The Department of Virology at AFRIMS has a robust and technically advanced sequencing laboratory and bioinformatics core that allows the department to be a regional asset for next generation sequencing. In addition to the Illumina MiSeq and Oxford Nanopore MinIon platforms on hand, the Bioinformatics group utilizes an automated, in-house designed software pipeline for the alignment, assembly, analysis and interpretation of sequencing data. This capability not only provides advanced characterization of pathogens of interest, but to also develops and answers specific research questions through the utilization of their analysis capabilities to include:
  • Consensus sequence generation
  • Reference mapping
  • De novo assembly
  • Genome gene annotation
  • Multiple sequence alignment and comparison
  • Phylogenetic tree reconstruction
  • Effective population size reconstruction
  • Pathogen-specific analyses
Beyond the Department of Virology, the facilities are used to assist laboratory personnel from the Department of Bacterial and Parasitic Diseases and the Department of Entomology in enhancing the effectiveness of next generation sequencing in the study of bacteria, parasites and mosquito genomes.

Within this advanced molecular biology core, the sequencing platforms and servers are an integral part of a wider disease surveillance network that extends throughout South, East and Southeast Asia. The resources of this section are routinely used to:
  • Support regional influenza surveillance to investigate the effectiveness of the current vaccine strain selection
  • Provide genetic characterization of the SARS-CoV-2 virus
  • Provide advanced characteristics of numerous arboviruses to include dengue, Zika and chikungunya viruses
  • Provide analytical training to colleagues within the Institute, at external sites within our surveillance network, and with our government, military and academic collaborators, upon request.
Bioinformatics works with partners across Southeast Asia and around the world including partner militaries, U.S. government and DOD agencies, non- and intergovernmental organizations, academic universities and industry laboratories. 
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