The risk of scaling back COVID-19 genomic surveillance too soon

With the easing of COVID-19 restrictions countries are reducing genomic surveillance, limiting the data necessary to prepare for new variants.

Two years into the COVID-19 pandemic, countries around the world are reopening and attempting to live with the virus. As restrictions like mask mandates ease, many countries are also scaling back their surveillance programs which were put into place to continuously and systematically collect health-related data which was then analyzed and interpreted to inform public health.

Surveillance programs not only include the reporting frequencies for COVID-19 cases and deaths, but also genomic sequencing efforts – a tool necessary to prepare for new SARS-CoV-2 variants. However, experts worry that it is too soon to make such dramatic cutbacks to these programs and doing so could leave us unprepared for the emergence of new, potentially harmful variants.

Taking our eye off the ball

This decrease in monitoring is unfortunate considering the remarkable effort made by countries that have led the way in genomic sequencing. For example, the UK’s genomic surveillance initiative has served as a model for the world. It was a major contributor to the global monitoring effort – having submitting over two million sequences to GISAID, the global repository for SARS-CoV-2 sequences. However, the UK recently shut down two routine virus surveys and dramatically scaled back a third. The timing of these actions seem counterintuitive when the UK’s infection rate is spiking, with approximately 1 in 13 people testing positive in the end of March 2022.

Furthermore, linking patient records with SARS-CoV-2 sequencing information is essential for COVID-19 research, epidemiological surveillance, and patient care – a topic discussed at length in IMO’s insight brief, What’s in a variant? The complexity of generating and using accurate COVID-19 data. Until recently, the UK model was working well to provide that link.

In the early stages of the pandemic, the UK ramped up their genomic sequencing and leveraged their centralized healthcare system to connect individual patient records directly to genomic sequences. Their robust surveillance program allowed for the quick identification of the Alpha variant and the Omicron sub-variant BA.2. But more importantly, linking patient information from the EHR directly with variant sequences enabled the UK to determine the impact of specific variants on patient health.

The US turns their monitoring efforts to wastewater

Looking across the pond, the initiative to establish a link between patient and variant is even more challenging. Monitoring efforts in the US have been hampered due to varying reporting requirements across states, a lackluster effort to sequence samples (the US ranked 43rd in the world for genomic sequencing in 2021), and an outdated data infrastructure. These factors have made it difficult to share health and sequencing information with public health agencies.

Now, the country is shifting its genomic surveillance strategy to focus on wastewater sampling, which can detect the presence of a variant within a community. However, this approach fails to provide the direct patient link that is critical for understanding the impacts of variants on human health. It also does nothing to solve the data infrastructure problems that have long plagued surveillance efforts. If we are to truly see the end of the pandemic, these issues must be addressed.

To learn more about the complexity of COVID-19 variant data, click here.

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