SARS-CoV-2 monitoring on mink farms in Poland

Voivodeship	2021 (February–December)		2022 (January–March)		Total		Number of positive farms
Voivodeship	No. of farms	No. of swabs	No. of farms	No. of swabs	No. of farms	No. of swabs	Number of positive farms
Mazowieckie	58	1,160	28	420	86	1,580	0
Podkarpackie	8	160	5	75	13	235	1
Lubuskie	35	700	19	295	54	995	0
Wielkopolskie	117	2,340	87	1,472	204	3,812	1
Zachodniopomorskie	54	1,080	8	420	62	1,500	3
Pomorskie	19	380	1	20	20	400	1
Dolnośląskie	14	280	0	0	14	280	0
Kujawsko-Pomorskie	24	480	0	0	24	480	1
Lubelskie	36	1,120	22	356	58	1,476	2
Łódzkie	6	120	1	15	7	135	1
Małopolskie	7	140	1	15	8	155	0
Opolskie	6	120	0	0	6	120	0
Podlaskie	10	200	0	0	10	200	1
Świętokrzyskie	6	120	13	185	19	305	0
Warmińsko-Mazurskie	1	20	0	0	1	20	0
Śląskie	8	160	0	0	8	160	0
Total	409	8,580	185	3,273	594	11,853	11

Locations of inspected mink farms (marked as grey dots) and those which were SARS-CoV-2 positive (marked as red dots)

Table 2

A summary of the analysis of positive mink farms

				rRT-PCR
No	Date of sample collection	Voivodeship	Location	Positive/Tested	Ct value range*
			Wisznice (house 1)	2/20	21.8–25.5
1	16/06/2021	Lubelskie	Wisznice (house 2)	1/20	28.9
2	22/11/2021	Kujawsko-Pomorskie	Kraczki	1/20	28.9
3			Zieleniewo1	1/20	30.5
4	30/11/2021	Zachodniopomorskie	Zieleniewo2	13/20	24.7–36.8
5			Ołużna	19/20	18.9–37.3
6	01/12/2021	Wielkopolskie	Biadki	18/20	17.6–36.4
7	14/12/2021	Podkarpackie	Janowiec	20/20	28.1–30.4
8	15/12/2021	Podlaskie	Kościuki	2/20	32.1–35.3
9	20/12/2021	Pomorskie	Leźno	10/20	19.1–26.3
10	20/12/2021	Lubelskie	Kłoczew	5/20	28.9–30.2
11	20/01/2022	Łódzkie	Stefanów	2/20	20.5–21.8

[i] Ct – threshold cycle; * – results for E gene rRT-PCR

Table 3

Results of oral swab and serum sample analysis collected in two houses in Wisznice in the Lubelskie voivodeship

Collected	Positive
	16/06/2021		20	2	21.8–25.5	10
1	19/07/2021	Oral swab	90	1	28.8	1.1
	02/08/2021	Serum of kitten	15	15	1.25	100
		Serum of adult	15	14	1.64	93.3
	16/06/2021		20	2	28.5–30.7	10
	19/07/2021	Oral swab	60	0	-	0
2		Serum of kitten	15	15	1.04	100
	02/08/2021	Serum of adult	15	14	1.25	93.3

[i] * – results for E gene rRT-PCR/mean OD values obtained using Ingezim ELISA test

Maximum-likelihood phylogenic tree constructed using the SARS-CoV-2 sequences from all Polish mink farms obtained in this and previous studies. The tree was processed with the Nextclade open source tool (https://clades.nextstrain.org/tree)

Table 4

Molecular characteristics of SARS-CoV-2 detected in farmed mink in Poland in the studied period

