Lab Matters Spring 2022 - Page 15


APHL Conducts Global Bioinformatics Virtual Training for SARS-CoV-2

By Noah Hull , PhD , MPH , laboratory technical manager , Global Health ; Beth Skaggs , PhD , laboratory team lead , Division of Global Health Protection , Thailand MOPH-US Centers for Disease Control and Prevention ; and Eugene Yeboah , MSc , senior specialist , Global Health
On September 30 , 2021 , two international cohorts completed a seven-week SARS-CoV-2 / COVID-19 bioinformatics and genomic epidemiology training course organized by APHL . The virtual course was conducted in collaboration with Theiagen Genomics , a company specializing in next-generation sequencing ( NGS ) and bioinformatics and an APHL Platinum level sustaining member . It was funded by the US Centers for Disease Control and Prevention ( CDC ) Division of Global Health Protection , Bangkok , Thailand , through an APHL-CDC cooperative agreement to strengthen public health laboratories internationally .
Starting Small
The training courses are part of US efforts to strengthen multilateral cooperation in response to and recovery from the COVID-19 pandemic by building capacity in global health . APHL staff served as faculty , providing foundational virtual training on key NGS concepts , terminology and wet-bench methodologies for nucleic acid extraction and library preparation . The bioinformatics and genomic epidemiology training utilized the Terra . bio platform , which allowed participants to work hands-on with COVID-19 data and whole-genome sequences of SARS-CoV-2 to identify genomically-linked clusters of outbreaks . The Terra . bio platform was developed by the Broad Institute at the Massachusetts Institute of Technology and Harvard . This same platform has been rolled out to all interested US public health laboratories through an agreement with CDC and Theiagen Genomics .
Course participants learned new skills from bioinformatics and genomic epidemiology to utilize raw sequencing files to generate actionable public health data pertaining to the COVID-19 pandemic response and other infectious disease-associated outbreaks .
Opening session of the virtual Genomic Epidemiology course for particpants from the Asia Pacific Region , co-hosted by APHL and Theiagen Genomics
Additionally , participants were able to visualize outbreak-specific data and assess for novel or emerging variants of SARS-CoV-2 . Participants receive ongoing access to resources and computational infrastructure thanks to a donation from Google . org , and ad-hoc support from APHL , CDC and Theiagen Genomics .
A Bigger Impact
These cohorts are part of a larger SARS-CoV-2 education for the Asia Pacific Region , which began May 2021 . To date , a total of 223 participants from 14 countries ( Brunei , Cambodia , Ghana , Indonesia , Jamaica , Malaysia , Myanmar , Nepal , Pakistan , Philippines , Singapore , Thailand , Trinidad and Tobago , and Vietnam ) have been represented . This training has enabled the improved operation of SARS-CoV-2 genomic sequencing laboratories within these countries . Since the inception of these courses , over 15,000 unique SARS-CoV-2 genomes have been analyzed . In addition , several of the trained countries identified their first Omicron variants within their borders using the Terra . bio platform and Theiagen workflows .
As countries continue building their SARS-CoV-2 genomic infrastructure , a subset of countries has begun to pivot and utilize workflows for other infectious agents and use cases . Countries are beginning to explore workflows for HIV to assess phylogenetics and antiretroviral resistance , antimicrobial resistance in hospital-acquired infections , and for tuberculosis to assess phylogenetics and antimicrobial resistance in clinical specimens . In addition , other countries are looking at onboarding wastewater surveillance for SARS-CoV-2 using the Terra . bio platform and various workflows available for analysis .
The Terra . bio training courses will continue into 2022 and will remain dynamic based on the needs of the regions and the progression of the COVID-19 pandemic and associated responses . Additional trainings will also be delivered to meet increasing need for sequencing and genomic epidemiology . •
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