Influenza A virus transmission in swine farms and during transport in
the swine supply chain
Abstract
The last influenza pandemic in 2009 emerged from swine and surveillance
of swine influenza is important for pandemic preparedness. Movement of
swine during husbandry, trade or marketing for slaughter provide
opportunities for transfer and possible genetic reassortment of swine
influenza viruses. Over 90% of the swine slaughtered at the central
swine abattoir in Hong Kong are imported from farms located in multiple
provinces in mainland China. There is opportunity for virus
cross-infection during this transport and slaughter process. Of the
26,980 swabs collected in the slaughterhouse in Hong Kong from 5
th January 2012 to 15 th December
2016, we analyzed sequence data on influenza A (H3N2) virus isolates (n
= 174) in conjunction with date of sampling and originating farm.
Molecular epidemiology provided evidence of virus cross-infection
between swine originating from different farms during transport and also
evidence of a virus lineage persisting in a swine farm for over 2 years.
We used virus serology and isolation data from 4,226 paired pig serum
and nasal swabs collected from swine originating from Guangdong Province
to compare the force of infection (FOI) during transport and within
farms. The mean weekly FOI during transport was λ t =
0.0286 (95% CI = 0.0211-0.0391) while the weekly FOI in farms was λ
f = 0.0089 (95% CI = 0.0084-0.0095), assuming a
duration of stay in farm of 28 weeks, suggesting increased force of
infection during the transport process. Potential risk factors for
infection including the duration in transport, length of stay at
slaughterhouse and farm-level seroprevalence were also assessed by
multivariable logistic regression analysis. Transport may increase virus
cross-infection rates and provide opportunities for virus reassortment
potentially increasing zoonotic risk to those involved in the
transportation and slaughtering processes.