A comparison of sampling and testing approaches for the surveillance of SARS-CoV-2 in farmed American mink

Abstract

Surveillance for SARS-CoV-2 in American mink (Neovison vison) is a global priority because outbreaks on mink farms have potential consequences for animal and public health. Surveillance programs often focus on screening natural mortalities; however, significant knowledge gaps remain regarding sampling and testing approaches. Using 76 mink from 3 naturally infected farms in British Columbia, Canada, we compared the performance of 2 reverse-transcription real-time PCR (RT-rtPCR) targets (the envelope [E] and RNA-dependent RNA polymerase [RdRp] genes) as well as serology. We also compared RT-rtPCR and sequencing results from nasopharyngeal, oropharyngeal, skin, and rectal swabs, as well as nasopharyngeal samples collected using swabs and interdental brushes. We found that infected mink were generally RT-rtPCR-positive on all samples; however, Ct values differed significantly among sample types (nasopharyngeal < oropharyngeal < skin < rectal). There was no difference in the results of nasopharyngeal samples collected using swabs or interdental brushes. For most mink (89.4%), qualitative (i.e., positive vs. negative) serology and RT-rtPCR results were concordant. However, mink were positive on RT-rtPCR and negative on serology and vice versa, and there was no significant correlation between Ct values on RT-rtPCR and percent inhibition on serology. Both the E and RdRp targets were detectable in all sample types, albeit with a small difference in Ct values. Although SARS-CoV-2 RNA can be detected in multiple sample types, passive surveillance programs in mink should focus on multiple target RT-rtPCR testing of nasopharyngeal samples in combination with serology.

Keywords: American mink; COVID-19; Neovison vison; RT-rtPCR; SARS-CoV-2; population surveillance; serology.

Figure 1.

Comparison of SARS-CoV-2 E gene RT-rtPCR Ct values for different sample types obtained from mink. Midlines represent the median value, with outer bounds of boxes delineating the interquartile range (IQR) of Ct values for a sample type. Error bars show the most extreme point within 1.5*IQR; outliers beyond this range are signified by dots.

Figure 2.

Genome completeness of SARS-CoV-2 collected using nasal brush, nasal swab, oral swab, rectal swab, and skin swab from 35 mink across 3 farms. Midlines represent the median value, with outer bounds of boxes delineating the interquartile range (IQR) of genome completeness (min. depth per site = 10 reads) for a sample type. Error bars show the most extreme point within 1.5*IQR; data beyond this range are outliers. The color of a point shows whether that sample had a Ct value of < 20 (blue), 21–29 (pink), or ≥ 30 (orange) for the RdRp gene. Significance codes: *** p < 0.001, * p < 0.05.