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Highly pathogenic influenza A virus (HPIAV) H5N1 within the genetic clade 2.3.4.4b has emerged in wild birds in different regions of the world, leading to the death of >70 million birds. When these strains spread to pinniped species a remarkable mortality has also been observed. A detailed genetic characterization of HPIAV isolated from pinnipeds is essential to understand the potential spread of these viruses to other mammalian species, including humans. To gain insight into these matters a detailed phylogenetic analysis of HPIAV H5N1 2.3.4.4b strains isolated from pinniped species was performed. The results of these studies revealed multiple transmission events from birds to pinnipeds in all world regions. Different evolutionary histories of different genes of HPIAV H5N1 2.3.4.4b strains gave rise to the viruses infecting pinnipeds in different regions of the world. European strains isolated from pinnipeds represent a completely different genetic lineage from strains isolated from South American ones. All strains isolated from pinnipeds bear characteristics of a highly pathogenic form for of avian influenza in poultry. Amino acid substitutions, previously shown to confer an adaptive advantage for infecting mammals, were observed in different genes in all pinniped species studied.

The ongoing H5N1 outbreak in the Americas caused by clade 2.3.4.4 is causing unprecedented impact in poultry and wild birds. In November 2022, a highly pathogenic avian influenza A outbreak was declared in poultry in Ecuador, affecting more than 1.1 million heads of poultry in two farms by February 2023. Phylogenetic analysis shows that the virus clade is 2.3.4.4b, and to the best of our knowledge, this is the first scientific publication reporting this clade in South America.

Hepatitis C virus (HCV) remains a significant global health challenge, affecting millions of people worldwide, with chronic infection a persistent threat. Despite the advent of direct-acting antivirals (DAAs), challenges in diagnosis and treatment remain, compounded by the lack of an effective vaccine. The HCV genome, characterized by high genetic variability, consists of eight distinct genotypes and over ninety subtypes, underscoring the complex dynamics of the virus within infected individuals. This study delves into the intriguing realm of HCV genetic diversity, specifically exploring the phenomenon of mixed infections and the subsequent detection of recombinant forms within the conserved internal ribosome entry site (IRES) region. Previous studies have identified recombination as a rare event in HCV. However, our findings challenge this notion by providing the first evidence of 1a/3a (and vice versa) inter-genotypic recombination within the conserved IRES region. Utilizing advanced sequencing methods, such as deep sequencing and molecular cloning, our study reveals mixed infections involving genotypes 1a and 3a. This comprehensive approach not only confirmed the presence of mixed infections, but also identified the existence of recombinant forms not previously seen in the IRES region. The recombinant sequences, although present as low-frequency variants, open new avenues for understanding HCV evolution and adaptation.

Since the safety of new-generation polyester-based internal coatings regarding the migration of non-intentionally added substances (NIAS) is poorly documented, studies are needed to identify NIAS originating from these food-contact materials (FCM). The aim of this study was to identify volatile and semi-volatile NIAS from polyester-based coatings in order to assess their hazard and ensure consumers' safety with regard to exposure from canned food. Extraction and migration tests were carried out on a single polyester-coated tin plate (5 batches) using two solvents: acetonitrile and ethanol 95%, then FCM's extracts and migrates were analysed by GC-MS. An antioxidant degradation (hydrolysis) product, 3-(3,5-di-tert-butyl-4-hydroxyphenyl)propionic acid or fenozan (CAS RN: 20170-32-5), was identified and confirmed by reference standard in all migrates. To assess fenozan's toxicity, several in vitro bioassays, such as the Ames test (to assess point mutation), the micronucleus assay (to detect chromosomal aberrations), and the iodide uptake assay (to study one mode of action for thyroid disruption) were conducted. Fenozan was negative in the Ames test on three strains of S. typhimurium (TA98, TA100, and TA1535) and on one strain of E.coli (WP2), with and without metabolic activation system (S9 mix) using direct incorporation and pre-incubation methods. The in vitro micronucleus assay conducted on HepG2 cells also exhibited a negative response following a 4-hour treatment with the S9 mix, and a 48-hour treatment without the S9 mix. A weak inhibitory effect was obtained when testing fenozan in the iodide uptake assay using rat thyroid FRTL-5 cells. Significant inhibition started from 800 µM of fenozan, with a maximal inhibition of almost 47% at 1000 µM. The findings indicate that fenozan exhibits an anti-thyroid activity in vitro. [ABSTRACT FROM AUTHOR]

