Single assay for simultaneous detection and differential identification of human and avian influenza virus types, subtypes, and emergent variants.
For more than four decades the cause of most type A influenza virus infections of humans has been attributed to only two viral subtypes, A/H1N1 or A/H3N2. In contrast, avian and other vertebrate species are a reservoir of type A influenza virus genome diversity, hosting strains representing at least 120 of 144 combinations of 16 viral hemagglutinin and 9 viral neuraminidase subtypes. Viral genome segment reassortments and mutations emerging within this reservoir may spawn new influenza virus strains as imminent epidemic or pandemic threats to human health and poultry production. Traditional methods to detect and differentiate influenza virus subtypes are either time-consuming and labor-intensive (culture-based) or remarkably insensitive (antibody-based). Molecular diagnostic assays based upon reverse transcriptase-polymerase chain reaction (RT-PCR) have short assay cycle time, and high analytical sensitivity and specificity. However, none of these diagnostic tests determine viral gene nucleotide sequences to distinguish strains and variants of a detected pathogen from one specimen to the next. Decision-quality, strain- and variant-specific pathogen gene sequence information may be critical for public health, infection control, surveillance, epidemiology, or medical/veterinary treatment planning. The Resequencing Pathogen Microarray (RPM-Flu) is a robust, highly multiplexed and target gene sequencing-based alternative to both traditional culture- or biomarker-based diagnostic tests. RPM-Flu is a single, simultaneous differential diagnostic assay for all subtype combinations of type A influenza viruses and for 30 other viral and bacterial pathogens that may cause influenza-like illness. These other pathogen targets of RPM-Flu may co-infect and compound the morbidity and/or mortality of patients with influenza. The informative specificity of a single RPM-Flu test represents specimen-specific viral gene sequences as determinants of virus type, A/HN subtype, virulence, host-range, and resistance to antiviral agents.
Department of Respiratory Diseases Research, Naval Health Research Center, San Diego, California, United States of America.
David
D
Metzgar
Christopher A
CA
Myers
Kevin L
KL
Russell
Dennis
D
Faix
Patrick J
PJ
Blair
Jason
J
Brown
Scott
S
Vo
David E
DE
Swayne
Colleen
C
Thomas
David A
DA
Stenger
Baochuan
B
Lin
Anthony P
AP
Malanoski
Zheng
Z
Wang
Kate M
KM
Blaney
Nina C
NC
Long
Joel M
JM
Schnur
Magdi D
MD
Saad
Lisa A
LA
Borsuk
Agnieszka M
AM
Lichanska
Matthew C
MC
Lorence
Brian
B
Weslowski
Klaus O
KO
Schafer
Clark
C
Tibbetts
D000818:Animals; D001483:Base Sequence; D001717:Birds; D002460:Cell Line; D002642:Chick Embryo; D020869:Gene Expression Profiling / Q000379:methods; D015967:Gene Expression Regulation, Viral; D006801:Humans; D009980:Influenza A virus / Q000145:classification / Q000235:genetics*; D005585:Influenza in Birds / Q000175:diagnosis* / Q000821:virology; D007251:Influenza, Human / Q000175:diagnosis* / Q000821:virology; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D057089:Pathology, Molecular / Q000379:methods*; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid