International travel poses an ongoing challenge for limiting SARS-CoV-2 transmission across borders. Some countries, like the UK, have established a traveler screening program for SARS-CoV-2 surveillance, with PCR-based detection tests for passenger screening and next-generation sequencing (NGS) for genomic analysis of positive samples. When coupled with information about travelers’ age and vaccination status, genomic surveillance can provide insights on how the virus is spreading in different populations.
The UK’s screening program tests all international arrivals twice with nasopharyngeal swabs, on day 2 and day 8 after entry. Oncologica™ was the first organization to gain certification for performing these tests, and their recently published study highlights the advantage of a rapid, integrated workflow for large-scale genomic testing and surveillance and provided early data on the correlation between vaccinations and viral lineage.
A total of 203,065 swabs were collected from arriving international passengers between March 11 and April 14, 2021. After multiplex real-time PCR-based testing, positive samples collected on day two were selected for next-generation sequencing (NGS). All samples were analyzed at Oncologica’s UK laboratory, which was able to rapidly identify and monitor SARS-CoV-2 variants with turnaround times of 48-72 hours.
SARS-CoV-2 RNA was detected in 3,855 samples, and 49 different variants were identified. The Alpha variant (B.1.1.7) was by far the most prevalent strain (over 80%), followed by the Beta variant (B.1.351, 4.2%) and Delta variant (B.1.617.2, 1.7%).
Interestingly, the vaccinated population had a greater percentage of infections with high-risk variants (Beta, Delta, and Eta (B.1.525)) than the unvaccinated population, suggesting that current vaccines are less effective in preventing infection by high-risk variants than by the Alpha strain. The data also showed that two doses appeared to be more effective than one, and that travelers over 60 years old had a higher likelihood of infection post-vaccination than younger populations. Lastly, even though Ct values did not appear to vary significantly between vaccinated and unvaccinated individuals, early detection of the Delta variant showed and on average a 10X increase in viral load by PCR.
When it comes to public health interventions, timing is key to performing effective contact tracing and isolating those with exposure. By performing detection and sequencing in the same laboratory, Oncologica’s efficient and integrated NGS workflow avoided any logistical delays or transportation-related sample degradation, eliminated the need for repeated PCR amplification at additional sites, and avoided variability due to differences in protocols or equipment at multiple laboratories. While the UK was the first country to implement test-and-sequence surveillance in real time, SARS-CoV-2 genomic surveillance with NGS can inform public health decisions anywhere to limit transmission of high-risk variants and will become an increasing priority worldwide as the SARS-CoV-2 virus continues to mutate and evolve.
Learn more about Thermo Fisher’s COVID-19 surveillance solutions
Learn more about Thermo Fisher’s COVID-19 testing solutions
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