Evaluation of the broad-range PCR-electrospray ionization mass spectrometry (PCR/ESI-MS) system and virus microarrays for virus detection

Lanyn P Taliaferro; Teresa A Galvin; Hailun Ma; Syed Shaheduzzaman; Dhanya K Williams; Dustin R Glasner; Arifa S Khan

doi:10.3390/v6051876

Evaluation of the broad-range PCR-electrospray ionization mass spectrometry (PCR/ESI-MS) system and virus microarrays for virus detection

Viruses. 2014 Apr 25;6(5):1876-96. doi: 10.3390/v6051876.

Authors

Lanyn P Taliaferro¹, Teresa A Galvin², Hailun Ma³, Syed Shaheduzzaman⁴, Dhanya K Williams⁵, Dustin R Glasner⁶, Arifa S Khan⁷

Affiliations

¹ Laboratory of Retroviruses, Division of Viral Products, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 8800 Rockville Pike, HFM-454, Bethesda, MD 20892, USA. lanyn.taliaferro@fda.hhs.gov.
² Laboratory of Retroviruses, Division of Viral Products, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 8800 Rockville Pike, HFM-454, Bethesda, MD 20892, USA. teresa.galvin@fda.hhs.gov.
³ Laboratory of Retroviruses, Division of Viral Products, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 8800 Rockville Pike, HFM-454, Bethesda, MD 20892, USA. hailun.ma@fda.hhs.gov.
⁴ Laboratory of Retroviruses, Division of Viral Products, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 8800 Rockville Pike, HFM-454, Bethesda, MD 20892, USA. syed.shaheduzzaman@fda.hhs.gov.
⁵ Laboratory of Retroviruses, Division of Viral Products, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 8800 Rockville Pike, HFM-454, Bethesda, MD 20892, USA. dhanya.williams@fda.hhs.gov.
⁶ Laboratory of Retroviruses, Division of Viral Products, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 8800 Rockville Pike, HFM-454, Bethesda, MD 20892, USA. drglasner@berkeley.edu.
⁷ Laboratory of Retroviruses, Division of Viral Products, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 8800 Rockville Pike, HFM-454, Bethesda, MD 20892, USA. arifa.khan@fda.hhs.gov.

Abstract

Advanced nucleic acid-based technologies are powerful research tools for novel virus discovery but need to be standardized for broader applications such as virus detection in biological products and clinical samples. We have used well-characterized retrovirus stocks to evaluate the limit of detection (LOD) for broad-range PCR with electrospray ionization mass spectrometry (PCR/ESI-MS or PLEX-ID), RT-PCR assays, and virus microarrays. The results indicated that in the absence of background cellular nucleic acids, PLEX-ID and RT-PCR had a similar LOD for xenotropic murine retrovirus-related virus (XMRV; 3.12 particles per µL) whereas sensitivity of virus detection was 10-fold greater using virus microarrays. When virus was spiked into a background of cellular nucleic acids, the LOD using PLEX-ID remained the same, whereas virus detection by RT-PCR was 10-fold less sensitive, and no virus could be detected by microarrays. Expected endogenous retrovirus (ERV) sequences were detected in cell lines tested and known species-specific viral sequences were detected in bovine serum and porcine trypsin. A follow-up strategy was developed using PCR amplification, nucleotide sequencing, and bioinformatics to demonstrate that an RD114-like retrovirus sequence that was detected by PLEX-ID in canine cell lines (Madin-Darby canine kidney (MDCK) and Cf2Th canine thymus) was due to defective, endogenous gammaretrovirus-related sequences.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Diagnostic Tests, Routine / methods*
Endogenous Retroviruses / genetics
Endogenous Retroviruses / isolation & purification*
Humans
Microarray Analysis / methods*
Polymerase Chain Reaction / methods*
Sensitivity and Specificity
Spectrometry, Mass, Electrospray Ionization / methods*
Virology / methods*