TY - JOUR

T1 - Emergence and spread of SARS-CoV-2 variants from farmed mink to humans and back during the epidemic in Denmark, June-November 2020

AU - Rasmussen, Thomas Bruun

AU - Qvesel, Amanda Gammelby

AU - Pedersen, Anders Gorm

AU - Olesen, Ann Sofie

AU - Fonager, Jannik

AU - Rasmussen, Morten

AU - Sieber, Raphael Niklaus

AU - Stegger, Marc

AU - Calvo-Artavia, Francisco Fernando

AU - Goedknegt, Marlies Jilles Francine

AU - Thuesen, Esben Rahbek

AU - Lohse, Louise

AU - Mortensen, Sten

AU - Fomsgaard, Anders

AU - Boklund, Anette

AU - Bøtner, Anette

AU - Belsham, Graham J.

N1 - Funding Information: Funding: This research was funded by the Danish Veterinary and Food Administration (FVST) as part of the agreement for commissioned work between the Danish Ministry of Food and Agriculture and Fisheries and the University of Copenhagen and the Statens Serum Institut. Further funding has been received from the Danish National Research Foundation (grant number DNRF170) to A.G.P. The funders did not play any role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. Publisher Copyright: Copyright: © 2024 Rasmussen et al.

PY - 2024/7

Y1 - 2024/7

N2 - The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) not only caused the COVID-19 pandemic but also had a major impact on farmed mink production in several European countries. In Denmark, the entire population of farmed mink (over 15 million animals) was culled in late 2020. During the period of June to November 2020, mink on 290 farms (out of about 1100 in the country) were shown to be infected with SARS-CoV-2. Genome sequencing identified changes in the virus within the mink and it is estimated that about 4000 people in Denmark became infected with these mink virus variants. However, the routes of transmission of the virus to, and from, the mink have been unclear. Phylogenetic analysis revealed the generation of multiple clusters of the virus within the mink. Detailed analysis of changes in the virus during replication in mink and, in parallel, in the human population in Denmark, during the same time period, has been performed here. The majority of cases in mink involved variants with the Y453F substitution and the H69/V70 deletion within the Spike (S) protein; these changes emerged early in the outbreak. However, further introductions of the virus, by variants lacking these changes, from the human population into mink also occurred. Based on phylogenetic analysis of viral genome data, we estimate, using a conservative approach, that about 17 separate examples of mink to human transmission occurred in Denmark but up to 59 such events (90% credible interval: (39–77)) were identified using parsimony to count cross-species jumps on transmission trees inferred using Bayesian methods. Using the latter approach, 136 jumps (90% credible interval: (117–164)) from humans to mink were found, which may underlie the farm-to-farm spread. Thus, transmission of SARS-CoV-2 from humans to mink, mink to mink, from mink to humans and between humans were all observed.

AB - The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) not only caused the COVID-19 pandemic but also had a major impact on farmed mink production in several European countries. In Denmark, the entire population of farmed mink (over 15 million animals) was culled in late 2020. During the period of June to November 2020, mink on 290 farms (out of about 1100 in the country) were shown to be infected with SARS-CoV-2. Genome sequencing identified changes in the virus within the mink and it is estimated that about 4000 people in Denmark became infected with these mink virus variants. However, the routes of transmission of the virus to, and from, the mink have been unclear. Phylogenetic analysis revealed the generation of multiple clusters of the virus within the mink. Detailed analysis of changes in the virus during replication in mink and, in parallel, in the human population in Denmark, during the same time period, has been performed here. The majority of cases in mink involved variants with the Y453F substitution and the H69/V70 deletion within the Spike (S) protein; these changes emerged early in the outbreak. However, further introductions of the virus, by variants lacking these changes, from the human population into mink also occurred. Based on phylogenetic analysis of viral genome data, we estimate, using a conservative approach, that about 17 separate examples of mink to human transmission occurred in Denmark but up to 59 such events (90% credible interval: (39–77)) were identified using parsimony to count cross-species jumps on transmission trees inferred using Bayesian methods. Using the latter approach, 136 jumps (90% credible interval: (117–164)) from humans to mink were found, which may underlie the farm-to-farm spread. Thus, transmission of SARS-CoV-2 from humans to mink, mink to mink, from mink to humans and between humans were all observed.

UR - http://www.scopus.com/inward/record.url?scp=85197211094&partnerID=8YFLogxK

U2 - 10.1371/journal.ppat.1012039

DO - 10.1371/journal.ppat.1012039

M3 - Journal article

C2 - 38950065

AN - SCOPUS:85197211094

VL - 20

JO - P L o S Pathogens (Online)

JF - P L o S Pathogens (Online)

SN - 1553-7374

IS - 7 July

M1 - e1012039

ER -