Impact of SARS-CoV-2 variants on unvaccinated and vaccinated U.S. military personnel


Researchers in the United States conducted a study on a cohort of United States military personnel and healthcare system beneficiaries and found significantly higher levels of infectious severe acute respiratory syndrome coronavirus 2 (SARS -CoV-2) in breakthrough vaccine infections (BBIs) involving the Delta variant compared to BBIs involving other variants.

They also found higher levels of viable virus in nasal swab samples from VBIs with Delta compared to unvaccinated personnel infected with other variants.

Based on the extreme difference in titers between Delta and other strains, the team suggests that the increased transmissibility of the Delta variant could be attributed in part to higher amounts of viral shedding.

Study: Genomic and virological characterization of SARS-CoV-2 variants in a subset of unvaccinated and vaccinated <a class=US military personnel. Image Credit: Aleksandar Malivuk / Shutterstock” class=”rounded-img” height=”800″ data-src=”https://d2jx2rerrg6sh3.cloudfront.net/images/news/ImageForNews_699930_16399963031651480.jpg” data-srcset=”https://d2jx2rerrg6sh3.cloudfront.net/image-handler/ts/20211220053146/ri/1200/src/images/news/ImageForNews_699930_16399963031651480.jpg 1200w, https://d2jx2rerrg6sh3.cloudfront.net/image-handler/ts/20211220053146/ri/1150/src/images/news/ImageForNews_699930_16399963031651480.jpg 1150w, https://d2jx2rerrg6sh3.cloudfront.net/image-handler/ts/20211220053146/ri/950/src/images/news/ImageForNews_699930_16399963031651480.jpg 950w, https://d2jx2rerrg6sh3.cloudfront.net/image-handler/ts/20211220053146/ri/750/src/images/news/ImageForNews_699930_16399963031651480.jpg 750w, https://d2jx2rerrg6sh3.cloudfront.net/image-handler/ts/20211220053146/ri/550/src/images/news/ImageForNews_699930_16399963031651480.jpg 550w, https://d2jx2rerrg6sh3.cloudfront.net/image-handler/ts/20211220053146/ri/450/src/images/news/ImageForNews_699930_16399963031651480.jpg 450w” sizes=”(min-width: 1200px) 673px, (min-width: 1090px) 667px, (min-width: 992px) calc(66.6vw – 60px), (min-width: 480px) calc(100vw – 40px), calc(100vw – 30px)” title=”Study: Genomic and virological characterization of SARS-CoV-2 variants in a subset of unvaccinated and vaccinated US military personnel. Image Credit: Aleksandar Malivuk / Shutterstock” width=”1200″/>Study: Genomic and virological characterization of SARS-CoV-2 variants in a subset of unvaccinated and vaccinated US military personnel. Image Credit: Aleksandar Malivuk / Shutterstock

A pre-printed version of the study has been published on the website medRxiv* server, while the article is subject to peer review.

Fund

Based on mutations that may impact coronavirus disease 2019 (COVID-19) countermeasures such as vaccines, therapeutics and diagnostics, the World Health Organization (WHO) has ranked as many variants of SARS-CoV-2 as variants of concern (VOC) or variants of interest (VOI). Current VOCs include B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta) and, more recently, B.1.1.529 (Omicron), which was designated as a VOC on November 26, 2021.

As the emergence of new variants of SARS-CoV-2 continues to complicate control measures for the COVID-19 pandemic, increased genomic surveillance is crucial for the early detection of emerging variants, tracking their movement, and monitoring their movement. monitoring the effectiveness of countermeasures.

In addition, information on the concentration of infectious viral particles present in clinical samples is also essential to understand the impact of variants on viral shedding and transmissibility.

Since viral RNA levels as a measure of viral load do not always correlate with the amount of viable virus present in a given sample, the team used the in vitro viral culture on sensitive cell lines to quantify infectious virus.

The study

Nasal swab samples were collected from a cohort of U.S. military personnel and beneficiaries stationed around the world between March 2020 and early November 2021 as part of the Defense Health Agency’s Global Emerging Infections Surveillance (GEIS) program ( DHA). Samples were derived from both unvaccinated and vaccinated individuals (after EUA approval of COVID-19 vaccines) during this time period.

Samples positive for SARS-CoV-2 qRT-PCR were characterized for genomic variations by Illumina MiSeq-next-generation sequencing. A subset of samples was then reported for virus isolation and quantification of viable viruses on Vero E6 / TMPRSS2 cells.

Results

Among the samples collected from March 2020 to early November 2021, the team sequenced more than 2,300 nasal swab samples. Of these, 1,304 complete genomes have been successfully assembled for which the Pango lines have been determined.

The first samples sequenced in March and April 2020 were found to be similar to the strains causing the pandemic (lineage A and sublines), referred to as the “other” Pango lineage, which contained a lineage with 12 representatives or less. The great European line B.1 was detected in six samples in April 2020 and was also included in the “other” category.

Alpha VOC (B.1.1.7) was the predominant strain found in circulation between February and June 2021. The older VOC, Iota (B.1.526), ​​was detected from March to June 2021 in 29 samples. Delta VOC (B.1.617.2) was first detected in May 2021 in a sample taken in Portsmouth, Virginia, and later an increasing number was detected from June 2021 and into July 2021, Delta was the dominant variant detected in all samples received. with several sublines which have increased over time.

The team did not detect the Omicron variant during the period of this study.

Quantification of the virus in unvaccinated individuals demonstrated 3.2 logten PFU / mL mean amount of virus, which was similar to that detected from VBIs associated with all variants (3.1 logten PFU / mL) except Delta. The average amount of virus detected in VBIs associated with the Delta variant was 4.6 logten PFU / mL, which was significantly higher compared to the amount of virus detected in unvaccinated personnel before the emergence of VOCs.

The amount of virus detected in VBIs associated with the Delta variant was also significantly higher compared to VBIs with other variants.

Our data demonstrating that we detected 40 times more infectious virus in VBIs involving Delta compared to unvaccinated personnel with non-Delta infections before the availability of EUA and FDA approved vaccines suggests that the increased amount of viable virus is due to the variant and not the vaccine status, ”the team emphasizes.

Comparing the results by vaccine manufacturer, the team observed a statistically significant difference in viral titers for unvaccinated individuals with non-Delta variants compared to VBI samples associated with the Delta variant from individuals with received the Pfizer and Johnson & Johnson vaccines. However, the BVIs associated with the Delta variant that received the Moderna vaccine were not statistically significant compared to the unvaccinated group. The team points out that the inference may reflect the limited number of samples, derived from VBIs associated with the Moderna vaccine, in the analyzes.

Conclusion

Based on the results, the team suggests that the increased transmissibility of the Delta variant could be in part due to higher amounts of virus shedding. Significantly higher levels of infectious virus were found in Delta-associated VBIs compared to VBI / unvaccinated personnel infected with non-Delta variants. The results are consistent with other studies for the rest of the general population in the United States where the Delta variant is the predominant strain and is more than twice as infectious as previous strains. The study helps explain the rapid spread of the Delta variant and provides the impetus to increase control measures, including vaccine recalls and social distancing requirements.

*Important Notice

medRxiv publishes preliminary scientific reports that are not peer reviewed and, therefore, should not be considered conclusive, guide clinical practice / health-related behavior, or treated as established information.


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