PMID- 31817886
OWN - NLM
STAT- MEDLINE
DCOM- 20200921
LR  - 20221207
IS  - 1999-4915 (Electronic)
IS  - 1999-4915 (Linking)
VI  - 11
IP  - 12
DP  - 2019 Dec 7
TI  - Rapid, Unbiased PRRSV Strain Detection Using MinION Direct RNA Sequencing and 
      Bioinformatics Tools.
LID - 10.3390/v11121132 [doi]
LID - 1132
AB  - Prompt detection and effective control of porcine reproductive and respiratory 
      syndrome virus (PRRSV) during outbreaks is important given its immense adverse 
      impact on the swine industry. However, the diagnostic process can be challenging 
      due to the high genetic diversity and high mutation rate of PRRSV. A diagnostic 
      method that can provide more detailed genetic information about pathogens is 
      urgently needed. In this study, we evaluated the ability of Oxford Nanopore 
      MinION direct RNA sequencing to generate a PRRSV whole genome sequence and detect 
      and discriminate virus at the strain-level. A nearly full length PRRSV genome was 
      successfully generated from raw sequence reads, achieving an accuracy of 96% 
      after consensus genome generation. Direct RNA sequencing reliably detected the 
      PRRSV strain present with an accuracy of 99.9% using as few as 5 raw sequencing 
      reads and successfully differentiated multiple co-infecting strains present in a 
      sample. In addition, PRRSV strain information was obtained from clinical samples 
      containing 10(4) to 10(6) viral copies or more within 6 hours of sequencing. 
      Overall, direct viral RNA sequencing followed by bioinformatic analysis proves to 
      be a promising approach for identification of the viral strain or strains 
      involved in clinical infections, allowing for more precise prevention and control 
      strategies during PRRSV outbreaks.
FAU - Tan, Shaoyuan
AU  - Tan S
AUID- ORCID: 0000-0002-9880-8213
AD  - Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, 
      University of Minnesota, St. Paul, MN 55108, USA.
FAU - Dvorak, Cheryl M T
AU  - Dvorak CMT
AUID- ORCID: 0000-0001-8900-8348
AD  - Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, 
      University of Minnesota, St. Paul, MN 55108, USA.
FAU - Murtaugh, Michael P
AU  - Murtaugh MP
AD  - Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, 
      University of Minnesota, St. Paul, MN 55108, USA.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20191207
PL  - Switzerland
TA  - Viruses
JT  - Viruses
JID - 101509722
RN  - 0 (RNA, Viral)
SB  - IM
MH  - Animals
MH  - *Computational Biology/methods
MH  - Evolution, Molecular
MH  - Genome, Viral
MH  - Genomics/methods
MH  - Porcine Reproductive and Respiratory Syndrome/*virology
MH  - Porcine respiratory and reproductive syndrome virus/*genetics/isolation & 
      purification
MH  - *RNA, Viral
MH  - Sequence Analysis, DNA
MH  - Swine
MH  - *Exome Sequencing
PMC - PMC6950593
OTO - NOTNLM
OT  - MinION
OT  - PRRSV
OT  - analytical sensitivity
OT  - bioinformatics
OT  - co-infection
OT  - direct RNA sequencing
OT  - quantitation
OT  - strain level detection
OT  - whole genome sequencing
COIS- The authors declare no conflict of interest.
EDAT- 2019/12/11 06:00
MHDA- 2020/09/22 06:00
PMCR- 2019/12/01
CRDT- 2019/12/11 06:00
PHST- 2019/11/14 00:00 [received]
PHST- 2019/12/04 00:00 [revised]
PHST- 2019/12/05 00:00 [accepted]
PHST- 2019/12/11 06:00 [entrez]
PHST- 2019/12/11 06:00 [pubmed]
PHST- 2020/09/22 06:00 [medline]
PHST- 2019/12/01 00:00 [pmc-release]
AID - v11121132 [pii]
AID - viruses-11-01132 [pii]
AID - 10.3390/v11121132 [doi]
PST - epublish
SO  - Viruses. 2019 Dec 7;11(12):1132. doi: 10.3390/v11121132.