Comparison of individual, group and environmental sampling strategies to conduct influenza surveillance in pigs

In this new scientific publication from Dr. Jorge Garrido, PhD candidate from the Torremorell lab, numerous sampling strategies to monitor influenza were compared. the following individual, litter, and environmental samples were included in the study:

  • Nasal swabs
  • Nasal wipes
  • Oropharyngeal swabs
  • Oral fluids
  • Surface wipes
  • Udder wipes
  • Airborne particle deposition
  • Air


Samples were collected in six breed-to-wean farms, from pigs aged between 18 to 21 days and from six wean-to-finish facilities, from pigs aged 35 to 45 days old. Herds were located in the Midwest and selected based on their history of influenza infection. Individual samples including 54 nasal swabs, 57 nasal wipes, and 51 oropharyngeal swabs were collected in the sow farms whereas 42 nasal swabs and 51 nasal wipes were collected in wean-to-finish facilities. . In sow farms, 24 udder wipes were collected whereas oral fluids were collected from both sow farms (6 samples) and wean-to-finish (20 samples). Lastly, 21 and 24 surface wipes, 26 and 19 air samples, and 24 and 21 airborne particle deposition samples were collected from sow farms and wean-to-finish facilities respectively.

All samples were tested by RT-PCR and selected PCR positive samples were selected for virus isolation. Hemagglutinin and neuraminidase influenza A virus gene segments were targeted for sequencing.


Overall, 20% to 100% of the sample types were positive for influenza if the farm status was positive. The litter or environmental samples had better detection rates than nasal swabs pooled by 3. However,oroparhyngeal swabs and udder wipes in the farrowing rooms or nasal swabs and nasal wipes in growing pigs were the most successful to obtain an isolate. The distribution of the Ct-value by sample types and by type of farms can be found in the figure below. Note: The samples were considered positive for a Ct-value equal or below 35.

The level of agreement between sample types varied but the authors noted, in growing pigs:

  • a substantial agreement between pooled nasal swabs and pooled nasal wipes,
  • a moderate agreement between oral fluids and surface wipes, and
  • a slight agreement between airborne particle deposition and pooled nasal swabs.

When compared to pooled nasal swabs, the probability of finding a positive sample was much higher for udder wipes, oral fluids, oropharyngeal swabs, and surface wipes (odds ratio of 16.5, 9.8, 8.07, 3.87 respectively).


Group and environmental sample types were most suited for influenza surveillance as they showed a higher probability of detection compared to pooled nasal swabs whereas individual samples were better at isolating and sequencing the virus.


Background: Influenza A virus (IAV) is an important pathogen in pigs that affects productivity and has important public health implications because of its zoonotic nature. Surveillance is central to the control of influenza, however, detection of IAV infections can be challenging in endemically infected herds with low prevalence of infection.
Methods: In groups of suckling (18–21 days of age) and growing (35–45 days of age) pigs, we compared various sampling approaches to detect, isolate and sequence IAV using individual (nasal swabs, nasal wipes and oropharyngeal swabs), group (oral fluids, surface wipes and sow udder skin wipes) and environmental (airborne particles deposited on surfaces and air samples) sampling approaches. All samples were tested by IAV rRT-PCR and a subset was used for virus isolation and direct sequencing.
Results: In general, environmental and group samples resulted in higher odd ratios (range = 3.87–16.5, p-value < 0.05) of detecting a positive sample by rRT-PCR compared to individual pooled samples, except for oropharyngeal swabs (OR = 8.07, p-value < 0.05). In contrast, individual samples were most likely to yield a viral isolate by cell culture. Oropharyngeal swabs in suckling pigs (78.4%), and nasal swabs (47.6%) or nasal wipes (45%) in growing pigs, and udder wipes in lactating sows (75%) were the preferred samples to obtain an isolate.
Conclusions: Our findings indicate that group and environmental sampling strategies should be considered in influenza surveillance programs in particular if the goal is just to detect infection. This study provides new information on sampling approaches to conduct effective influenza surveillance in pigs and identifies udder wipes from lactating sows as a novel sample type that offers a convenient, cheap and sensitive manner to monitor IAV in litters prior to weaning.

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