Infection, recovery and re-infection of farmed mink with SARS-CoV-2

Abstract

Mink, on a farm with about 15,000 animals, became infected with SARS-CoV-2. Over 75% of tested animals were positive for SARS-CoV-2 RNA in throat swabs and 100% of tested animals were seropositive. The virus responsible had a deletion of nucleotides encoding residues H69 and V70 within the spike protein gene as well as the A22920T mutation, resulting in the Y453F substitution within this protein, seen previously in mink. The infected mink recovered and after free-testing of 300 mink (a level giving 93% confidence of detecting a 1% prevalence), the animals remained seropositive. During further follow-up studies, after a period of more than 2 months without any virus detection, over 75% of tested animals again scored positive for SARS-CoV-2 RNA. Whole genome sequencing showed that the viruses circulating during this re-infection were most closely related to those identified in the first outbreak on this farm but additional sequence changes had occurred. Animals had much higher levels of anti-SARS-CoV-2 antibodies in serum samples after the second round of infection than at free-testing or during recovery from initial infection, consistent with a boosted immune response. Thus, it was concluded that following recovery from an initial infection, seropositive mink were readily re-infected by SARS-CoV-2.

Fig 1. Timeline for infection of mink on Farm 4.

The percentage of live and dead mink assayed by RT-qPCR that tested positive is shown throughout the period of August to November 2020, together with the proportion of live mink that tested positive by ELISA for anti-CoV-2 antibodies. The numbers of animals tested on each date are shown in Table 1. Dotted lines have been used to connect the data points for clarity but should not be used to infer intermediate percentage levels.

Fig 2. Assessment of anti-SARS CoV-2 antibody levels in mink sera.

Panel A. Anti-SARS-CoV-2 antibody titres were measured by ELISA. Selected sera from mink collected at the time of initial diagnosis (blue circles), at free-testing (grey circles) and following re-infection (red circles), on 19-08-20, 05-10-20 and 06-11-20 respectively, that scored positive when assayed undiluted were titrated and assayed again by ELISA. The reciprocals of the highest dilution yielding a positive signal are plotted (on a log2 scale). Mean (+/- SEM) values are indicated by horizontal black lines. Panel B. The same serum samples were also assayed in virus neutralization assays and the calculated antibody titres are plotted (on a log2 scale) using the same colour scheme. The statistical significance of the differences between anti-CoV-2 antibody levels was determined using the Kruskal-Wallis test (see Materials and Methods).

Fig 3. Phylogenetic trees showing the relationships between the full genome sequences of SARS-CoV-2 samples from Danish mink farms with the lineage B.1.1.298 variants.

Panel A. All known SARS-CoV2 lineage B.1.1.298 genome sequences (436 in total) from Danish mink along with the Wuhan reference sequence (NC_045512.2) were included in this analysis. Sequences from the re-infection on Farm 4 (collected in November) are indicated by open red triangles while samples collected in August are indicated by blue triangles. Sequences from Farm 1 are indicated with green squares and the Wuhan reference strain with a black filled circle. The GISAID accession IDs are listed in S1 Table. Panel B. The Maximum Likelihood phylogenetic relationships between the viruses collected on Farm 4 and those from Farms 1–3 are shown. The GISAID accession IDs are listed in S2 Table.