Audacity
GISAID is a global data science initiative and the primary source of genomic and associated metadata of the pandemic coronavirus.
AudacityInstant makes it possible to determine – in real-time – how any SARS-CoV-2 genome (COVID-19) is related to the nearly 12 million sequences currently available in GISAID’s EpiCoV™ database.
The tool allows custom comparative genomics queries against all of EpiCoV™ with summary results being instantly downloadable as a PDF report.
AudacityInstant enables users to explore the results by phylogenetic lineage, location and collection date. It also provides further details including an interactive display of the amino acid substitutions in the context of the 3-D spike protein model.
“AudacityInstant is useful for those looking to learn more about individual genome sequences in the context of GISAID’s global database and those working in public health trying to better understand the source of an outbreak,” says GISAID Vice President Ben Branda.
“With the growing demand on genomic surveillance around the globe, it is of paramount importance to intelligently process the unprecedented number of sequences.
“The Dragonfly team has done a remarkable job working closely with GISAID’s developers and bioinformatics experts to strike just the right balance of smart software algorithms and real hardware ingenuity.”
AudacityInstant visualises a phylogenetic tree of related COVID-19 sequences and maps user-uploaded sequences to those it is most related to. Different views show how variants have changed over time and which country they came from.
A feature in development displays a visualisation of any spike protein mutations. These are labelled with how they might affect the behaviour of the virus, such as increased virulence or transmissibility.
“We regard Dragonfly’s team as a critical spoke in GISAID’s worldwide ecosystem. We hope the government of New Zealand will take note of the role Dragonfly plays through GISAID in global health security.”
Since the first whole-genome sequences were made available through GISAID on 10th January 2020, nearly 12 million genomes of the pandemic coronavirus from 210 countries and territories have been shared via GISAID, enabling the development of lifesaving countermeasures to COVID-19 at unprecedented speed. These include the first vaccines (Polack et al 2020) and the first diagnostic tests (Bohn et al 2020, Carter et al 2020). The World Health Organisation (WHO) Chief Scientist called GISAID a “game-changer” (Swaminathan 2020).
More information about GISAID
The GISAID Initiative is an independent, non-profit, public-private partnership that involves various governments with in-kind contributions from Brazil, China, France, Germany, Indonesia, Senegal, Singapore, South Africa, the United Kingdom and United States.
GISAID receives public grants, for example from the WHO and Rockefeller Foundation, but also private and corporate donors.
GISAID is an essential asset for the Global Influenza Surveillance and Response System (GISRS) and for post-regulatory quality control of manufacturer seed viruses relative to candidate vaccine viruses.