Researchers in the United States have conducted a study on a cohort of United States (U.S.) military personnel and healthcare system beneficiaries and have found significantly higher levels of infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in vaccine breakthrough infections (VBIs) involving Delta variant compared to VBIs 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 increased transmissibility of the Delta variant could be attributed in part to higher amounts in virus shedding.

Study: Genomic and Virological Characterization of SARS-CoV-2 Variants in a Subset of Unvaccinated and Vaccinated U.S. Military Personnel. Image Credit: Aleksandar Malivuk/Shutterstock

A pre-print version of the study has been published on the medRxiv* server, while the article undergoes peer review.

Background

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

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

Moreover, information on the concentration of infectious virus particles present in the clinical samples is also vital in understanding the impact of variants on viral shedding and transmissibility.

As viral RNA levels as a measurement of viral load do not always correlate to the amount of viable virus present in a given sample, the team made use of the in vitro viral culture on susceptible cell lines to quantitate infectious virus.

The study

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

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

Findings

Of the samples collected from March 2020 until early November 2021, the team sequenced more than 2,300 nasal swab samples. Of these, 1,304 complete genomes were successfully assembled for which Pango lineages were determined.

Initial samples sequenced in March and April 2020 were found to be similar to strains at the root of the pandemic (lineage A and sublineages), designated as Pango lineage “other”, that contained any lineage with 12 or fewer representatives. The large European lineage B.1 was detected in six samples in April 2020 and was also included in the “other” category.

The Alpha VOC (B.1.1.7) was the predominant strain found circulating between February and June 2021. The former VOC, Iota (B.1.526), was detected from March to June 2021 in 29 samples. The Delta VOC (B.1.617.2) was first detected in May 2021 in one sample collected from Portsmouth, Virginia, and later increasing numbers were detected starting in June 2021 and by July 2021, Delta was the dominant variant detected in all samples received with multiple sublineages which increased over time.

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

Quantification of virus in unvaccinated individuals demonstrated 3.2 log₁₀ PFU/mL mean amount of virus, which was similar to that detected from VBIs associated with all variants (3.1 log₁₀ PFU/mL) except Delta. The mean amount of virus detected in VBIs associated with the Delta variant was 4.6 log₁₀ PFU/mL, which was significantly higher when compared to the amount of virus detected in unvaccinated personnel prior to 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-fold more infectious virus in VBIs involving Delta compared to unvaccinated personnel with non-Delta infections prior to the availability of vaccines granted EUA and FDA  approval suggests that the increase in the amount of viable virus is due to the variant and not the vaccination status” the team highlights.

On comparing the results according to the vaccine manufacturers, the team observed a statistically significant difference in viral titers for unvaccinated individuals with non-Delta variants compared to samples from VBI associated with the Delta variant from individuals that received the Pfizer and Johnson & Johnson vaccines. However, the VBIs associated with the Delta variant that received the Moderna vaccine were not statistically significant when compared to the unvaccinated group. The team highlights that the inference could be a reflection of the limited number of samples, derived from VBIs associated with the Moderna vaccine, in the analyses.

Conclusions

Based on the findings, 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 VBIs associated with Delta when compared to VBIs/unvaccinated personnel infected with non-Delta variants. The results are in concordance with other studies for the rest of the general population in the U.S. where the Delta variant poses the predominant strain and is more than twice as infectious as previous strains. The study helps to explain the rapid spread of the Delta variant and provides the impetus to increase control measures including vaccine boosters and social distancing requirements.

*Important notice

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

Written by

Namita Mitra

After earning a bachelor’s degree in Veterinary Sciences and Animal Health  (BVSc) in 2013, Namita went on to pursue a Master of Veterinary Microbiology from GADVASU, India. Her Master’s research on the molecular and histopathological diagnosis of avian oncogenic viruses in poultry brought her two national awards. In 2013, she was conferred a doctoral degree in Animal Biotechnology that concluded with her research findings on expression profiling of apoptosis-associated genes in canine mammary tumors. Right after her graduation, Namita worked as Assistant Professor of Animal Biotechnology and taught the courses of Animal Cell Culture, Animal Genetic Engineering, and Molecular Immunology.