Broiler chickens with clinical signs of uneven growth, depression, and dull feathers were submitted to our laboratory and, at necropsy, lesions in proventriculus, gizzard, and intestines were detected. Fowl adenovirus serotype 1 (FAdV-1) was isolated from digestive tissues. The virus, assigned as FAdV-PL/G068/08, showed 99.5% nucleotide homology and 99.2% amino acid homology in hexon gene with chicken embryo lethal orphan (CELO) strain classified as the European reference of FAdV-1. One-day-old and 21-d-old SPF chickens were inoculated with FAdV-PL/068/08 by both nasal and ocular routes and then observed daily and examined by necropsy at 6, 10, and 14 d postinoculation. Experimental infection with isolated virus was fatal for younger chickens and major lesions occurred in the gizzards. No clinical or pathological changes were observed in chickens infected at 21 d of age, but the presence of intranuclear inclusion bodies in gizzard epithelial cells was detected. Molecular characterization was based on the long and short fibers genes sequencing and comparison of obtained sequences with other FAdV-1 strains. The homology between FAdV-PL/G068/08 and other sequences available in GenBank was between 98.9 and 99.8% (short fiber region) and 99.0 and 99.7% (long fiber region) at nucleotide level and between 98.4 and 100% (short fiber region) and 99.3 and 99.9% (long fiber region) at amino acid level. No correlation between identified amino acid changes in short and long fiber proteins and pathogenicity of studied FAdV-1 strains was observed. Although short and long proteins were indicated as factors influencing virus pathogenicity, the role of identified sequence differences in infectivity determination remain unclear.

Avian astroviruses (aAstVs) are divided into three species, Avastrovirus 1, Avastrovirus 2, and Avastrovirus 3, but there are a few strains are waiting to be assigned to an official taxonomic group. This study presents the molecular characterization of chicken astrovirus (CAstV), PL/G059/2014, which is involved in the induction of “white chicks” condition. The 7382-nucleotide-long genome sequence was determined by next-generation sequencing using an Illumina MiSeq System. Phylogenetic analysis showed that it has the characteristics that are typical of avian astroviruses. However, overall degree of nucleotide sequence identity was 43.6 % to 73.7 % between PL/G059/2014 and other available genome sequences of aAstV strains. The amino acid sequences of the proteins encoded by ORF1a and ORF1b of the studied strain were very similar (86.5-93.8 % identity) to those of CAstVs 4175 and GA2011, but they were only 32.7-35.2 % identical in the case of ORF2, which is used officially for astrovirus species demarcation. These features could suggest that the PL/G059/2014 strain should be assigned to a new species in the genus Avastrovirus. Moreover, the different phylogenetic topology of PL/G059/2014 and its nucleotide sequence similarity in different genomic regions could suggest that a recombination event occurred during its evolution and that it has ancestors in common with duck astroviruses.

Persistence of H5N1 high pathogenicity avian influenza virus (HPAIV), isolated during the epidemic in wild birds in Poland in 2006, was evaluated in three water samples derived from the sources known to host wild water birds (city pond, Vistula river mouth, and Baltic Sea). The virus was tested at two concentrations (10(4) and 10(6) median tissue culture infective dose per milliliter) and at three temperatures (4 C, 10 C, and 20 C), representing average seasonal temperatures in Poland. All tested water samples were filtered before virus inoculation, and one unfiltered sample (Baltic seawater) was also tested. Infectivity was determined twice a week over a 60-day trial period by microtiter endpoint titration. The persistence of the virus varied considerably depending on its concentration and also on physico-chemical parameters of the water, such as temperature and salinity. Avian influenza virus survival was the highest at 4 C and the lowest at 20 C. Prolonged infectivity of the virus in Baltic seawater (brackish, 7.8 ppt) was also seen. In distilled water, the virus retained its infectivity beyond the 60-day study period. Interestingly, a devastating effect of the unfiltered fraction of seawater was seen as the virus disappeared in this fraction the quickest in all studied combinations; thus, biologic factors may also affect infectivity of HPAIV.

