The Changing Landscape of COVID-19 — What's Next? Part 1 in a Series

Posted by ApolloLIMS on Jun 09, 2021

Viral genomic sequencing and covid-19

The United States is reaching a transition point in the COVID-19 pandemic due to a rise in the SARS-CoV-2-immune population (via vaccination or infection) and the onset of warmer weather.

As a result, the COVID-19 cases in the United States are expected to decrease over the next few months. However, this year’s autumn and winter will see unvaccinated children back in the classroom and adults back in the office. We anticipate a more complex landscape of upper respiratory infections in the fall and winter. Diagnostic laboratories need to stay ahead of the curve as the United States returns to “normal” and the landscape for COVID-19 testing shifts.

Anticipated COVID-19 Trends

In the coming months, we expect the number of COVID-19 cases to decrease, similar to what we saw during this time in 2020. The growing SARS-CoV-2-immune population and an increase in people spending time outdoors during the warmer months will drive down the number of active COVID-19 cases. As summer turns to fall, we can expect to see a rise in upper respiratory infections.

Unlike the 2020-2021 cold and flu season, we anticipate an increase in influenza and other respiratory tract infections to return during this year’s colder months, as more people return to school, work, and daily life. Also, we expect that the pockets of non-immune populations will increase the cases of COVID-19 during this time. This shifting dynamic and integration of COVID-19 into the normal milieu of upper respiratory infections will lead to a complex situation for the treating physicians and the laboratories that serve them.

Expanded Upper Respiratory Panel—Integration of SARS-CoV-2

To prepare for the colder months, diagnostic laboratories will expand into panel-based differential testing for common upper respiratory pathogens, including SARS-CoV-2, Influenza A, Influenza B, and others. BioFire’s Respiratory Panel 2.1 includes SARS-CoV-2 along with its extensive list of upper respiratory pathogens and has received FDA clearance (March 2021) via the De Novo pathway. Other tests are available to differentiate influenza viruses from SARS-CoV-2 under the current EUA for COVID-19. We anticipate that diagnostic laboratories are adapting their test menus right now for differential testing for the fall and winter.

Screening and Specimen Pooling

Although we can expect laboratory-based diagnostic testing for COVID-19 to continue into the autumn and winter, more economical approaches to molecular testing are likely to be implemented.

As children return to the classroom and adults return to the workplace, laboratories will be asked to continue screening asymptomatic individuals. As long as the infection rates among these populations remain low, the laboratory may consider the benefit of specimen pooling as a way to increase turn-around time and lower costs. Many laboratories have already validated screening tests and various pooling strategies and have been very successful with faster results delivery and lowering laboratory costs. We expect to see a shift toward increased screening and pooling in the autumn and winter months.

If your laboratory is planning to implement screening or pooling, be sure your laboratory information management system (LIMS) provider can support your plans and knows how to work with your laboratory to identify COVID-19-positive specimens in a pool.

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Variant Characterization Using Sequencing

Many diagnostic laboratories are gearing up to support the public health initiative to monitor the SARS-CoV-2 strains using next-generation sequencing (NGS) to identify new variants, define the population distribution for each variant, and search for any potential vaccine break-through variants.

Laboratory-based diagnostic testing algorithms for SARS-CoV-2 that include viral genomic sequencing will emerge as a critical aspect of COVID-19 testing as populations persist in a non-immune state and as a way to monitor for break-through cases. As more and more individuals receive the vaccine, others refuse, and other populations do not have vaccine access, attention will turn to characterizing SARS-CoV-2 variants and monitoring the rate of break-through infections caused by new variants.

Laboratories that are pursuing variant characterization via NGS need to ensure that their LIMS provider has the capability to support the NGS workflow, especially the volume of data and the processing support to do the analysis efficiently. The ApolloLIMS platform is flexible and can be adapted to fit the needs of your laboratory and its workflow. Take a look at our product offerings to see how ApolloLIMS will meet your laboratory’s workflow and NGS needs.

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Topics: LIMS, COVID-19

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