Viral load of SARS-CoV-2 Omicron BA.5 is lower than that of BA.2 despite the higher infectivity of BA.5

Abstract

Sublineage BA.5 of the SARS-CoV-2 Omicron variant rapidly spread and replaced BA.2 in July 2022 in Tokyo. A high viral load can be a possible cause of high transmissibility. Therefore, the copy numbers of SARS-CoV-2 in nasopharyngeal swab samples obtained from all patients visiting the hospital where this research was conducted were measured using quantitative polymerase chain reaction (qPCR). Viral genotypes were determined using PCR-based melting curve analysis. Next, whole-genome sequencing was performed using approximately one-fifth of the samples to verify the viral genotypes determined using PCR. Then, the copy numbers of the BA.1, BA.2, and BA.5 cases were compared. Contrary to expectations, the copy numbers of the BA.5 cases (median 4.7 X 104copies/uL, n = 290) were significantly (p = 0.001) lower than those of BA.2 cases (median 1.1 X 105copies/uL, n = 184). There was no significant difference between the BA.5 and BA.1 cases (median, 3.1 X 104copies/uL; n = 215). The results presented here suggest that the increased infectivity of BA.5 is not caused by higher viral loads, but presumably by other factors such as increased affinity to human cell receptors or immune escape due to its L452R mutation.

Epidemiology and Characteristics of SARS-CoV-2 Variants of Concern: The Impacts of the Spike Mutations

“…Sublineage BA.5 replaced BA.2 in April 2022 due to increased affinity for ACE2 and increased immune escape, probably related to selection of the L452R substitution [ 75 , 77 , 78 ], one of the major mutations responsible for the increased transmissibility of the Delta variant, as well as the 69/70 deletion, the F486V substitution, and reversion to the wild type amino acid at position Q493. Treatment sensitivity and vaccine efficacy remained similar.…”