Standing up Sequencing for SARS-CoV-2 by Christin Hanigan , PhD , senior specialist , Advanced Molecular Detection
Variants of concern are viral variants that exhibit evidence of an increase in transmissibility , more severe disease ( increased hospitalizations or deaths ), significant reduction in neutralization by antibodies generated during previous infection or vaccination , reduced effectiveness of treatments or vaccines , or diagnostic detection failures . As these variants are discovered and spread , the demand to boost sequencing activities has increased .
In the United States , this necessity became apparent in December 2019 with the identification of the SARS-CoV-2 B . 1.1.7 variant in the United Kingdom . The Massachusetts State Public Health Laboratory
( MA SPHL ) had taken time to stand up sequencing for SARS-CoV-2 before the utility was fully recognized . Molecular Diagnostics and Virology Division Director Glen Gallagher , PhD and his team knew that viruses by nature evolve , and understanding and studying genetic drift is important . Sequencing would allow for greater tracking of outbreak clusters . In a previous collaboration with the Broad Institute , Massachusetts had seen the value of genomic sequencing in a number of events , including studying a COVID-19 super-spreader event from a biotech company meeting that infected over 100 people across several states .
Responding and Collaborating
MA SPHL was well-poised to onboard sequencing for a new pathogen . An existing relationship with the Broad Institute allowed for collaboration and having a partner to help with validation and troubleshooting was invaluable . Thanks to Epidemiology and Laboratory Capacity funding from the US Centers for Disease Control and Prevention
( CDC ), MA SPHL had dedicated sequencing staff that could focus on developing the new SARS-CoV-2 sequencing assay . While MA SPHL was a laboratory that only routinely sequences PulseNet organisms , it had participated in a number of different projects from rabies to Legionella to unexplained respiratory outbreaks and
The sequencing team ( from l to r ): APHL COVID-19 Fellow Kristine Tran , Microbiologist III Stephanie Baez , Microbiologist V and NBS Sequencing Supervisor Timelia Fink , and Microbiologist II Patrick Beauchamp . Photo : MA SPHL
had experience in method development for a new pathogen . Because of the various projects they have undertaken , it prepared them for the challenging optimization of the wet-lab protocols of SARS-CoV-2 sequencing .
Massachusetts was not the first state public health laboratory to onboard sequencing , and knowing that other public health laboratories had gone before them gave them additional confidence that it was doable . Communication and collaboration with other public health laboratories was critical in bringing on SARS-CoV-2 sequencing . As a CDC Office of Advanced Molecular Detection
( OAMD ) Bioinformatics Regional Resource and Training Lead , MA SPHL also wanted to ensure the processes and tools developed would be accessible to others . As it worked to onboard this pathogen , it was also constantly thinking about how to train others in the region and to learn from its experiences . Sequencing SARS-CoV-2 is not a one-size fits all approach as laboratories have different funding and staffing constraints . So MA SPHL tried to identify the bare minimum that was needed for states to onboard sequencing , allowing for differences in workflows , instrumentation and expertise . It was also able to put the workflow on Terra . Bio
, allowing other states to access and analyze sequences even if they did not have in-house bioinformatics support or computing resources .
Massachusetts began the process in May 2020 , started sequencing in July and was fully operational by September . Massachusetts is now running 194 samples each week , utilizing a three-day process with two days dedicated to wet lab and one day to sequence , and then analysis . MA SPHL is fortunate to have an in-house bioinformatician who modified existing bioinformatics workflows for SARS-CoV-2 sequence analysis to suit its needs for logging and tracking the outputs . The Broad Institute was also instrumental in helping them learn how to do custom Nextstrain builds and interpret the results .
Sequencing of SARS-CoV-2 answers multiple questions and will continue to aid in the understanding of this virus . From cluster analysis to variant detection , sequencing opens the door to answering a wide variety of questions . Public health laboratories use of sequencing for detection and surveillance of SARS-CoV-2 is another tool to aid in the understanding of this virus and stop its spread . n
20 LAB MATTERS Spring 2021