(CoviSurveTM* is a dashboard by Strand Life Sciences, a leader in delivering precision genomics to the people, to track emergence, introduction and spread of SARS-CoV-2 variants locally)
SARS-CoV-2, the coronavirus that caused the COVID-19 pandemic is proving to be an elusive moving target. The virus has picked up multiple mutations in keys genes since it was first detected at the end of 2019. In popular culture “a new mutant COVID virus” is now a looming villain
and the general population is overly familiar with SARS-CoV-2 variants and variants of concern(VOCs), even with their tongue twister names such as B.1.1.7 and B.1.6171.2.
Genomic surveillance for SARS-CoV-2, the science of reading the SARS-CoV-2 genome and tracking how it is changing and spreading can play an important role in shaping pandemic response and aid preparedness.
So what are the key challenges preventing this tool from achieving its full potential in the Indian context or at an even more local scale – within the city of Bengaluru?
1. Number of sequences – We are not sequencing enough – given that the virus picks up new mutations every few weeks; the large number of people infected – we need to sequence more to be able to track how the virus is changing and spreading.
2. Timeliness – Analysis of sequencing data and overlay of this information with other epidemiological data – such as travel history, age, pre-existing conditions, hospitalizations needs to be done in a timely manner.
3. Data integration and visualization – The lack of tools that can convert genomic data into information that can be understood by non-experts and convert to actionable insights.
Why is this important?
Variants of SARS-CoV-2 that emerge in any part of the world are likely to spread to other parts of the world. Making an integrated global surveillance of SARS-CoV-2 variants becomes a necessary next step in responding to the COVID-19 pandemic. Late last year, within a space of just a few weeks, three SARS-CoV-2 variants were announced to the world. Alpha (first detected in UK), Beta (first detected in South Africa) and Gamma (first detected in Brazil) brought us face to face with new challenges with the COVID-19 pandemic.
The emergence of variants with increased transmission, variants that can escape immune response from previous infection or post vaccination or those that cause more severe disease are a cause for concern as countries begin to open up and focus on vaccinating their populations.
Some variants of SARS-CoV-2 (Alpha & Delta) have spread globally from the countries where they were first described. So combining how the virus is changing, with where it is spreading (domestic/international travel), and who is presently infected (vaccinated individuals, children etc), is critical to a holistic outbreak response strategy.
In India we grappled with our own harrowing experience with the delta variant , which has now been shown to be one of the most transmissible variants of SARS-CoV-2. The lessons are the following-
We need to detect variants early and track their spread locally and globally
We must build tools that can convert this detection event to actionable information rapidly.
One outcome of this would be the identification of variants of concern and communicating with key stake holders such as the state government, as well as informing the general population.
CoviSurveTM* is a platform by Strand Life Sciences, a leader in high precision medicine, that allows the visualization of SARS-CoV-2 sequences through time and at a fine spatial resolution – such as a city or city blocks. It can be used to display the emergence and introduction of new variants into a city, highlighting the places that can then be targeted for detailed surveillance – both for cases (epidemiological surveillance) and virus genomes (genomic surveillance). This in turn can inform decision makers in a data based and visual way, highlighting trends and suggesting strategies.
Concerted efforts are currently underway to leverage the genome capacity present in different parts of the country to trace the emergence of variants/ “mutants” and track mutations. Over 40,000 SARS-CoV-2 genomes from India are now available in the GISAID database, a global resource available to researchers across the world. A national surveillance effort namely INSACOG is currently operational and expanding to include more labs for continued monitoring of SARS-CoV-2 genomes.
The next step is to leverage genomic data on the virus to guide public health decisions by combining it with local epidemiology- who is infected, when and where. These can then be overlaid with indicators of susceptibility/past-exposures suggested by sero-surveys to target surveillance efforts. There are few tools that allow visualization of the data in a way that is accessible to decision makers and the general population. CoviSurveTM* is an attempt to bridge this gap from data to actionable information. It aims to provide an integrated view of the state of the COVID-19 pandemic that will help shape pandemic preparedness response starting at a local scale.
Covi-Surve is a highly customisable application, that can be tailor-made to interpret data from accessible global databases, as well as from individual uploads. To know more about the features of the application, get a demo, or any additional queries, do reach out to us on +91 98450 90555 or email us at hello@strandls.com.
*The trademark application has already been submitted & pending registration