RESUMO
Hepatitis E virus (HEV) infection is prevalent among domestic pigs and wild boar in Europe. This study focused on the genetic diversity of HEV subtypes 3c, 3e and 3f among swine and wild boar in Europe as well as their circulation. Phylogenetic analysis and Bayesian phylogenetic inference were applied on the selected ORF2 capsid HEV sequences to co-estimate the viral circulation, the mean evolutionary rates and the dated trees. The estimated mean values of the HEV ORF2 capsid gene evolutionary rate were 8.29 x 10-3, 5.96 x 10-3, and 1.107 x 10-2 substitutions/site/year, respectively for 3c, 3e and 3f. The majority of the HEV 3c and 3e supported clusters did not show intermixing between swine and wild boar. Thus, although the intermixing observed in a minority of HEV 3c and 3e supported clusters suggests that transmission/circulation of these subtypes between swine and wild boar can potentially occur, 3c and 3e European wild boar HEV populations remained mainly segregated. In contrast, one half of the HEV 3f supported clusters showed intermixing between swine and wild boar, providing evidence for transfer/circulation to swine. The data suggest that continued virologic surveillance in swine and wild boar is necessary, together with targeted measures to reduce the chance of HEV transmission to humans.
Assuntos
Vírus da Hepatite E , Hepatite E , Filogenia , Sus scrofa , Doenças dos Suínos , Animais , Vírus da Hepatite E/genética , Vírus da Hepatite E/classificação , Vírus da Hepatite E/isolamento & purificação , Suínos , Europa (Continente) , Sus scrofa/virologia , Hepatite E/veterinária , Hepatite E/virologia , Hepatite E/epidemiologia , Doenças dos Suínos/virologia , Doenças dos Suínos/epidemiologia , Variação GenéticaRESUMO
In this work, we studied the selective pressure and evolutionary analysis on the SARS-CoV-2 BF.7 and BQ.1.1 lineages circulating in Italy from July to December 2022. Two different datasets were constructed: the first comprised 694 SARS-CoV-2 BF.7 lineage sequences and the second comprised 734 BQ.1.1 sequences, available in the Italian COVID-19 Genomic (I-Co-Gen) platform and GISAID (last access date 15 December 2022). Alignments were performed with MAFFT v.7 under the Galaxy platform. The HYPHY software was used to study the selective pressure. Four positively selected sites (two in nsp3 and two in the spike) were identified in the BF.7 dataset, and two (one in ORF8 and one in the spike gene) were identified in the BQ.1.1 dataset. Mutation analysis revealed that R408S and N440K are very common in the spike of the BF.7 genomes, as well as L452R among BQ.1.1. N1329D and Q180H in nsp3 were found, respectively, at low and rare frequencies in BF.7, while I121L and I121T were found to be rare in ORF8 for BQ.1.1. The positively selected sites may have been driven by the selection for increased viral fitness, under circumstances of defined selective pressure, as well by host genetic factors.
RESUMO
INTRODUCTION: A COVID-19 outbreak occurred at the end of October 2021 among pilgrims returning from Medjugorje (Bosnia and Herzegovina). METHODOLOGY: Whole genome sequencing (WGS) of SARS-CoV-2, epidemiological data, and phylogenetic analysis were used to reconstruct outbreak dynamics. RESULTS: The results suggest that only in one case, associated with the SARS-CoV-2 sub-lineage AY.9.2, it is possible to trace back the place of contagion to Medjugorje, while the other cases were likely to be acquired in the country of origin. CONCLUSIONS: The combined use of phylogenetic data derived from WGS, and epidemiological data allowed us to study epidemic dynamics and to formulate a possible hypothesis on the place of exposure to SARS-CoV-2. The identification of different sub-lineages of the SARS-CoV-2 Delta variant also suggested that different chains of transmission contributed to the outbreak.
Assuntos
COVID-19 , Humanos , COVID-19/epidemiologia , SARS-CoV-2/genética , Filogenia , Surtos de DoençasRESUMO
The "Investigating and translating genomic evidence for public health response to SARS-CoV-2 (INSIDE SARS-CoV-2)" project is part of the initiative "Joint science and technology cooperation call for joint project proposals for the years 2021-2023" promoted by the Italian Ministry of Foreign Affairs and International Cooperation (MAECI) and the Republic of India. To start the project activities, the pandemic response and the epidemiological situation in Italy and in India, together with the genomic surveillance strategies for SARS-CoV-2 virus in the two countries, are here described.