Rapid differential detection of H1 and H3 subtype swine influenza
viruses by a TaqMan-MGB based duplex one-step real time RT-PCR assay
Abstract
Background: Swine influenza is not only an economically important
respiratory disease in swine, but also constantly poses a threat to
human health. Hence, developing a rapid, sensitive and efficient
detection method of swine influenza virus (SIV) is highly essential.
Method: By aligning the HA gene sequences of SIV circulating in China in
recent 10 years, a H1 primer-probe set targeting both Eurasian
avian-like H1N1 (EA H1N1) and Pandemic 2009 H1N1 (Pdm09 H1N1) lineages
plus a H3 prime-probe set targeting the prevalent human-like H3N2 (HL
H3N2) subtype were designed, respectively. Further, a TaqMan-MGB based
duplex one-step real time RT-PCR (RRT-PCR) assay was established, and
the sensitivity, specificity and repeatability were evaluated. Results:
The duplex RRT-PCR exhibited good sensitivity with the detection limit
of 5 copies/μL HA plasmid for each of the EA H1N1, Pdm09 H1N1 and HL
H3N2 subtype SIVs, and matched a detection accuracy of 94.4% (17/18)
with traditional virus isolation through chicken embryo inoculation
using experimentally infected mice lung samples. Besides, the method
showed high repeatability both within-run and between-runs, and no
cross-reactivity against some commonly circulated porcine viruses in
China. Furthermore, the duplex RRT-PCR method revealed a relatively
higher prevalent rate of H1 than H3 subtype SIV in 166 nasal swabs from
pigs in some slaughterhouse during October~December,
2019. Conclusions: This developed assay could be very helpful for rapid
differential detection and routine surveillance of EA H1N1, Pdm H1N1 and
HL H3N2 subtype SIVs in China.