Phylodynamic and phylogeographic analysis of the complete genome of the West Nile virus lineage 2 (WNV-2) in the Mediterranean basin.

BACKGROUND: The West Nile virus is a highly contagious agent for a wide range of hosts. Its spread in the Mediterranean region raises several questions about its origin and the risk factors underlying the virus's dispersal. MATERIALS AND METHODS: The present study aims to reconstruct the temporal and spatial phylodynamics of West Nile virus lineage 2 in the Mediterranean region using 75 complete genome sequences from different host species retrieved from international databases. RESULTS: This data set suggests that current strains of WNV-2 began spreading in South Africa or nearby regions in the early twentieth century, and it migrated northwards via at least one route crossing the Mediterranean to reach Hungary in the early 2000s, before spreading throughout Europe. Another introduction event, according to the data set collected and analyses performed, is inferred to have occurred in around 1978. Migratory birds constitute, among others, additional risk factors that enhance the geographical transmission of the infection. CONCLUSION: Our data underline the importance of the spatial-temporal tracking of migratory birds and phylodynamic reconstruction in setting up an efficient surveillance system for emerging and reemerging zoonoses in the Mediterranean region.

Phylogenetic analysis of the neuraminidase segment gene of Influenza A/H1N1 strains isolated from Monastir Region (Tunisia) during the 2017-2018 outbreak.

Influenza A/H1N1 is widely considered to be a very evolutionary virus causing major public health problems. Since the pandemic of 2009, there has been a rapid rise in human Influenza virus characterization. However, little data is available in Tunisia regarding its genetic evolution. In light of this fact, our paper aim is to genetically characterize the Neuraminidase, known as the target of antiviral inhibitors, in Tunisian isolates circulating in Monastir region during 2017-2018. In total of 31 positive Influenza A/H1N1 detected by multiplex real-time PCR, RT-PCR of neuraminidase was performed. Among the 31 positive samples, 7 samples representing fatal and most severe cases were conducted for sequencing and genetic analysis. The results thus obtained showed genetic evolution of the A/H1N1 neuraminidase between 2009 and 2010 and 2018-2019 outbreaks. All Tunisian isolates were genetically related to the recommended vaccine strain with a specific evolution. Moreover, the phylogenetic analysis demonstrated that France and especially Italian strains were the major related strains. Interestingly, our results revealed a specific cluster of Tunisian isolates where two intragroup were evolved in correlation with the severity and the fatalities cases. From the outcome of our investigation, this study confirms the genetic evolution of the Influenza A virus circulating in Tunisia and gives a preliminary analysis for a better comprehension of new emerging Tunisian strain's virulence and thus, a more appropriate monitoring of Influenza virus A/H1N1 during each round of outbreaks. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11756-021-00723-y.