File Download
Supplementary

Conference Paper: Deep sequencing of PRRSV isolates: rapid and large-scale characterization of viral genomes

TitleDeep sequencing of PRRSV isolates: rapid and large-scale characterization of viral genomes
Authors
Issue Date2012
Publisher2012 IPRRSS/NSIF Conference.
Citation
The 2012 Joint Meetings of the International PRRS Symposium (IPRRSS) and National Swine Improvement Federation (NSIF) Conference, Kansas, MO., 29-30 November 2012. In Conference Program, 2012, p. 43, abstract no. 24 How to Cite?
AbstractPorcine reproductive and respiratory syndrome virus (PRRSV) is a single stranded, positive sense RNA virus with a genome size of approximately 15 kb. Much of the genetic characterization or viral genotyping of PRRSV isolates is limited to one or two viral genes only (ORF5 and/or ORF7) for a number of reasons, for example: (1) characterizing one or two ORFs is sufficient for diagnostics; (2) genome characterization is laborious because traditional (Sanger) sequencing yields only a single sequence of 800-1000 bases per reaction; (3) large-scale genome characterization is time-consuming and costly. Collectively, this hinders the study of PRRSV genomic evolution at different levels (host, regional, and global). We demonstrate here the use of 454 technology to rapidly sequence PRRSV genomic nucleic acid from different sources (cell culture and swine tissue), genotypes (type 1 and type 2), and genome structure (non-deletion vs. deletion variants). Samples (n=16) were multiplexed to bring down cost per genome sequence. Assembly of sample specific reads resulted in a single contig in almost all instances (15 out of 16). Average genome coverage was 96.7% with reference to prototype isolates (Lelystad virus for type 1 and ATCC VR2332 for type 2). Average sequence depth was 405 reads per nucleotide position. This high sequence depth allowed characterization of variants from quasispecies that occurred at frequencies even lower than 1%. In summary, next generation sequencing technology offers unparalleled opportunity to quickly and efficiently characterize near complete length PRRSV genomes in an economical manner. This allows experiments to be designed with considerations to viral genomic evolution rather than those with limited insights from select viral genes only.
Persistent Identifierhttp://hdl.handle.net/10722/190674

 

DC FieldValueLanguage
dc.contributor.authorBrar, MSen_US
dc.contributor.authorShi, Men_US
dc.contributor.authorLeung, FCCen_US
dc.date.accessioned2013-09-17T15:34:49Z-
dc.date.available2013-09-17T15:34:49Z-
dc.date.issued2012en_US
dc.identifier.citationThe 2012 Joint Meetings of the International PRRS Symposium (IPRRSS) and National Swine Improvement Federation (NSIF) Conference, Kansas, MO., 29-30 November 2012. In Conference Program, 2012, p. 43, abstract no. 24en_US
dc.identifier.urihttp://hdl.handle.net/10722/190674-
dc.description.abstractPorcine reproductive and respiratory syndrome virus (PRRSV) is a single stranded, positive sense RNA virus with a genome size of approximately 15 kb. Much of the genetic characterization or viral genotyping of PRRSV isolates is limited to one or two viral genes only (ORF5 and/or ORF7) for a number of reasons, for example: (1) characterizing one or two ORFs is sufficient for diagnostics; (2) genome characterization is laborious because traditional (Sanger) sequencing yields only a single sequence of 800-1000 bases per reaction; (3) large-scale genome characterization is time-consuming and costly. Collectively, this hinders the study of PRRSV genomic evolution at different levels (host, regional, and global). We demonstrate here the use of 454 technology to rapidly sequence PRRSV genomic nucleic acid from different sources (cell culture and swine tissue), genotypes (type 1 and type 2), and genome structure (non-deletion vs. deletion variants). Samples (n=16) were multiplexed to bring down cost per genome sequence. Assembly of sample specific reads resulted in a single contig in almost all instances (15 out of 16). Average genome coverage was 96.7% with reference to prototype isolates (Lelystad virus for type 1 and ATCC VR2332 for type 2). Average sequence depth was 405 reads per nucleotide position. This high sequence depth allowed characterization of variants from quasispecies that occurred at frequencies even lower than 1%. In summary, next generation sequencing technology offers unparalleled opportunity to quickly and efficiently characterize near complete length PRRSV genomes in an economical manner. This allows experiments to be designed with considerations to viral genomic evolution rather than those with limited insights from select viral genes only.-
dc.languageengen_US
dc.publisher2012 IPRRSS/NSIF Conference.-
dc.relation.ispartof2012 International PRRS Symposium/NSIF Conference Programen_US
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.titleDeep sequencing of PRRSV isolates: rapid and large-scale characterization of viral genomesen_US
dc.typeConference_Paperen_US
dc.identifier.emailLeung, FCC: fcleung@hkucc.hku.hken_US
dc.identifier.authorityLeung, FCC=rp00731en_US
dc.description.naturepostprint-
dc.identifier.hkuros225008en_US
dc.identifier.spage43-
dc.identifier.epage43-
dc.publisher.placeUnited states-

Export via OAI-PMH Interface in XML Formats


OR


Export to Other Non-XML Formats