Study identifies lower viral load in the nasopharyngeal samples of patients infected with SARS-CoV-2 Omicron variant

By Dr. Priyom Bose, Ph.D.Feb 8 2022Reviewed by Aimee Molineux

The evolution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), due to genomic mutations, has led to the emergence of several SARS-CoV-2 variants.

This virus is the causal agent of the ongoing coronavirus disease 2019 (COVID-19) pandemic, which has claimed more than 5.7 million lives worldwide. The World Health Organization (WHO) has categorized these variants as variants of concern (VOC) and variants of interest (VOI), in accordance with their infectiousness, and virulence.

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources

Background

At the end of 2020, the SARS-CoV-2 Alpha variant was the dominant circulating strain and was, subsequently, replaced by the Delta variant. Both of these variants have been regarded as VOCs as they have a higher rate of transmission than the original SARS-CoV-2 strain that was reported in China, in 2019.

The increased infectivity has been associated with a higher affinity for the ACE2 cellular receptor of the host. Additionally, a higher viral burden was found in the respiratory tract samples of patients infected by VOCs than in the case of the original strain. Recently, another VOC, namely, the SARS-CoV-2 Omicron variant has replaced the Delta strain. This variant has rapidly become the dominantly circulating strain in the majority of countries across the world.

Scientists have reported that the Omicron variant contains a large number of mutations in the spike protein compared to the original SARS-CoV-2 strain. These mutations are responsible for the higher rate of transmission and evasion of immune responses induced via immunization or natural infection. Researchers revealed that this strain is the most contagious among all the SARS-CoV-2 variants known so far. However, it is not yet known if the Omicron variant is also related to a higher viral load compared to other SARS-CoV-2 variants.

A new study

Researchers have addressed the aforementioned gap in research and posted their findings on the medRxiv* preprint server. The authors determined if the higher transmission rate of the Omicron variant is due to a higher viral load compared to the Delta variant.

Nasopharyngeal swab samples were collected from a screening center, completely dedicated to health care workers and families, at the University Hospital of Lyon, France. During the time of the sample collection, the Delta variant was predominantly circulating and the Omicron variants had also been introduced in Lyon. These samples were subjected to RT-PCR tests and the whole-genome of the COVID-19 positive samples were sequenced. Researchers used cycle threshold (Ct) values for the RdRp target as a proxy to evaluate SARS-CoV-2 viral load.

Findings

Scientists revealed that patients infected with the Omicron variant exhibited a lower viral load (higher Ct value) compared to patients infected with the Delta variant. Significant viral load differences were observed in the group of patients who were over 40 years of age with higher viral loads and patients infected by the Delta variant. This finding is in line with a previous study that reported patients infected by the Delta variant (average Ct value of 20.5) exhibited higher viral loads than those who were infected by the Omicron variant (average Ct value of 23.3).

In order to prevent biased results due to vaccination, researchers categorized patients into five groups, according to the French vaccination strategy, i.e., not vaccinated, partially vaccinated (one dose or one COVID-19 infection), completely vaccinated (2 doses or one dose and one infection), boosted (three doses or two doses and one infection), and an unknown group (unavailable date).

Scientists reported that completely vaccinated individuals, infected by the Omicron variant showed lower viral loads compared to those who were infected by the Delta variant. Interestingly, an inverse trend was found in the group of patients who received the booster vaccine, i.e., a higher viral load was found during the Omicron infection.

Conclusion

The present study has several limitations including the estimation of the viral load by using Ct values without specific quantification and normalization. The inverse trend, i.e., individuals who received the booster vaccine and were infected with the Omicron variant showed a higher viral load compared to the Delta variant, could be due to lower susceptibility to neutralizing antibodies for the Omicron variant compared to the Delta variant.

The authors of this study revealed that the higher infectiousness of the Omicron variant might not be related to an increased viral load as reported for previous variants. In the future, more studies related to the mechanisms driving the higher transmissibility of the Omicron variant are required.

Additionally, more studies are required taking into account the vaccination status, time of vaccination, and antibody levels to better understand the efficacy of immune responses against SARS-CoV-2 variants.

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources