Announcement of two complete coding genomes of mink coronavirus and one partial coding genome of mink enteric calicivirus from mink in Denmark

ABSTRACT

Two complete coding genomes of mink coronavirus and one partial coding genome of the sapovirus mink enteric calicivirus were assembled from metagenomic sequencing data from mink on different farms with diarrhea outbreaks in 2015 in Denmark.

ANNOUNCEMENT

Mink coronaviruses (MCoVs) belonging to the species Alphacoronavirus neovisontis, family Coronaviridae has previously been associated with gastrointestinal disorders in farmed mink (Neogale vison) (1). Few complete sequences of MCoV strains and even fewer and only partial genome sequences of mink enteric calicivirus (MEC), belonging to the genus Sapovirus (genotype GXII) in the Caliciviridae family, appear presently in GenBank. This virus has also been linked to disease, as it has been isolated from diarrheic mink (2), and the replication and location of mink sapovirus in the crypts and basis of the villi of the small intestine from diarrheic mink kits has been visualized by in situ hybridization (3).

This report describes the detection and sequencing of complete coding genomes of MCoV strains and a partial coding genome of MEC from two minks on different farms sampled in 2015 in Denmark.

Mink feces samples, from farms experiencing problems with diarrhea, were collected in July 2015. The samples were diluted in PBS to 10% and homogenized in a TissueLyser II (QIAGEN, Denmark). Nucleic acids were extracted using the QIAsymphony DSP Virus/Pathogen Mini Kit (QIAGEN, Denmark) on a QIAsymphony (QIAGEN, Denmark). The presence of coronavirus was tested with a broadly reactive panCoV RT-qPCR assay (4, 5). Two RNA samples testing positive for coronavirus were selected for sequencing using a non-targeted metagenomic protocol as previously described (6). Briefly, dsDNA was generated using the NEBNext mRNA second strand synthesis kit (New England Biolabs), library preparation performed with the Nextera-XT DNA library Preparation kit, and sequencing done on a MiSeq machine with Reagent Kit v3 600 bp (Illumina Inc, San Diego, CA, USA).

Taxonomic identification on read level was performed with Kaiju (7) (Table 1), read quality assessed using FastQC (8), and trimming performed with BBDuk (9) (default parameters) using Geneious Prime (10). Trimmed reads were de novo assembled using the SPAdes plugin v. 3.10.0 for metagenomic data (default parameters) (11). A single contig covering the complete coding genome of MCoV was generated for each of the two samples 11917-2 and 11918-1, as well as a single contig with the partial coding genome of MEC in sample 11917-2 (Table 1). Contigs were polished using trimmed reads, and consensus sequences were extracted after visual evaluation. These were queried by BLASTn, aligned to the highest scoring reference genomes, and annotated.

TABLE 1.

Overview of samples, read data, and assemblies described in this study

Parameters	Data set	Data set
Sample number	11918-1	11917-2
Total reads	453,092	2,728,992
Trimmed reads	420,000	2,300,000
Read length (min.–max.)	35–301	35–301
Relevant results from Kaiju analysis	Alphacoronavirus	Alphacoronavirus, Sapovirus
Virus strain	MCoV1/11918-1/DK/2015	MCoV1/11917-2/DK/2015	MEC/11917-2/DK/2015
Trimmed reads mapped (approx. count)	85,600	460,000	1,700
Mean mapped read length (approx. bp)	180	170	160
Mean read coverage depth	546	2,800	37
Assembled genome length (bp)	28,914	28,910	7,327
GC content (%)	37.1	37.2	57.0
Closest BLASTn match (by % ID)	PQ451285, Mink coronavirus isolate MCoV/46351- 1_Case/DK/2019	PQ451290, Mink coronavirus isolate MCoV/46367- 5_Case/DK/2019	KX000385, Sapovirus GXII/WD1237
Identity to BLASTn match; E-value	91.94%; E 0.0	93.69%; E 0.0	83.60%; E 0.0 (78 % query coverage length)

The MCoV shared 91% nucleotide identity and 92% amino acid identity, indicating two different strains. Concerning the MEC, conserved motifs previously described for sapoviruses (12, 13) were used to roughly identify the different non-structural and structural viral protein CDS in the genome. Hereby, it was possible to determine that the 5′-end of ORF1 encoding the polyprotein and 3′-end of ORF2 encoding VP2 were missing. MEC reads identified in publicly available metagenomic data from farmed mink in Denmark (14) were used to confirm the MEC sequence assembly. Assembly and read information are shown in Table 1.

AFTER EPUB

[This article was published on 12 November 2025 with errors in the third affiliation. The affiliation was corrected in the current version, posted on 28 November 2025.]

DATA AVAILABILITY

The data and sequences have been deposited and have been publicly available in GenBank since June 2020 under the BioProject PRJNA577843, nucleotide sequences MN535737, MN535736, and MN543743.