No	Mink farm	Gisaid_ID	Clade	Pango lineage	Nucleotide		Frame shifts	Amino acid
No	Mink farm	Gisaid_ID	Clade	Pango lineage	substit.	delet.	Frame shifts	substit.	delet.
1	Wisznice, house 2,	EPI_ISL_3218555	GR/20B	B.1.1	31	0	0	18	0
	Lubelskie	EPI_ISL_3218557			31	0	0	18	0
2	Kraczki, Kujawsko-Pomorskie	EPI_ISL_7721854	GK/21J (Delta)	AY.43	44	13	0	34	4
		EPI_ISL_8693906			38	13	0	33	4
3	Ołużna, Zachodniopomorskie	EPI_ISL_8693911	GK/21J (Delta)	AY.43	40	14	1	34	4
		EPI_ISL_8693912			38	13	0	33	4
4	ZieleniewoZachodniopomorskie 1,	EPI_ISL_8693816	GK/21J (Delta)	AY.43	38	13	0	33	4
		EPI_ISL_8693913			41	13	0	34	4
5	Biadki, Wielkopolskie	EPI_ISL_8693914	GK/21J (Delta)	AY.43	41	13	0	34	4
		EPI_ISL_8693915			41	13	0	34	4
		EPI_ISL_9640028			51	104	1	37	34
6	Janowiec, Podkarpackie	EPI_ISL_9640033	GK/21J (Delta)	AY.126	50	107	1	37	34
		EPI_ISL_9640052			50	107	1	37	34
7	Kościuki, Podlaskie	EPI_ISL_9640055	GRY/20I (Alpha, V1)	B.1.1.7	52	37	0	30	11
8	Leźno, Pomorskie	EPI_ISL_9640059	GK/21J (Delta)	B.1.617.2	47	16	0	37	5
		EPI_ISL_9640062			45	47	1	36	12
9	Kłoczew, Lubelskie	EPI_ISL_9640065	GK/21J (Delta)	AY.122	41	16	0	32	4
		EPI_ISL_10337406			74	53	0	51	12
10	Stefanów, Łódzkie	EPI_ISL_10337127	GRA/21L (Omicron)	BA.2	72	53	0	51	12

Table 5

Sequence mutations in SARS-CoV-2 detected in farmed mink in Poland in the studied period

No	Mink farm	Pango lineage	Nonsynonymous mutations in the S protein in comparison to the Wuhan reference strain
1	Wisznice, Lubelskie house 2,	B.1.1	Q183R, Y453F, K558N, *D614G*, C1236F
2	Kraczki, Kujawsko- Pomorskie	AY.43	T19R, E96A, G142D, R158G, L452R, T478K, D614G, P681R, D950N, E156-, F157-
3	Ołużna, Zachodniopomorskie	AY.43	T19R, G142D, R158G, L452R, T478K, *D614G*, P681R, D950N, E156-, F157-
4	Zieleniewo1, Zachodniopomorskie	AY.43	T19R, G142D, R158G, L452R, T478K, *D614G*, P681R, D950N, E156-, F157-
5	Biadki, Wielkopolskie	AY.43	T19R, G142D, R158G, L452R, T478K, *D614G*, P681R, D950N, E156-, F157-
6	Janowiec, Podkarpackie	AY.126	T19R, T95I, G142D, R158G, G181V, L452R, T478K, N532S, *D614G*, P681R, I850L, D950N, K1045N E156-, F157-
7	Kościuki, Podlaskie	B.1.1.7	S94F, Y453F, N501Y, A570D, *D614G*, P681H, T716I, S982A, D1118H H69-, Y144-, H245-, S247-, V70-, L244-, R246-, Y248-
8	Leźno, Pomorskie	B.1.617.2	T19R, T95I, G142D, R158G, L452R, T478K, *D614G*, P681R, D950N, E156-, F157-
9	Kłoczew, Lubelskie	AY.122	T19R, G142D, R158G, L452R, T478K, *D614G*, P681R, D950N E156-, F157-
10	Stefanów, Łódzkie	BA.2	T19I, A27S, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, *D614G*, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K L24-, P25-, P26-

[i] bold – Y453F mutation; italic and bold – D614G mutation; underlined – substitutions in position 681

References

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Articles in this issue

DOI: https://doi.org/10.2478/jvetres-2022-0066 | Journal eISSN: 2450-8608 (formerly 2300-3235)

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Language: English

Page range: 449 - 458

Submitted on: Apr 13, 2022

Accepted on: Nov 15, 2022

Published on: Dec 3, 2022

Published by: National Veterinary Research Institute in Pulawy

In partnership with: Paradigm Publishing Services

Keywords:

SARS-CoV-2,

surveillance,

mink,

whole-genome sequencing,

Poland.

Related subjects:

Life sciences,

Molecular biology,

Microbiology and virology,

Life sciences, other,

Medicine,

Veterinary medicine

© 2022 Katarzyna Domańska-Blicharz, Anna Orłowska, Marcin Smreczak, Bas Oude Munnink, Paweł Trębas, Wojciech Socha, Krzysztof Niemczuk, Magdalena Kawiak-Sadurska, Justyna Opolska, Anna Lisowska, Aleksandra Giza, Arkadiusz Bomba, Ewelina Iwan, Marion Koopmans, Jerzy Rola, published by National Veterinary Research Institute in Pulawy
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Volume 66 (2022): Issue 4 (December 2022)

SARS-CoV-2 monitoring on mink farms in Poland

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Table 2

Table 3

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Table 4

Table 5

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