After nearly two months, the state of Karnataka has finally started to see a sustained decline in cases. From reporting nearly 26,000+ daily cases in end April and May, cities and towns are now consistently reporting less than 2,000 daily cases. However, this isn't the time to be lax. In fact, this is when governments and healthcare authorities must focus on ramping up vaccination rates, and more importantly, prepare for a possible third wave. 

The Mutation Crisis

The biggest challenge of the COVID-19 resurgence has been the emergence of new virus variants across the globe. In the fall of 2020, the United Kingdom (UK) identified a fast-spreading variant called B.1.1.7, which has since been detected in many countries around the world. Experts believe it may potentially carry an increased risk of death compared to other variants. In South Africa, another variant called B.1.351, detected in early October 2020, shares some mutations with B.1.1.7. Cases of this variant were reported in the US at the end of January 2021. In Brazil, a variant called P.1 was identified during routine screening at a Japanese airport in early January. This variant contains a set of additional mutations that may be able to escape natural antibodies. It was first detected in the USA at the end of January 2021. The Indian government in April announced a new coronavirus variant detected amid a new surge of Covid-19 cases across several states. This is a unique “double mutant” coronavirus variant with a combination of mutations not found anywhere in the world. However, it is still to be established if it increases infectivity or severity of COVID-19. Genome sequencing of a section of virus samples by a consortium of 10 labs across the country, called the Indian SARS-CoV-2 Consortium on Genomics (INSACOG), revealed two mutations, E484Q and L452R together, in at least 200 virus samples from Maharashtra, as well as a handful in Delhi, Punjab and Gujarat. 

Stringent genomics surveillance and monitoring of the viral epidemiology and genetic diversity can help explain why people respond to Covid-19 in different ways, thereby helping design more effective health care strategies to better protect those at greater risk. Genomic analysis will help public health officials develop efficient vaccination strategies, develop antiviral drugs in response to emerging mutations and interpret changes in viral pathogenesis. 

Karnataka Deems Genomic Surveillance Necessary To Manage Public Health Crisis 

In a circular sent to key public health authorities, biologists, state and district level administrative officers, the government of Karnataka has deemed genomic surveillance necessary to develop effective control and preventative measures in the wake of a possible third wave. Following the Govt of India mandate of deploying genomic surveillance for 5% of COVID-19 cases, the government of Karnataka has decided to set up a COVID-19 Genomic Surveillance Committee that will prepare a sero-surveillance strategy for Karnataka, prioritise COVID-19 genome sequencing to study virus and mutations, validate RT-PCR tests across virus mutants and provide an in-depth analysis of genome surveillance and vaccination plans to identify immune escape versions of the virus and their spread. 

Committee member Dr. Vishal Rao, Dean, Centre of Academic Research, HCG Cancer Hospital says, "We do not have any genetic surveillance system operational in India, but it is undoubtedly the need of the hour. Whole viral genome sequencing allows for better understanding of the virus transmission, including the knowledge of whether it is mutating and becoming a larger threat. In addition, genomics can help explain why people respond to Covid-19 in different ways."

Could AI & Analytics Be The Key To Genomic Surveillance? 

Dr Rao is of the firm opinion that in a country the size of India, it is imperative to rely on machine learning models and AI algorithms to execute genomic surveillance efficiently. Some developments have taken place that support the role of analytics and machine learning in successful genome surveillance. The Chan Zuckerberg Initiative (CZI) and Chan Zuckerberg (CZ) Biohub heavily invested in two approaches to understand the spread of the virus - rampant testing and genomic analysis of COVID19 patients to understand mutation. The California Covid Tracker, launched by CZI and the CZ Biohub along with the state of California, is a statewide COVID tracking programme which has made genome sequencing and analysis freely available to all primary healthcare centres, with the goal to enable public health officers better manage the spread of the virus. More recently, CZI and CZ Biohub launched Aspen, a new open-source free software tool with access to powerful analysis tools built by the scientific community. Aspen does not require coding or any local infrastructure build — it aggregates data and provides easy access to analytics and interpretation for scientists and non-scientists alike. 

Meanwhile, COG-UK and the Sanger Institute have raised £12.2m from the Testing Innovation Fund of the Department of Health and Social Care for creating a real-time surveillance system of emerging outbreaks. This system will be supported by new software being developed by the Sanger Institute and involving researchers from across the consortium’s network.

Dr Rao recommends that genomic surveillance data from INSACOG, clinical correlation of Aarogya Setu, vaccination information from CoWin, vaccination supply management information from eWIn and data integration from NCDIR need to be aligned to catch new variants early, warn clinicians of atypical symptomology, and prevent wide-spread community transmission.

Early last year, Google's DeepMind utilised its deep learning system AlphaFold to predict SARS CoV-2's protein structures, becoming one of the most significant breakthroughs in genomic structures and Artificial Intelligence. Perhaps, genomic surveillance aided by AI and advanced analytics could be one step closer to the way out of this really long and arduous phase in our lives brought upon by COVID-19.