Context: The contamination of feedstuffs with multi-mycotoxins and their transfer to milk is an important concern because it can affect the health of both animals and humans. Aims: This study determined the nutrient composition and quantified the mycotoxins present in dairy feedstuffs and in cow's milk. Methods: Samples of feedstuffs and milk were collected from 11 dairy farms in northern Tunisia for physicochemical composition and mycotoxin analyses. The extraction of mycotoxins was performed by the QuEChERS procedure and the presence of 26 mycotoxins was checked using liquid or gas chromatography with tandem mass spectrometry (LC–MS/MS and GC–MS/MS). Key results: Nutrient contents differ among feedstuffs (P < 0.05). The pH values of oat, ryegrass and pulp silages varied from 4.6 to 5.3. Dry-matter (DM) content was highest for concentrate feeds and hay (90% and 86% DM respectively). Crude protein (CP) content was highest in concentrate feeds (15.8% DM). The neutral detergent fibre, acid detergent fibre and acid detergent lignin contents were highest in green grass, hay, and silage. Eight Fusarium mycotoxins, enniatins (ENA1, ENB, ENB1), beauvericine (BEA), HT-2 toxin (HT-2), deoxynivalenol (DON), 15-acetyldeoxynivalenol (15-ADON), Fumonisin B2 (FB2) and one Alternaria mycotoxin tentoxin (TENT) were detected at low concentrations. There was a significant (P < 0.05) difference in the levels of contamination by ENB between the samples of forages and concentrate feeds. The ENs (ENA1, ENB, ENB1) were the most frequently detected combination of mycotoxins. Milk analysis for fat, CP, lactose and dehydrated dry extract averaged 3.49%, 3.10%, 4.71%, and 8.77% respectively; urea concentration was of 34.01 mg/dL, milk pH was 6.5, and a somatic cell count of 1168.63 103 cells/mL was found. Most milk samples (82%) were contaminated with ENB. Conclusions: The levels of mycotoxin contamination in feedstuffs and milk were low and do not present a risk for dairy cattle and consumer health. Implications: Mycotoxins in feedstuffs and milk should be regularly analysed to make sure that quality and safety standards are met. The safety and nutritional quality of milk for human consumption depends on the quality of the feed sources consumed by dairy cattle. Our study has shown that mycotoxins, harmful toxins, detected in some feed sources (e.g. forage silages, hay and concentrates) could be transferred to milk. Strategies for efficient management of feed sources should be developed and the transferability of mycotoxins to milk should be controlled to ensure that the food supply chain is safe and free from harmful toxins. [ABSTRACT FROM AUTHOR]

Abstract Background Direct-Acting agents (DAAs) target and inhibit essential viral replication proteins. They have revolutionized the treatment of Hepatitis C virus (HCV) infection reaching high levels of sustained virologic response. However, the detection of basal resistance-associated substitutions (RASs) to DAAs in naïve patients could be important in predicting the treatment outcome in some patients exhibiting failures to DAA-based therapies. Therefore, the aim of this work was to evaluate the presence of RASs as minority variants within intra-host viral populations, and assess their relationship to response to therapy on a multiple times relapser patient infected chronically with HCV. Case presentation A male HCV infected-patient with a genotype 1a strain was evaluated. He had previously not responded to dual therapy (pegylated interferon-α plus ribavirin) and was going to start a direct-acting agent-based therapy (DAAs). He showed no significant liver fibrosis (F0). Viral RNA was extracted from serum samples taken prior and after therapy with DAAs (sofosbubir/ledipasvir/ribavirin). NS5A and NS5B genomic regions were PCR-amplified and the amplicons were sequenced using Sanger and next-generation sequencing (NGS) approaches. RASs were searched in in-silico translated sequences for all DAAs available and their frequencies were determined for those detected by NGS technology. Sanger sequencing did not reveal the presence of RASs in the consensus sequence neither before nor after the DAA treatment. However, several RASs were found at low frequencies, both before as well as after DAA treatment. RASs found as minority variants (particularly substitutions in position 93 within NS5A region) seem to have increased their frequency after DAA pressure. Nevertheless, these RASs did not become dominant and the patient still relapsed, despite perfect adherence to treatment and having no other complications beyond the infection (no significant fibrosis, no drug abuse). Conclusions This report shows that some patients might relapse after a DAA-based therapy even when RASs (pre- and post-treatment) are detected in very low frequencies (

