Objective To analyze epidemiological characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant infections in Pudong New Area, Shanghai during January – June 2023 for improving regional containment of coronavirus disease 2019 (COVID-19) epidemic.
Methods Whole-genome sequencing was conducted on 1 080 throat swabs positive for SARS-CoV-2 nucleic acid sampled at medical institutions (n = 751) or customs (n = 329) in Pudong New Area, Shanghai during January – June 2023. The information on 381 cases with laboratory-confirmed Omicron variant infection were collected via phone interviews and analyzed using descriptive statistics.
Results All the SARS-CoV-2 strains were Omicron variants for 947 specimens successfully sequenced. Omicron BA.5 and BF.7 variant and their subtypes were dominant strains in January and February and Omicron XBB subvariant occurred first in March and became the dominant strain gradually till June in Pudong New Area. The top 3 Pangolin types (ratio, number of positive specimens) identified among the 875 specimens collected during March – June were XBB.1.16 (29.49%, 258), XBB.1.9 (16.22%, 142), and XBB.1.5 (16.22%, 142). Of the 381 eligible phone interview respondents (mainly aged 21 – 40 years) with Omicron XBB variant infections, 49 (12.86%) reported having no clinical symptoms and the proportion (number) of the respondents reporting fever, pharyngalgia, and cough were 79.27% (302), 36.48% (139) , and 34.12% (130), respectively; the majority (80.58%) of the respondents considered that the Omicron XBB infection was their first experienced COVID-19 illness. In terms of registered COVID-19 vaccination, 16.54% of the respondents were not been vaccinated; 4.72%, 30.45%, and 48.29% received one, two, and three or more doses. The results of multivariate logistic regression analysis showed the respondents experiencing the first COVID-19 illness were more likely to have clinical symptoms due to the Omicron XBB variant infection.
Conclusion The study results indicated that SARS-CoV-2 Omicron XBB variant and its subvariants were the dominant strains for the COVID-19 epidemic in Pudong New Area of Shanghai during January – June 2023; the XBB variant infection resulted mainly in upper-respiratory symptoms and experiencing first COVID-19 illness may be a risk factor for the incidence of clinical symptoms of the infection.
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