Accurate strand-specific quantification of viral RNA

PLoS ONE

Volumn 4, Issue 10, 2009, Pages

  Plaskon, Nicole E ^a   Adelman, Zach N ^a   Myles, Kevin M ^a  

^a Fralin Life Science Institute   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; PRIMER DNA; VIRUS RNA; COLORING AGENT; DNA; ORGANIC COMPOUND; SYBR GREEN I;

ACCURACY; ARTICLE; CONTROLLED STUDY; DNA STRAND; DNA TRANSCRIPTION; HYDROLYSIS; INTERMETHOD COMPARISON; MOLECULAR PROBE; NONHUMAN; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RNA STRUCTURE; SENSITIVITY AND SPECIFICITY; VIRUS INFECTION; VIRUS REPLICATION; CHIKUNGUNYA ALPHAVIRUS; EPIDEMIC; GENETIC PROCEDURES; GENETICS; HUMAN; INDIAN OCEAN; METABOLISM; METHODOLOGY; MICROBIOLOGICAL EXAMINATION; POLYMERASE CHAIN REACTION; REPRODUCIBILITY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

CHIKUNGUNYA VIRUS; RNA VIRUSES;

CHIKUNGUNYA VIRUS; COLORING AGENTS; DISEASE OUTBREAKS; DNA; DNA, COMPLEMENTARY; GENETIC TECHNIQUES; HUMANS; HYDROLYSIS; INDIAN OCEAN; MICROBIOLOGICAL TECHNIQUES; ORGANIC CHEMICALS; POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, VIRAL;

EID: 70449601770     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0007468     Document Type: Article

References (26)

1. Strauss JH, Strauss EG (1994) The alphaviruses: gene expression, replication, and evolution. Microbiol Rev 58: 491-562.
2. Sawicki DL, Sawicki SG (1980) Short-lived minus-strand polymerase for Semliki Forest virus. J Virol 34: 108-118.
3. Kim KH, Rumenapf T, Strauss EG, Strauss JH (2004) Regulation of Semliki Forest virus RNA replication: a model for the control of alphavirus pathogenesis in invertebrate hosts. Virology 323: 153-163.
4. Shirako Y, Strauss JH (1994) Regulation of Sindbis virus RNA replication: uncleaved P123 and nsP4 function in minus-strand RNA synthesis, whereas cleaved products from P123 are required for efficient plus-strand RNA synthesis. J Virol 68: 1874-1885.
5. Yuki N, Matsumoto S, Tadokoro K, Mochizuki K, Kato M, et al. (2006) Significance of liver negative-strand HCV RNA quantitation in chronic hepatitis C. J Hepatol 44: 302-309.
6. Wang WK, Sung TL, Tsai YC, Kao CL, Chang SM, et al. (2002) Detection of dengue virus replication in peripheral blood mononuclear cells from dengue virus type 2-infected patients by a reverse transcription-real-time PCR assay. J Clin Microbiol 40: 4472-4478.
7. Richardson J, Molina-Cruz A, Salazar MI, Black Wt (2006) Quantitative analysis of dengue-2 virus RNA during the extrinsic incubation period in individual Aedes aegypti. Am J Trop Med Hyg 74: 132-141.
8. Purcell MK, Hart SA, Kurath G, Winton JR (2006) Strand-specific, real-time RT-PCR assays for quantification of genomic and positive-sense RNAs of the fish rhabdovirus, Infectious hematopoietic necrosis virus. J Virol Methods 132: 18-24.
9. Komurian-Pradel F, Perret M, Deiman B, Sodoyer M, Lotteau V, et al. (2004) Strand specific quantitative real-time PCR to study replication of hepatitis C virus genome. J Virol Methods 116: 103-106.
10. Hashimoto Y, Valles SM (2008) Detection and quantitation of Solenopsis invicta virus-2 genomic and intermediary replicating viral RNA in fire ant workers and larvae. J Invertebr Pathol 98: 243-245.
11. Gu C, Zheng C, Shi L, Zhang Q, Li Y, et al. (2007) Plus- and minus-stranded foot-and-mouth disease virus RNA quantified simultaneously using a novel real-time RT-PCR. Virus Genes 34: 289-298.
12. Castillo I, Rodriguez-Inigo E, Lopez-Alcorocho JM, Pardo M, Bartolome J, et al. (2006) Hepatitis C virus replicates in the liver of patients who have a sustained response to antiviral treatment. Clin Infect Dis 43: 1277-1283.
13. Campbell CL, Keene KM, Brackney DE, Olson KE, Blair CD, et al. (2008) Aedes aegypti uses RNA interference in defense against Sindbis virus infection. BMC Microbiol 8: 47.
14. Bartolome J, Lopez-Alcorocho JM, Castillo I, Rodriguez-Inigo E, Quiroga JA, et al. (2007) Ultracentrifugation of serum samples allows detection of hepatitis C virus RNA in patients with occult hepatitis C. J Virol 81: 7710-7715.
15. Anwar A, August JT, Too HP (2006) A stem-loop-mediated reverse transcription real-time PCR for the selective detection and quantification of the replicative strand of an RNA virus. Anal Biochem 352: 120-128.
16. Anderson JR, Rico-Hesse R (2006) Aedes aegypti vectorial capacity is determined by the infecting genotype of dengue virus. Am J Trop Med Hyg 75: 886-892.
17. Lin L, Fevery J, Hiem Yap S (2002) A novel strand-specific RT-PCR for detection of hepatitis C virus negative-strand RNA (replicative intermediate): evidence of absence or very low level of HCV replication in peripheral blood mononuclear cells. J Virol Methods 100: 97-105.
18. Afonina I, Ankoudinova I, Mills A, Lokhov S, Huynh P, et al. (2007) Primers with 5′ flaps improve real-time PCR. Biotechniques 43: 770, 772, 774.
19. Timofeeva AV, Skrypina NA (2001) Background activity of reverse transcriptases. Biotechniques 30: 22-24, 26, 28.
20. Peyrefitte CN, Pastorino B, Bessaud M, Tolou HJ, Couissinier-Paris P (2003) Evidence for in vitro falsely-primed cDNAs that prevent specific detection of virus negative strand RNAs in dengue-infected cells: improvement by tagged RT-PCR. J Virol Methods 113: 19-28.
21. Gunji T, Kato N, Hijikata M, Hayashi K, Saitoh S, et al. (1994) Specific detection of positive and negative stranded hepatitis C viral RNA using chemical RNA modification. Arch Virol 134: 293-302.
22. Wittwer CT, Herrmann MG, Moss AA, Rasmussen RP (1997) Continuous fluorescence monitoring of rapid cycle DNA amplification. Biotechniques 22: 130-131, 134-138.
23. Higuchi R, Fockler C, Dollinger G, Watson R (1993) Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. Biotechnology (N Y) 11: 1026-1030.
24. Holland PM, Abramson RD, Watson R, Gelfand DH (1991) Detection of specific polymerase chain reaction product by utilizing the 5′ - 3′ exonuclease activity of Thermus aquaticus DNA polymerase. Proc Natl Acad Sci U S A 88: 7276-7280.
25. Powers AM, Logue CH (2007) Changing patterns of chikungunya virus: re-emergence of a zoonotic arbovirus. J Gen Virol 88: 2363-2377.
26. Enserink M (2008) Entomology. A mosquito goes global. Science 320: 864-866.