Co-circulation of Hepatitis E Virus (HEV) Genotype 3 and Moose-HEV-Like Strains in Free-Ranging-Spotted Deer (Axis axis) in Uruguay.

Hepatitis E caused by hepatitis E virus (HEV) is considered an emerging foodborne zoonosis in industrialized, non-endemic countries. Domestic pigs and wild boars are considered the main reservoir of HEV. However, HEV can also infect an ever-expanding host range of animals, but they exact role in transmitting the virus to other species or humans is mostly unknown. In this work, we investigated the spread of HEV in free-living and captive spotted deer (Axis axis) from Uruguay in a 2-year period (2020-2022) and examined the role of this invasive species as a new potential reservoir of the virus. In addition, with the aim to gain new insights into viral ecology in the context of One Health, by using camera trapping, we identified and quantified temporal and spatial coexistence of spotted deer, wild boars, and cattle. In free-living animals, we detected an anti-HEV seropositivity of 11.1% (6/54). HEV infection and viral excretion in feces were assessed by RT-PCR. Thirteen of 19 samples (68.4%) had HEV RNA. Six samples were amplified using a broadly reactive RT-PCR and sequenced. No captive animal showed evidence of HEV infection. Additionally, HEV RNA was detected in a freshwater pond shared by these species. Phylogenetic and p-distance analysis revealed that zoonotic HEV genotype 3 strains circulate together with unclassified variants related to moose HEV whose potential risk of transmission to humans and other domestic and wild animals is unknown. The data presented here suggest that spotted deer (A. axis) may be a novel host for zoonotic HEV strains.

An evolutionary insight into Severe Acute Respiratory Syndrome Coronavirus 2 Omicron variant of concern.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel virus that belongs to the family Coronaviridae. This virus produces a respiratory illness known as coronavirus disease 2019 (COVID-19) and is to blame for the pandemic of COVID-19. Due to its massive circulation around the world and the capacity of mutation of this virus, genomic studies are much needed in to order to reveal new variants of concern (VOCs). On November 26th, 2021, the WHO announced that a new SARS-CoV-2 VOC, named Omicron, had emerged. In order to get insight into the emergence, spread and evolution of Omicron SARS-CoV-2 variants, a comprehensive phylogenetic study was performed. The results of these studies revealed significant differences in codon usage among the S genes of SARS-CoV-2 VOCs Alfa, Beta, Gamma, Delta and Omicron, which can be linked to SARS-CoV-2 genotypes. Omicron variant did not evolve out of one of the early VOCs, but instead it belongs to a complete different genetic lineage from previous ones. Strains classified as Omicron variants evolved from ancestors that existed around May 15th, 2020, suggesting that this VOC may have been circulating undetected for a period of time until its emergence was observed in South Africa. A rate of evolution of 5.61 × 10-4 substitutions/site/year was found for Omicron strains enrolled in these analyses. The results of these studies demonstrate that S genes have suitable genetic information for clear assignment of emerging VOCs to its specific genotypes.

Phylogenetic analysis of SARS-CoV-2 viruses circulating in the South American region: Genetic relations and vaccine strain match.

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.

Molecular accuracy vs antigenic speed: SARS-CoV-2 testing strategies.

The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has hit every corner of the world faster than any infectious disease ever known. In this context, rapid and accurate testing of positive cases are essential to follow the test-trace-isolate strategy (TETRIS), which has proven to be a key approach to constrain viral spread. Here, we discuss how to interpret and combine molecular or/and antigen-based detection methods for SARS-CoV-2 as well as when they should be used. Their application can be cleverly designed as an algorithm to prevent viral dissemination according to distinct epidemiological contexts within surveillance programs.

Hepatitis E Virus (HEV) infection in captive white-collared peccaries (Pecari tajacu) from Uruguay.

Hepatitis E virus (HEV) infection is a major cause of acute hepatitis worldwide. Clinical presentation of hepatitis E mainly occurs as an acute and self-limited disease, though chronic cases are now being commonly reported in immunocompromised individuals. In high-income developed areas and non-endemic regions, HEV is mainly transmitted by the zoonotic route through direct contact with infected animals or by consumption of contaminated meat products. Although pigs and wild boars are the main reservoirs of the disease, HEV can also infect deer, camels, and rats and seems to have an ever-expanding host range. Peccaries (Tayassuidae family, superfamily Suoidea), the 'new world pigs', share susceptibility to several pathogens with domestic pigs and wild boars. Herein, we performed a serological and molecular survey of two captive populations of white-collared peccaries (Pecari tajacu) from Uruguay, with the aim to assess the role of the species as an HEV reservoir. One-hundred and one serum samples were analysed for anti-HEV antibodies. Further evidences of active HEV infection were investigated in stool by RT-nested PCR. Animals from both wildlife reserves were exposed to HEV with an overall prevalence of 24.7%. Moreover, HEV RNA could be detected in peccaries' stool samples from one of the reserves. Phylogenetic analysis clustered the strains within HEV-3, closely related to both human and swine isolates. Our work provides the first evidences supporting the notion that white-collared peccaries are susceptible to HEV. However, these data should not be overinterpreted. Further research is needed concerning the role of peccaries in the transmission of HEV.