Community Protocol Sharing Evolves with COVID19
Community – no other word makes more sense in times when a pandemic like COVID19 is affecting the whole world. It’s with the concept of community in mind that nextstrain.org1 was built. Nextstrain is designed to provide real-time information on genetic data of multiple pathogens, such as SARS-CoV-2, the virus that causes COVID19.
Nextstrain focuses in sharing open source datasets from scientific studies, namely sequencing data obtained by analyzing samples from infected sources linked to the location of collection. Tracking locations where the virus was detected and differences in its sequence, allows scientists to learn more about how fast it is evolving, whether there are new mutations, determine how it spreads and overall perform surveillance. This is remarkably important in predicting how the virus will likely continue to evolve and how we can further prevent its spread.
Nextstrain makes its data widely available and uses a simplified and interactive interface. Data can be accessed by anyone in the world with an Internet connection, and its especially relevant for community scientists, virologists, epidemiologists, and public health officials.
Behind the scenes, scientists have been working tirelessly to sequence any incidences of the virus in order to provide sequencing information to those making public health decisions. Another community-based online platform, the Artic Network 2 , helps organize established sequencing methodologies. It provides easily accessible sequencing protocols that can save precious time by eliminating the need to dig through large amounts of articles to obtain step-by-step methods.
In an effort to provide a more modern experience, groups have turned to shared platforms like protocols.io to provide researchers with a site to view, ask questions, discuss and comment on protocols. This allows effective revisions and upgrades so all users can effectively obtain high quality results using user-optimized methods.
For example, in this nCoV-2019 sequencing protocol3, Josh Quick from the University of Birmingham, shared a sequencing protocol for the MinIon™ sequencer. On the page, the community of scientists can log whether the protocol works for their lab, can bookmark the protocol to follow any updates, can ask questions, and read comments and answers posted by other researchers.
Josh Quick’s protocol makes use of the Quick-RNA Viral kit, which is able to purify RNA from multiple samples types (swabs, saliva, blood, etc.). Additionally, the kit efficiently purifies samples with low virus abundance and yields ultra-pure RNA, which increases sensitivity for direct use in downstream applications such as RT-PCR, and library prep for Next-Gen Sequencing.
In times where we are all asked to maintain social distancing, a sense of community has become increasingly important. During times of great need such as the COVID-19 pandemic, participation on platforms to share protocols, ideas, questions and answers will continue and aid scientists worldwide.
Learn more about the Quick-RNA Viral Kits
- James Hadfield, Colin Megill, Sidney M Bell, John Huddleston, Barney Potter, Charlton Callender, Pavel Sagulenko, Trevor Bedford, Richard A Neher, Nextstrain: real-time tracking of pathogen evolution, Bioinformatics, Volume 34, Issue 23, 01 December 2018, Pages 4121–4123, https://doi.org/10.1093/bioinformatics/bty407
- Josh Quick (2020). nCoV-2019 sequencing protocol (single sample). protocols.io dx.doi.org/10.17504/protocols.io.bdbfi2jn