Chicken astrovirus (CAstV) was recently indicated as the factor of the "white chicks" condition associated not only with increased embryo/chick mortality but also with weakness and white plumage of hatched chicks. In February 2014, organ samples (livers and kidneys) from dead-in-shell embryos, as well as 1-day-old whitish and normal chicks, were delivered from one hatchery in Poland for disease diagnosis. The samples originated from the same 30-week-old breeder flock in which the only observed abnormal signs were 4-5% decrease in the number of hatched chickens and the presence (about 1%) of weaker chicks with characteristic whitish plumage among normal ones. CAstV was detected in submitted samples and was then isolated in 10-day-old embryonated specific pathogen free (SPF) chicken eggs. We also reproduced an infection model for the "white chicks" condition in SPF layer chickens using the isolated PL/G059/2014 strain as the infectious agent. Results of experimental reproduction of the "white chicks" condition were somewhat more serious than field observation. The administration of the CAstV material into the yolk sac of 8-day-old SPF chicken eggs caused delay and prolongation of hatching, as well as death of embryos/chicks, and also a change of plumage pigmentation. Only two chicks of a total of 10 inoculated SPF eggs survived and were observed for 2 months. A gradual elimination of the CAstV genome was noted in this period. Moreover, a few contact-naive SPF chicks, which had been placed in the same cage, were infected with CAstV. Molecular characterization of detected CAstV was performed by nucleotide sequencing of the full ORF2 region encoding the capsid precursor protein gene. Phylogenetic studies showed that the PL/G059/2014 isolate clustered in the subgroup Aiii of CAstV. In the light of the new classification rules, the Polish PL/G059/2014 CAstV isolate could be assigned to a new species of the Avastrovirus genus.

Fig. 1 Structure of the p1643_10 plasmid. Circular map of the p1643_10 plasmid. Genes are 1 colour-coded depending on functional annotations: plasmid replication (blue boxes), plasmid 2 maintenance (pink), DNA methylation (light pink), conjugative plasmid transfer (green), 3 transposition/recombination (yellow), resistance (red), others (light blue). The two external box-4 circles depicture coding strands; the third circlepeseudogenes. The inner black circle indicate 5 regions identical (min. 99%) with pTC2, another IncA/C plasmid (GenBank Acc. No.

We examined 884 wild birds mainly from the Anseriformes, Charadriiformes and Galliformes orders for infectious bronchitis (IBV)-like coronavirus in Poland between 2008 and 2011. Coronavirus was detected in 31 (3.5%) of the tested birds, with detection rates of 3.5% in Anseriformes and 2.3% in Charadriiformes and as high as 17.6% in Galliformes. From the 31 positive samples, only 10 gave positive results in molecular tests aimed at various IBV genome fragments: five samples were positive for the RdRp gene, four for gene 3, eight for gene N and eight for the 3'-untranslated region fragment. All analysed genome fragments of the coronavirus strains shared different evolutionary branches, resulting in a different phylogenetic tree topology. Most detected fragment genes seem to be IBV-like genes of the most frequently detected lineages of IBV in this geographical region (i.e. Massachusetts, 793B and QX). Two waves of coronavirus infections were identified: one in spring (April and May) and another in late autumn (October to December). To our knowledge this is the first report of the detection of different fragment IBV-like genes in wild bird populations.

Variants assigned to GI-23 lineage of infectious bronchitis virus (IBV), formerly called Var2, have circulated for nearly 20 years only in countries of the Middle East. Strains of this lineage were first identified in Israel in 1998. More severe form of the virus appeared in 2006, when the second wave of Var2 epidemic has spread over the Middle East region. The present study describes the detection and detailed genetic characterization of the GI-23 viruses in Poland. The full-length genome of gammaCoV/Ck/Poland/G052/2016 strain consists of 27596 nucleotides and has typical organization for IBV (UTR5'-POl-S-3a-3b-E-M-4b-4c-5a-5b-N-UTR3'). The phylogenetic analysis of the complete sequence showed that it formed separate branch distinct from all of the full-length genome sequences analyzed in this study. Recombination analyses with other gammacoronaviruses revealed that Polish GI-23 strain may originate from recombination events and potential donors of build-in sequences are IBV of GI-1, GI-13 and G-19 lineages (Mass-, 793B- and QX-like strains, respectively). The 1a, 1b and N genes were involved in these recombination events. The source of virus introduction to the chicken population in Poland is unknown.

IntroductionSince April 2020, when the first SARS-CoV-2 infection was reported in mink and subsequently in mink farm workers in the Netherlands, it has been confirmed that human-to-mink and mink-to-human transmission can occur. Later, SARS-CoV-2 infections in mink were reported in many European and North American countries.Material and methodsSamples from 590 mink from a total of 28 farms were tested by real-time RT-PCR. Whole genome sequences from one positive farm were generated and genetic relatedness was established.ResultsSARS-CoV-2 RNA was detected on a breeder farm with stock of 5,850 mink. Active viraemia was confirmed in individually tested samples with Ct values respectively between 19.4 and 29.6 for E and N gene fragments. Further testing of samples from culled animals revealed 70% positivity in throat swabs and 30% seropositivity in blood samples. Phylogenetic analysis of full-length nucleotide sequences of two SARS-CoV-2 isolates revealed that they belong to the 20B Nextstrain clade. Several nucleotide mutations were found in analysed samples compared to the reference Wuhan HU-1 strain and some of them were nonsynonymous.ConclusionWe report the infection of mink with SARS-CoV-2 on one farm in Poland and the results of subsequent analysis of virus sequences from two isolates. These data can be useful for assessment of the epidemiological situation of SARS-CoV-2 in Poland and how it endangers public health.