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.

Since late 2021, the highly transmissible SARS-CoV-2 Omicron variant has driven a new surge of infections across the world. We used a case-ascertained study to determine the features of household transmission of SARS-CoV-2 Omicron variant in Shanghai, China. We collected detailed information on 323 pediatric cases and their 951 household members, all received consecutively intensive RT-PCR testing. We estimated the transmission parameters. Both secondary infection attack rates (SARI) and secondary clinical attack rates (SARC) among adult household contacts were computed, through which the transmission heterogeneities in infectivity and susceptibility were characterized and the vaccine effectiveness were estimated. The mean incubation period and serial interval of Omicron variant were estimated to be 4.6±2.1 days and 3.9±3.7 days. The overall SARI and SARC among adult household contacts were 77.11% (95% confidence interval [CI]: 73.58%-80.63%) and 67.03% (63.09%-70.98%). We found higher household susceptibility in females, while infectivity was not significantly different in primary cases by age, sex, vaccination status and clinical severity. Full vaccination and booster vaccination of inactivated vaccines were 14.8% (5.8%-22.9%) and 18.9% (9.0%-27.7%) effective against Omicron infection and 21.5% (10.4%-31.2%) and 24.3% (12.3%-34.7%) effective against symptomatic disease. Overall, we found high household transmission during the Omicron wave in Shanghai due to asymptomatic and pre-symptomatic transmission in the context of city-wide lockdown, indicating the importance of early detection and timely isolation of SARS-CoV-2 infections and quarantine of close contacts. Marginal effectiveness of inactivated vaccines against Omicron infection poses great challenge for prevention and control of the SARS-CoV-2 Omicron variant.

Objectives: To understand the epidemiological and clinical characteristics of pediatric SARS-CoV-2 infection during the early stage of Omicron variant outbreak in Shanghai. Study designs: This study included local COVID-19 cases<18 years in Shanghai referred to the exclusively designated hospital by the end of March 2022 since emergence of Omicron epidemic. Clinical data, epidemiological exposure and COVID-19 vaccination status were collected. Relative risks (RR) were calculated to assess the effect of vaccination on symptomatic infection and febrile disease. Results: A total of 376 pediatric cases of COVID-19 (median age:6.0±4.2 years) were referred to the designated hospital during the period of March 7-31, including 257 (68.4%) symptomatic cases and 119 (31.6%) asymptomatic cases. Of the 307 (81.6%) children ≥3 years eligible for COVID-19 vaccination, 110 (40.4%) received 2-dose vaccines and 16 (4.0%) received 1-dose vaccine. The median interval between 2-dose vaccination and infection was 3.5 (IQR: 3, 4.5) months (16 days-7 months). Two-dose COVID-19 vaccination reduced the risks of symptomatic infection and febrile disease by 35%(RR 0.65, 95% CI: 0.53-0.79) and 33% (RR 0.64, 95% CI: 0.51-0.81). Two hundred and sixteen (83.4%) symptomatic cases had fever (mean duration:1.7±1.0.8 days), 104 (40.2%) had cough, 16.4% had transient leukopenia; 307 (81.6%) had an epidemiological exposure in household (69.1%) , school (21.8%) and residential area (8.8%). Conclusion: The surge of pediatric COVID-19 cases and multiple transmission model reflect wide dissemination of Omicron variant in the community. Asymptomatic infection is common among Omicron-infected children. COVID-19 vaccination can offer some protection against symptomatic infection and febrile dise