Surveillance of the Roots and Routes of the COVID-19 Pandemic

Every week, labs around Britain send refrigerated left over material from the COVID-19 tests across the country to genome-sequencing facility in Cambridgeshire, eastern England. This operation is part of UK’s surveillance system for tracking mutations.

Late November of last year, England’s public health institutions were strained by a puzzling outbreak of coronavirus cases in Kent. A lockdown had brought down the virus across England, but not there.

Around summer time last year, doctors at the South African hospitals noticed an odd spike in the number of cases. Even though the COVID restrictions were eased and there were many violations of social distancing, the numbers were increasing a little too fast, prompting them to wonder the role of a new factor.

Early November, hospitals in Durban raised the distressing possibility of a new variant. This observation quickly led to rampant genetic investigation, also informing and sharing the news with Britain who were equally puzzling over surging cases in Kent.

Eventually, the tip off from Durban and Britain’s frantic surveillance led to the discovery of 23 mutations from the original Wuhan virus — enough to be considered a new variant. It was only in December 8, looking back, Britain concluded that the new strain had appeared as early as September when the country had lax restrictions.

Soon Britain sounded an alarm for the world, allowing countries to start searching for a variant that otherwise might have went unnoticed for months. British scientists soon after published studies that convinced the world of its potency.

The campaign for a platform for the surveillance and analysis of genomes, started way ahead by the scientific community in England, pushing the government to fund the project. In March, putting aside any rivalry and ego, the government and the research community went hand in hand to set up the world’s most powerful tool to track mutations.

Today, the country produces half the world’s data of coronavirus genomes, providing a detailed view of the history of the virus’s mutations, how people brought it into Britain and carried the variant out.

When a virus replicates inside a host, there is a chance of error in copying its genome. It is this faulty replication that causes mutations. In the case of RNA-viruses like SARS-CoV2, replication errors are more, since unlike other organisms, RNA-viruses do not have proof reading systems that weed out errors after replication. Thus, as the number of infections increase, the number of replications increase, causing an increase in mutations. As mutations occur inside infected humans, countries with the most infections tend to produce the most mutations.

The only way to identify variants in a timely manner is sequencing. In India, it’s not easy for scientists to pursue COVID-19 research due to difficulty in accessing data. The ICMR database is inaccessible to anyone outside of the government. On 29 April, the scientific community wrote to Prime Minister Narendra Modi, asking for better access to data such as COVID-19 test results and clinical outcomes of patients in hospitals (https://sites.google.com/view/corona-appeal/home). The same day, the matter was acknowledged by the government’s principal scientific adviser, a move welcomed by the scientists.

There should have been no need in the first place to send a letter of protest to the government. This is only to be expected since in the past too, the government has not responded well to the research community questioning its policy. This was reflected when the researchers urged an end to the government’s interference in the release of statistical government data. It does not do well when the research community has a difficult relationship with their country’s government, especially in the middle of a pandemic when quick and evidence based decisions and predictions are much needed. In Brazil too, an anti-scientific government led to the devastating rise in COVID cases.

Just as China failed to stop travellers from spreading the virus before the New Year last year, just as Britain had lowered its guard during the holidays thus failing to move fast enough to control the new variant’s spread, India too, despite being a witness to the experiences of the world and warnings from our scientific community, laxed its restrictions, in some cases promoting large gatherings, paving the way for a new pariah to the world.

It is a mark of the failure and missteps of major countries that it could not contain the spread of variants before its surge. Thus the Indian second wave is a threat not only to India, but to the world, and global consequences of ill-timed promotion of local COVID inappropriate behavior must be clearly acknowledged [1].

‘The longer the virus spreads among the unvaccinated, the more mutations it might collect gathering immunity against the vaccines’ effectiveness. Larger outbreaks in April 2021, has seen the rise of the B.1.1.7 and B.1.617 variants. The indigenous variant B.1.617, was independently found in Maharashtra and evoked global interest [2].’ Upon further research, it was noted that the earliest sequences of this lineage can be traced back to December 2020 .

SARS-COV2 Variants in India [1]

India is, therefore, likely to become a hotspot for rise of future variants of concern, unless things are rapidly brought under control. Even then, careful surveillance for an extended period must be observed.

Please note that vaccine alone will not be sufficient to get ahead of the virus: It will take years to vaccinate enough people to limit the evolution of the virus. In the meantime, simple things like masking, sanitizing and COVID appropriate behavior still remain key in the public health fight. This might avert devastating spikes in hospitalizations and deaths and buy the research community some time to study the variants of concern and its potential immunity to vaccine, thereby if and when needed, update the vaccines accordingly.

Constant surveillance and data sharing within the country and with the world (with appropriate safeguards for enabling patient privacy) is an unquestionable key to track the virus and be better prepared to tackle its surge. It would bode well to remember that denying or obscuring access to data, risks prolonging the pandemic.

An article by Sulthana Shams, PhD student Data Analytics and Privacy, Trinity College Dublin

REFERENCES

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