The pandemic of coronavirus disease 2019 (COVID-19) is caused by a novel member of the family Coronaviridae, now known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recent studies revealed the emergence of virus variants with substitutions in the spike and/or nucleocapsid and RNA-dependent RNA polymerase proteins that are partly responsible for enhanced transmission and reduced or escaped anti-SARS-CoV-2 antibodies that may reduce the efficacy of antibodies and vaccines against the first identified SARS-CoV-2 strains. In order to gain insight into the emergence and evolution of SARS-CoV-2 variants circulating in the South American region, a comprehensive phylogenetic study of SARS-CoV-2 variants circulating in this region was performed. The results of these studies revealed sharp increase in virus effective population size from March to April of 2020. At least 62 different genotypes were found to circulate in this region. Variants of concern (VOCs) Alpha, Beta, Gamma and Delta co-circulate in the region, together with variants of interest (VOIs) Lambda, Mu and Zeta. Most of SARS-CoV-2 variants circulating in the South American region belongs to B.1 genotypes and have substitutions in the spike and/or nucleocapsid and polymerase proteins that confer high transmissibility and/or immune resistance. 148 amino acid positions of the spike protein and 70 positions of the nucleocapsid were found to have substitutions in different variants isolated in the region by comparison with reference strain Wuhan-Hu-1. Significant differences in codon usage among spike genes of SARS-CoV-2 strains circulating in South America was found, which can be linked to SARS-CoV-2 genotypes.

The genetic material of the three domains of life (Bacteria, Archaea, and Eukaryota) is always double-stranded DNA, and their GC content (molar content of guanine plus cytosine) varies between ≈ 13% and ≈ 75%. Nucleotide composition is the simplest way of characterizing genomes. Despite this simplicity, it has several implications. Indeed, it is the main factor that determines, among other features, dinucleotide frequencies, repeated short DNA sequences, and codon and amino acid usage. Which forces drive this strong variation is still a matter of controversy. For rather obvious reasons, most of the studies concerning this huge variation and its consequences, have been done in free-living organisms. However, no recent comprehensive study of all known viruses has been done (that is, concerning all available sequences). Viruses, by far the most abundant biological entities on Earth, are the causative agents of many diseases. An overview of these entities is important also because their genetic material is not always double-stranded DNA: indeed, certain viruses have as genetic material single-stranded DNA, double-stranded RNA, single-stranded RNA, and/or retro-transcribing. Therefore, one may wonder if what we have learned about the evolution of GC content and its implications in prokaryotes and eukaryotes also applies to viruses. In this contribution, we attempt to describe compositional properties of ∼ 10,000 viral species: base composition (globally and according to Baltimore classification), correlations among non-coding regions and the three codon positions, and the relationship of the nucleotide frequencies and codon usage of viruses with the same feature of their hosts. This allowed us to determine how the base composition of phages strongly correlate with the value of their respective hosts, while eukaryotic viruses do not (with fungi and protists as exceptions). Finally, we discuss some of these results concerning codon usage: reinforcing previous results, we found that phages and hosts exhibit moderate to high correlations, while for eukaryotes and their viruses the correlations are weak or do not exist.

Abstract Background Host single-nucleotide polymorphisms (SNPs) near the interleukin 28B (IL28B) locus are associated with sustained virological response to antiviral therapy and with spontaneous Hepatitis C Virus (HCV) clearance. Prevalence of these SNPs varies depending on ethnicity. The impact of IL28B SNPs in HCV-infected patients is currently unknown in Uruguay. Therefore, the aim of this study was to evaluate and compare the distribution of polymorphisms in the IL28B gene (rs12979860 and rs8099917) among HCV-infected patients and healthy individuals in Uruguay and thus assess their possible association with the establishment of HCV infection. Methods DNA was recovered from 92 non-infected individuals and 78 HCV-infected patients and SNPs were determined by RFLP and allelic discrimination by real-time PCR. Results The distribution of rs12979860 genotypes for the infected population was 29.5%-CC, 47.4%-CT and 23.1%-TT and for the control group 45.7%, 42.4% and 11.9%, respectively. Prevalence in both infected and uninfected individuals is similar to that reported in other countries with admixed populations. The distribution of rs8099917 genotypes for the infected population was 57.7%-TT, 27.2%-TG and 14.1%-GG and for the control group 60.9%, 33.7% and 5.4%, respectively. The comparison of rs12979860 genotype distribution between the two populations evidenced a higher prevalence of the favourable genotype (CC) in the uninfected control group (p