology in a major natural reservoir. IMPORTANCEMigratory birds are a reservoir for antigenic and genetic diversity of influenza A viruses (AIVs) and are implicated in the spread of virus diversity that has contributed to previous pandemic events. Evidence for dispersal of avian-origin AIVs by migratory birds is rarely examined on temporal scales relevant to pandemic or panzootic threats. Therefore, characterizing AIV movement by hosts within a migratory season is important for implementing effective surveillance strategies. We conducted surveillance following birds along a major North American migratory route and observed that within a migratory season, AIVs rapidly reassorted and gene lineages were dispersed primarily within the migratory corridor. Patterns of regional persistence were observed across seasons for each gene segment. We show that dispersal of AIV gene lineages by migratory birds occurs quickly along migratory routes and that surveillance for AIVs threatening human and animal health should focus attention on these routes.

show abstract

Section: Methodsmentioning

confidence: 99%

Spread and Persistence of Influenza A Viruses in Waterfowl Hosts in the North American Mississippi Migratory Flyway

Fries

Nolting

Bowman

et al. 2015

J Virol

View full text Add to dashboard Cite

show abstract

“…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′). 18 SISPA NGS was used for defining RNA and DNA viruses including Rotavirus, Astrovirus, and Parvovirus. [19][20][21] Here, we attempted to establish SISPA NGS for the rapid recovery of HTNV tripartite genomic sequences identified from highly HFRS-endemic areas.…”

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

“…Viral RNA was extracted (Viral RNA Mini kit, QIAGEN) and then denatured at 97 C for 5 min. Reverse transcription (RT) was performed using AMV reverse transcriptase (Promega) with random hexamer, tailed by a common PCR primer sequence (Djikeng et al, 2008). PCR was carried out with Taq DNA polymerase (Thermo Scientific), applying the following thermal profile: initial denaturation (95 C for 3 min) was followed by 40 cycles of amplification (95 C for 30 s, 48 C for 30 s, 72 C for 2 min) and terminated at 72 C for 8 min.…”

Section: Methodsmentioning

confidence: 99%

Analysis of the full genome of human group C rotaviruses reveals lineage diversification and reassortment

Medici

Tummolo

Martella

et al. 2016

Journal of General Virology

View full text Add to dashboard Cite

Group C rotaviruses (RVC) are enteric pathogens of humans and animals. Whole-genome sequences are available only for few RVCs, leaving gaps in our knowledge about their genetic diversity. We determined the full-length genome sequence of two human RVCs (PR2593/ 2004 and PR713/2012), detected in Italy from hospital-based surveillance for rotavirus infection in 2004 and 2012. In the 11 RNA genomic segments, the two Italian RVCs segregated within separate intra-genotypic lineages showed variation ranging from 1.9 % (VP6) to 15.9 % (VP3) at the nucleotide level. Comprehensive analysis of human RVC sequences available in the databases allowed us to reveal the existence of at least two major genome configurations, defined as type I and type II. Human RVCs of type I were all associated with the M3 VP3 genotype, including the Italian strain PR2593/2004. Conversely, human RVCs of type II were all associated with the M2 VP3 genotype, including the Italian strain PR713/2012. Reassortant RVC strains between these major genome configurations were identified. Although only a few full-genome sequences of human RVCs, mostly of Asian origin, are available, the analysis of human RVC sequences retrieved from the databases indicates that at least two intra-genotypic RVC lineages circulate in European countries. Gathering more sequence data is necessary to develop a standardized genotype and intragenotypic lineage classification system useful for epidemiological investigations and avoiding confusion in the literature.

show abstract

Viral genome sequencing by random priming methods

Cited by 295 publications

References 18 publications

Spread and Persistence of Influenza A Viruses in Waterfowl Hosts in the North American Mississippi Migratory Flyway

Spread and Persistence of Influenza A Viruses in Waterfowl Hosts in the North American Mississippi Migratory Flyway

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

Analysis of the full genome of human group C rotaviruses reveals lineage diversification and reassortment

Contact Info

Product

Resources

About