Exploring viral loads of SARS-CoV-2 Omicron BA.5 and BA.2 sublineages

By Bhavana KunkalikarReviewed by Aimee MolineuxNov 1 2022

In a recent study posted to the medRxiv* preprint server, researchers compared the viral loads of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.5 and BA.2 sublineages.

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

In January 2022, the number of SARS-CoV-2 Omicron-infected patients rapidly increased in Tokyo, Japan. After BA.2 replaced BA.1 as the predominant strain in April 2022, the number of patients gradually declined. However, the infection rate of the sublineage BA.5 suddenly rose, and by July 2022, BA.5 had completely replaced BA.2. Although this phenomenon has been reported all around the world, its cause is still unknown. Therefore, it is important to look into the factors that make BA.5 more contagious than BA.1 and BA.2.

About the study

In the present study, researchers compared the virus copy number corresponding to infection samples from patients with SARS-CoV-2 Omicron BA.1, BA.2, and BA.5 sublineage infections.

Polymerase chain reaction (PCR) testing was used to detect 774 coronavirus disease 2019 (COVID-19) patients who visited the Tokyo Medical and Dental University (TMDU) hospital between 1 February 2021 and 31 August 2022. Samples from nasopharyngeal swabs were collected during the patient's initial outpatient visit. In this investigation, the first sample was collected from each patient. Reverse transcription-quantitative PCR (RT-qPCR) was used to determine the SARS-CoV-2 copy numbers in the samples without ribonucleic acid (RNA) purification. Applying the threshold cycle numbers corresponding to each specimen to the calibration line of the reference samples having known concentration facilitated the calculation of the copy number per 1 L sample.

The melting curve of the PCR products was analyzed to identify the variations and sublineage types present. Additionally, the team extracted RNA from the swab samples. For E484K, L452R, N501Y, and S371L/S373P, reverse transcription-PCR was conducted with fluorescently labeled probes and primers. Furthermore, melting temperatures (T_m) estimated with melting curve analysis defined the variant and sublineage types. One-fifth of the samples were used for whole-genome sequencing (WGS) to confirm the sublineage types and variants identified using PCR.

Results

In the study, 774 samples in total were examined. In the PCR samples, the S371L/S373P probe was employed to differentiate between SARS-CoV-2 Omicron BA.1 and BA.2/BA.4/BA.5 and other Omicron variants. The team found that all of the samples that produced PCR results were Omicron variants. The samples from the test period did not contain any of the Alpha or Delta variants.

In particular, 215 samples had the mutations 501Y, 484A, 452L, and 371L/373P, referred to as BA.1, whereas 184 samples had the mutations 501Y, 484A, 452L, and 371F/373P, referred to as BA.2. Individuals belonging to the BA.2 cohort, six BA.2.12.1 samples having 501Y, 484A, 452Q, and 371F/373P mutations, as well as ten unidentified BA.2 samples having 501Y, 484A, 452M, and 371F/373P mutations.

Furthermore, the variant PCR used in this investigation discovered 290 positive samples having 501Y, 484A, 452R, and 371F/373P mutations and were categorized as BA.5. Viruses of sublineage BA.5 also possess the F486V mutation. Due to this mutation, the T_m of the E484K probe changed to 37 °C, whereas the T_m of the BA.2 samples having 484A and 486F mutations remained consistent at 40 °C.

The genotyping results were similar to those resulting from PCR. The samples containing 501Y, 486V, 484A, 452R, and 371F/373P were classified as BA.5 in the subsequent analysis because WGS analysis did not detect the BA.4 sublineage in the samples. Furthermore, BA2.75⁴ was not detected by the WGS analysis either. Although the distribution of copy numbers for BA.1, BA.2, and BA.5 sublineages were widely scattered, contrary to predictions, the copy numbers observed in BA.5 cases were lower than those in BA.2 cases. The BA.5 and BA.1 cases, as well as the BA.2 and BA.1 cases, did not significantly differ from one another.

Overall, the study findings highlighted that compared to the viral loads displayed by earlier variants and sublineages, Omicron BA.5's enhanced infectivity is not primarily due to a higher viral burden. To restrict the spread of COVID-19, future research must investigate the specific mechanism underlying the high infectivity of 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