Recombination is one of the major sources of genetic variation in viruses. RNA viruses, such as rabbit hemorrhagic disease virus (RHDV), are among the viruses with the highest recombination rates. Several recombination events have been described for RHDV, mostly as a consequence of their genomic architecture. Here, we undertook phylogenetic and recombination analyses of French and Swedish RHDV strains from 1994 to 2016 and uncovered a new intergenotypic recombination event. This event occurred in the late 1990s/early 2000s and involved nonpathogenic GI.3 strains as donors for the nonstructural part of the genome of these recombinants, while pathogenic GI.1d strains contributed to the structural part. These GI.3P–GI.1d recombinant strains did not entirely replace GI.1d (nonrecombinant) strains, but became the dominant strains in France and Sweden, likely due to a fitness advantage associated with this genomic architecture. GI.3P–GI.1d (P stands for polymerase) strains persisted until 2013 and 2016 in Sweden and France, respectively, and cocirculated with the new genotype GI.2 in France. Since strains from the first GI.2 outbreaks were GI.3P–GI.2, we hypothesize that GI.3P–GI.1d could be the parental strain. Our results confirm the outstanding recombination ability of RHDV and its importance in the evolution of lagoviruses, which was only revealed by studying complete genomic sequences.

Increased evidence suggests that cattle are the primary host of Influenza D virus (IDV) and may contribute to respiratory disease in this species. The aim of this study was to detect and characterise IDV in the Swedish cattle population using archived respiratory samples. This retrospective study comprised a collection of a total 1763 samples collected between 1 January 2021 and 30 June 2024. The samples were screened for IDV and other respiratory pathogens using real-time reverse transcription quantitative PCR (rRT-qPCR). Fifty-one IDV-positive samples were identified, with a mean cycle threshold (Ct) value of 27 (range: 15–37). Individual samples with a Ct value of <30 for IDV RNA were further analysed by deep sequencing. Phylogenetic analysis was performed by the maximum likelihood estimation method on the whole IDV genome sequence from 16 samples. The IDV strains collected in 2021 (n = 7) belonged to the D/OK clade, whereas samples from 2023 (n = 4) and 2024 (n = 5) consisted of reassortants between the D/OK and D/660 clades, for the PB2 gene. This study reports the first detection of IDV in Swedish cattle and the circulation of D/OK and reassortant D/OK-D/660 in this population.

During routine sampling of northern pike, a male Esox lucius with circular blue-metallic granular spots mainly located on the head and back was identified. Histological investigations presented multifocally thickened epidermis rich in basophilic large structures with a granulated rim and a dense, non-granulated center. Other organs showed no signs of infection. Ultrastructural analysis of the skin revealed three different types of herpes-like structures predominantly located within enlarged vacuoles. PCR analysis and NGS of dissected skin tissue verified the presence of EsHV1 DNA. In this study, we describe the first identification of EsHV1 in mainland Europe. In addition, for the first time, full sequences of both the DNA polymerase and terminase of the virus is available, thus allowing for an improved phylogenetic placement of EsHV1 within the Alloherpesviridae family. In addition to the EsHV1 infected pike, we also observed that 11.1% of the pike were affected by lymphosarcoma, a hyperplasia-disease caused by retroviruses. In conclusion, viral infections in pike are relatively common and likely have consequences for the local population dynamics.

The alloherpesvirus esocid herpesvirus 1 (EsHV-1) causes epidermal hyperplasia on the skin and fins of northern pike (Esox lucius). For the first time, we present a near-complete genome sequence of EsHV-1, directly obtained from a pike skin sample. The 223,553 bp sequence of the genome has a GC-content of 56.47% and is organised into a long, unique segment (148,159 bp) and a short, unique segment (45,925 bp). The short segment is flanked by inverted repeat sequences (IRSs) of 14,733/6 bp, with the IRS length difference attributed to a codon deletion. The genome is predicted to contain 144 open reading frames, including eight duplicated within the IRSs. The leftmost third of the genome contains genes of unknown function, but many of which exhibit extensive inter-gene homology, suggesting gene duplication. Six paralogous groups were identified, each containing two to thirteen gene members. Homologues of all twelve alloherpesvirus core genes are present. The ATPase subunit of the terminase and the DNA polymerase is composed of three and two exons, respectively. However, an alternate splicing pattern is found, for which, speculatively, a role is suggested in the terminase assembly at the capsid portal.