Cryptic SARS-CoV-2 lineage identified on two mink farms as a possible result of long-term undetected circulation in an unknown animal reservoir, Poland, November 2022 to January 2023

Abstract

In late 2022 and early 2023, SARS-CoV-2 infections were detected on three mink farms in Poland situated within a few km from each other. Whole-genome sequencing of the viruses on two of the farms showed that they were related to a virus identified in humans in the same region 2 years before (B.1.1.307 lineage). Many mutations were found, including in the S protein typical of adaptations to the mink host. The origin of the virus remains to be determined.

SARS-CoV-2 Outbreaks on Mink Farms—A Review of Current Knowledge on Virus Infection, Spread, Spillover, and Containment

“…Nonetheless, experimentally infected pigs [ 24 , 33 ], horses [ 30 ], chickens [ 24 , 33 ], and ducks [ 24 ] are not susceptible to SARS-CoV-2. Additionally, natural infection of SARS-CoV-2 has been detected in cats [ 42 ], dogs [ 43 ], tigers and lions [ 29 ], white tailed deer [ 44 ], feral/free-roaming mink [ 45 , 46 , 47 ], and recently farmed mink [ 13 , 22 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 ]. Further, zoonotic spread of SARS-CoV-2 from experimentally [ 25 , 48 ] and naturally [ 22 , 59 , 60 ] infected animals to susceptible humans has been reported, and anthropozoonotic transmission of SARS-CoV-2 from infected humans to susceptible animals (i.e., farmed mink [ 22 , 52 , 53 , 61 ] and certain zoo animals [ 62 ]) has also been reported.…”

“…Following the culling of mink in the Netherlands and Denmark, Poland became the largest mink producer in the European Union and second in the world, after China [ 55 , 83 ]. As of March 2023, Poland had 166 mink farms, whereas there were 350 farms before the COVID-19 outbreak in 2019 [ 56 , 83 ]. In response to the WHO, European Center for Disease Prevention and Control, and World Organisation for Animal Health recommendations for monitoring and surveillance of mink farms for SARS-CoV-2 infection, the Polish government ordered active monitoring and close surveillance of mink farms across Poland beginning in fall 2020 [ 55 ].…”

“…In response to the WHO, European Center for Disease Prevention and Control, and World Organisation for Animal Health recommendations for monitoring and surveillance of mink farms for SARS-CoV-2 infection, the Polish government ordered active monitoring and close surveillance of mink farms across Poland beginning in fall 2020 [ 55 ]. Accordingly, the first outbreak of SARS-CoV-2 on mink farms in Poland was detected on 30 January 2021 on one mink farm in North Poland as a result of testing 28 mink farms between November 2020 and January 2021 [ 55 , 56 , 83 ]. Another 13 SARS-CoV-2-positive mink farms were detected through July 2022 [ 56 , 85 ], and an additional 3 positive farms were detected between September 2022 and January 2023 [ 56 ].…”

Human origin ascertained for SARS-CoV-2 Omicron-like spike sequences detected in wastewater: a targeted surveillance study of a cryptic lineage in an urban sewershed

“…13–14 Thus, it is plausible that wild animal reservoirs of cryptic lineages exist undetected, with ongoing virus transmission and exchange between animal species. 15…”

“…[13][14] Thus, it is plausible that wild animal reservoirs of cryptic lineages exist undetected, with ongoing virus transmission and exchange between animal species. 15 Alternately, cryptic SARS-CoV-2 lineage sequences in wastewater could be derived from people with unsampled infections. 16 In a recent cohort study, 49.2% of participants had viral RNA (vRNA) in stool in the first week of infection; vRNA remained detectable in stool four months later in 12.7% of individuals even though all had cleared vRNA from the nasopharynx.…”