From Clinical Specimen to Whole Genome Sequencing of A(H3N2) Influenza Viruses: A Fast and Reliable High-Throughput Protocol.

(1) Background: Over the last few years, there has been growing interest in the whole genome sequencing (WGS) of rapidly mutating pathogens, such as influenza viruses (IVs), which has led us to carry out in-depth studies on viral evolution in both research and diagnostic settings. We aimed at describing and determining the validity of a WGS protocol that can obtain the complete genome sequence of A(H3N2) IVs directly from clinical specimens. (2) Methods: RNA was extracted from 80 A(H3N2)-positive respiratory specimens.

Time and Mode of Epidemic HCV-2 Subtypes Spreading in Europe: Phylodynamics in Italy and Albania.

Hepatitis C virus (HCV) genotype 2 causes about 10% of global infections and has the most variable circulation profile in Europe. The history of "endemic" HCV-2 subtypes has been satisfactorily reconstructed, instead there is little information about the recent spread of the "epidemic" subtypes, including HCV-2c. To investigate the origin and dispersion pathways of HCV-2c, 245 newly characterized Italian and Albanian HCV-2 NS5B sequences were aligned with 247 publicly available sequences and included in phylogeographic and phylodynamic analyses using the Bayesian framework.

Origin and transmission of Feline coronavirus type I in domestic cats from Northern Italy: a phylogeographic approach.

Feline coronavirus (FCoV) is responsible, along with an inadequate immune response of the host, for Feline infectious peritonitis (FIP), one of the most frequent and deadly infectious feline disease worldwide. This study analyzed the genetic characteristics of the spike (S) gene of 33 FCoVs circulating in Northern Italy between 2011 and 2015 in cats with or without FIP. In order to reconstruct the most probable places of origin and dispersion of FCoV among Italian cats, a phylogeographic approach was performed based on 106 FCoV S gene partial sequences from cats, including the 33 novel Italian sequences and 73 retrieved from public databases.

Identification and Genetic Characterization of a Novel Respirovirus in Alpine Chamois (r).

The genus, family , includes respiratory viral pathogens. Here we report the identification and genetic characterization of a respirovirus in an Alpine chamois showing interstitial pneumonia associated with catarrhal bronchopneumonia. The full-genome characterization of this respirovirus, named ChamoisRV/IT2014, revealed low similarities to caprine respirovirus (77.

In-depth phylogenetic analysis of the hemagglutinin gene of influenza A(H3N2) viruses circulating during the 2016-2017 season revealed egg-adaptive mutations of vaccine strains.

: The authors conducted an in-depth phylogenetic analysis of the hemagglutinin (HA) gene of A(H3N2) identified during the 2016-2017 season to compare the circulating strains with both the egg-derived and cell-derived 2016-2017 candidate vaccine virus (CVV).: 162 HA1 sequences of H3N2 viruses identified during the 2016-2017 season were phylogenetically analyzed and compared with egg-/cell-derived CVV. The predicted vaccine efficacy (pVE) of egg-/cell-derived CVV against field strains was quantified by P model.