Presence of pandemic H1N1 influenza virus by qRT-PCR in samples collected at 3, 5, and 7 days post infection (dpi).^*

*<p>15 pigs were infected with either the A/CA/04/2009 (CA/09) or A/Mexico/4108/2009 (MX/09) pandemic H1N1 virus isolates. Number of pigs positive out of 5 is reported from each group euthanized on 3, 5, or 7 dpi; LN = inguinal lymph node tissue sample.</p

Presence of pandemic H1N1 influenza virus by virus isolation in samples collected at 3, 5, and 7 days post infection (dpi).^*

*<p>15 pigs were infected with either the A/CA/04/2009 (CA/09) or A/Mexico/4108/2009 (MX/09) pandemic H1N1 virus isolates. Number of pigs positive out of 5 is reported from each group euthanized on 3, 5, or 7 dpi; LN = inguinal lymph node tissue sample.</p

Arctic Lineage-Canine Distemper Virus as a Cause of Death in Apennine Wolves (<i>Canis lupus</i>) in Italy

<div><p>Canine distemper virus (CDV) infection is a primary threat affecting a wide number of carnivore species, including wild animals. In January 2013, two carcasses of Apennine wolves (<i>Canis lupus</i>) were collected in Ortona dei Marsi (L'Aquila province, Italy) by the local Veterinary Services. CDV was immediately identified either by RT-PCR or immunohistochemistry in lung and central nervous tissue samples. At the same time, severe clinical signs consistent with CDV infection were identified and taped (<b><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082356#pone.0082356.s001" target="_blank">Videos S1</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082356#pone.0082356.s003" target="_blank">S3</a></b>) from three wolves rescued in the areas surrounding the National Parks of the Abruzzi region by the Veterinary Services. The samples collected from these symptomatic animals also turned out CDV positive by RT-PCR. So far, 30 carcasses of wolves were screened and CDV was detected in 20 of them. The sequencing of the haemagglutinin gene and subsequent phylogenetic analysis demonstrated that the identified virus belonged to the CDV Arctic lineage. Strains belonging to this lineage are known to circulate in Italy and in Eastern Europe amongst domestic dogs. To the best of our knowledge this is the first report of CDV Arctic lineage epidemics in the wild population in Europe.</p></div

Map illustrating the distribution of CDV positive animals in Abruzzi region.

<p>Map was generated using Quantum GIS (QGIS) software, version 1.8.0.</p

Immunohistochemistry (IHC) for CDV on lung tissue of wolf Wa. Bronchiolar epithelial cells and inflammatory cells filling the airways show a strong and specific CDV immuno-reactivity.

<p>Scale bar = 100 µm.</p

Neighbour-joining tree inferred from multiple nucleotide sequence alignment of the H encoding gene of selected CDV strains retrieved from GenBank.

<p>Sequences obtained in this study are marked with a circle.</p

Immunohistochemistry (IHC) for CDV on cerebral cortex tissue of wolf Wa. xNeurons from the cerebral cortex show a strong and specific CDV immuno-reactivity.

<p>Scale bar = 100 µm.</p

Indirect immunofluorescence (IIF) for detection IgM antibodies performed on the serum sample of wolf W1.

<p>Scale bar = 100 µm.</p

Data_Sheet_3_The Delta variant wave in Tunisia: Genetic diversity, spatio-temporal distribution and evidence of the spread of a divergent AY.122 sub-lineage.PDF

IntroductionThe Delta variant posed an increased risk to global public health and rapidly replaced the pre-existent variants worldwide. In this study, the genetic diversity and the spatio-temporal dynamics of 662 SARS-CoV2 genomes obtained during the Delta wave across Tunisia were investigated.MethodsViral whole genome and partial S-segment sequencing was performed using Illumina and Sanger platforms, respectively and lineage assignemnt was assessed using Pangolin version 1.2.4 and scorpio version 3.4.X. Phylogenetic and phylogeographic analyses were achieved using IQ-Tree and Beast programs.ResultsThe age distribution of the infected cases showed a large peak between 25 to 50 years. Twelve Delta sub-lineages were detected nation-wide with AY.122 being the predominant variant representing 94.6% of sequences. AY.122 sequences were highly related and shared the amino-acid change ORF1a:A498V, the synonymous mutations 2746T>C, 3037C>T, 8986C>T, 11332A>G in ORF1a and 23683C>T in the S gene with respect to the Wuhan reference genome (NC_045512.2). Spatio-temporal analysis indicates that the larger cities of Nabeul, Tunis and Kairouan constituted epicenters for the AY.122 sub-lineage and subsequent dispersion to the rest of the country.DiscussionThis study adds more knowledge about the Delta variant and sub-variants distribution worldwide by documenting genomic and epidemiological data from Tunisia, a North African region. Such results may be helpful to the understanding of future COVID-19 waves and variants.</p

Image_1_The Delta variant wave in Tunisia: Genetic diversity, spatio-temporal distribution and evidence of the spread of a divergent AY.122 sub-lineage.TIF

IntroductionThe Delta variant posed an increased risk to global public health and rapidly replaced the pre-existent variants worldwide. In this study, the genetic diversity and the spatio-temporal dynamics of 662 SARS-CoV2 genomes obtained during the Delta wave across Tunisia were investigated.MethodsViral whole genome and partial S-segment sequencing was performed using Illumina and Sanger platforms, respectively and lineage assignemnt was assessed using Pangolin version 1.2.4 and scorpio version 3.4.X. Phylogenetic and phylogeographic analyses were achieved using IQ-Tree and Beast programs.ResultsThe age distribution of the infected cases showed a large peak between 25 to 50 years. Twelve Delta sub-lineages were detected nation-wide with AY.122 being the predominant variant representing 94.6% of sequences. AY.122 sequences were highly related and shared the amino-acid change ORF1a:A498V, the synonymous mutations 2746T>C, 3037C>T, 8986C>T, 11332A>G in ORF1a and 23683C>T in the S gene with respect to the Wuhan reference genome (NC_045512.2). Spatio-temporal analysis indicates that the larger cities of Nabeul, Tunis and Kairouan constituted epicenters for the AY.122 sub-lineage and subsequent dispersion to the rest of the country.DiscussionThis study adds more knowledge about the Delta variant and sub-variants distribution worldwide by documenting genomic and epidemiological data from Tunisia, a North African region. Such results may be helpful to the understanding of future COVID-19 waves and variants.</p