Characteristics of SARS-CoV-2 Omicron BA.5 variants in Shanghai after
ending the zero-COVID policy in December 2022: a clinical and genomic
An unprecedented surge of Omicron infections appeared nationwide in
China in December 2022 after the adjustment of COVID-19 response policy.
In this study, we report the clinical and virological characteristics of
SARS-CoV-2 Omicron BA.5 infections among children in Shanghai during the
outbreak in late December 2022. We sequenced the 64 SARS-CoV-2 positive
samples obtained from hospitalized children. The genomic monitoring
revealed that the current outbreak was driven by the BA.5.2.48 and
BF.7.14 subvariants. Additionally, children with BA.5.2.48 infection
were more frequently observed to experience vomiting/diarrhea compared
to those with BF.7.14 infection. The high-frequency unique
non-synonymous mutations were present in BA.5.2.48 (N: Q241K) and
BF.7.14 (nsp2: V94I, nsp12: L247F, S: C1243F, ORF7a: H47Y) with respect
to their parental lineages. Of these mutations, C1243F mutation in S
protein, L247F mutation in nsp12, and H47Y mutation in ORF7a protein
were predicted to have a deleterious effect on the protein function.
Besides, H47Y mutation was also found to increase the stability of ORF7a
protein. Therefore, attention should be paid to these specific
mutations, especially for H47Y mutation, which could serve as a viral
immune escape strategy due to the potential immunomodulatory ability of
the ORF7a protein. Continuous genomic monitoring and clinical
manifestation assessments of the emerging variants will be crucial for
effective responses to the ongoing COVID-19 pandemic.