The development of sequencing technologies dramatically changed the course of epidemiological studies of infectious diseases. Virus genomics have already been used to investigate infectious disease outbreaks for several decades. Since the introduction of Next-generation Sequencing (NGS), the viral or bacterial whole genomes can be sequenced in a matter of days. Now, thanks to advances in high-throughput sequencing and decreasing costs, most virus genomics studies utilize data sets containing tens to thousands of complete genomes. While well-established sequencing platforms still provide robust insights, the real-time sequencing approaches and analysis opens up entirely new applications in the field of molecular epidemiology.

The advances in genome sequence technologies have improved the ability to track and understand the bacterial and viral transmission of animal diseases. Phylogenetic analysis of these genomes can be used to clarify the key questions in infectious disease epidemiology, from the initial detection and characterization of outbreak viruses to transmission chain tracking and outbreak mapping, which can now be much more accurately addressed using recent advances in virus sequencing and phylogenetics. The threat of emerging and re-emerging infectious diseases continues to be a challenge to public and global health security as well as animal health, and highlights that sequencing is not just a critical tool in bio-surveillance, it can also play a major role in pandemic or outbreak response.

The scope of the Research Topic is to explore the current status and future perspectives of sequencing technologies in the control and prevention of infectious diseases, including the elucidation of diagnosis, molecular evolution, distribution, and transmission of important veterinary infectious diseases. The collection welcomes, but is not limited to, Original Research, Methods, and Reviews in the following areas:

- Molecular surveillance of specific infections at the local, national, and international levels;

- Rapid detection and characterization of emerging pathogens;

- Whole and partial genome sequencing of viral and bacterial isolates;

- Short- and long-read sequencing approaches for infectious diseases control and prevention;

- Development of new bioinformatic tools for NGS data analysis.

Volume I: Sequencing and Phylogenetic Analysis as a Tool in Molecular Epidemiology of Veterinary Infectious Diseases

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Frontiers in Veterinary Science

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