A method using subtree pruning and regrafting-based tree assessment (SPRTA), which considers evolutionary relationships between lineages, enhances interpretability of phylogenetic analyses such as those of SARS-CoV-2 variants.

Bats are natural reservoirs for a wide range of RNA viruses. Members of the genus Betacoronavirus, including Severe Acute Respiratory Syndrome virus 2 (SARS-CoV-2) and Middle East Respiratory Syndrome...

Phylogenetic studies examining the origins, emergence, and spread of viruses have arguably been one of the most active and successful areas of evolutionary biology and form the bedrock of the flourishing field of genomic epidemiology. This, in part, reflects the ability of viruses, particularly those with RNA genomes, to evolve at rates much greater than their cellular counterparts (1). The rapid rate at which viruses evolve and accumulate mutations enables evolutionary signals to be identified through comparative genomics at short timescales relevant for outbreak investigation and response. The integration of phylogenetics and epidemiology, known as phylodynamics, has become a vital tool in response to numerous viral outbreaks, epidemics, and pandemics, including Ebola (2), Zika (3), and, more recently, COVID-19 (4) and mpox (5).

npj Viruses - Characterization of A(H1N1)pdm09 influenza viruses isolated between 2016 and 2019

Author summary The discovery of brine shrimp virga-like virus 1 (BSVV1) challenges the conventional view that positive- and negative-sense RNA viruses are evolutionarily independent. Through genomic a...

Abstract. Animal genomes are characterized by extensive variation in size. RNA viruses similarly exhibit substantial genomic diversity, with genome lengths

npj Viruses - Influenza B viruses are more susceptible to high temperatures than influenza A viruses

We analyzed metagenomic sequencing data obtained from fecal samples of hooded cranes and wild ducks that winter on the Izumi Plain in Japan. Various organisms were identified in each sample, and thei...

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has spread worldwide since its emergence in late 2021, and its sub-lineages are established in human society. Compared ...