Jozef I. Nissimov

Cell-associated viral community composition and its functional potential in a dimictic lake on the Canadian Shield

The paper characterizes the seasonal dynamics of cell-associated viral communities in Big Turkey Lake, identifies their functional roles through auxiliary metabolic genes, and reconstructs viral genomes.

Gas-vacuolate Microcystis evolves cyanophage resistance under low nitrogen conditions

The paper shows gas-vacuolate Microcystis aeruginosa develops virus resistance under low nitrogen, with a mutation in a nitrogen transporter linked to this adaptation.

A jumbo cyanophage encodes the most complete ribosomal protein set in the known virosphere

The paper reannotates the genome of the jumbo cyanophage PhiMa05, revealing it encodes multiple ribosomal proteins and related genes, suggesting horizontal gene transfer to host bacteria.

A Genome Sequence Variant Monitoring Program for Seasonal Influenza A H3N2 and Respiratory Syncytial Virus A using Wastewater-Based Surveillance in Ontario, Canada

This paper develops and implements wastewater-based surveillance methods to monitor Influenza A H3N2 and respiratory syncytial virus A in Ontario, Canada, enabling real-time tracking of viral lineages and informing public health decisions.

Hybrid sequencing reveals the genome of a Chrysochromulina parva virus and highlight its distinct replication strategy

The paper reports the complete genome sequence of CpV-BQ1, a phycodnavirus infecting Chrysochromulina parva, and shows its phylogenetic relationship to other viruses in the Megaviricetes phylum.

AlphaFold 3 proteomic modelling reveals multiple photosystem structural homologs in freshwater cyanophages

The paper uses AlphaFold 3 and DALI to predict structures and functions of viral genes in cyanophages, identifying 28 new structural homologs including cyanobacteriochrome.

Structural models predict a significantly higher binding affinity between the NblA protein of cyanophage Ma-LMM01 and the phycocyanin of Microcystis aeruginosa NIES-298 compared to the host homolog

The paper uses structural modeling to show that the viral NblA protein from cyanophage Ma-LMM01 binds more strongly to host phycocyanin than the host's own NblA.

Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data

The paper evaluates nine computational tools for identifying SARS-CoV-2 lineages in wastewater sequencing data using simulated samples, finding most tools reliably detect lineages above 5% frequency.