Prevalence of SARS-CoV-2 Omicron variants and epidemiological characteristics of subvariant XBB infections in Pudong New Area, Shanghai during January – June 2023
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摘要:
目的 分析2023年1 — 6月上海市浦东新区新冠病毒变异株的流行病学特征，为完善防控策略和措施提供参考依据。 方法 对2023年1 — 6月上海市浦东新区1080份新冠病毒感染者核酸样本进行基因测序并对接受流行病学调查的381例XBB变异株感染者进行描述性流行病学特征分析。 结果 获得947份有效基因测序样本，毒株分型均为Omicron变异株。BA.5及其亚分支和BF.7及其亚分支是1 — 2月份的主要流行株；XBB及其亚分支于3月份首次检出，3 — 6月份Pangolin分型中占前3位的分别为XBB.1.16（29.49%，258/875）、XBB.1.9（16.22%，142/875）、XBB.1.5（16.22%，142/875），截至6月份，XBB及其亚分支已逐渐成为浦东新区绝对优势流行株。接受流行病学调查的381例XBB感染者中，年龄集中于21～40岁，49例（12.86%）自述无临床症状，临床症状以发热（79.27%）、咽痛（36.48%）、咳嗽（34.12%）等上呼吸症状为主；80.58%的感染者为首次感染；未接种新冠疫苗的感染者占16.54%，接种过1剂次者占4.72%，接种过2剂次者占30.45%，接种过3剂次及以上者占48.29%。多因素非条件logistic回归分析结果显示，首次感染是XBB感染者中出现临床症状的危险因素。 结论 XBB及其亚分支为浦东新区2023年3 — 6月份优势流行株，感染者临床表现以上呼吸道症状为主，既往未感染新冠病毒可能会增加感染者出现临床症状的风险。 Abstract: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. -
Key words:
- SARS-CoV-2 variant /
- epidemiological characteristics /
- Pudong New Area
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表 1 2023年1 — 6月上海市浦东新区新冠病毒感染者基因测序结果
Table 1. Month-specific subtype ratios of SARS-CoV-2 Omicron variants among 947 infections in Pudong New Area, Shanghai during January – June 2023 based on whole-genome sequencing
月份 有效测序病例数 BA.5及其亚分支 BF.7及其亚分支 BA.2及其亚分支 XBB及其亚分支 其他 a 例数 构成比（%） 例数 构成比（%） 例数 构成比（%） 例数 构成比（%） 例数 构成比（%） 1 62 32 51.61 28 45.16 0 0.00 0 0.00 2 3.23 2 10 4 40.00 3 30.00 2 20.00 0 0.00 1 10.00 3 70 18 25.71 23 32.86 0 0.00 26 37.14 3 4.29 4 188 27 14.36 33 17.55 14 7.45 106 56.38 8 4.26 5 285 0 0.00 3 1.05 8 2.81 274 96.14 0 0.00 6 332 0 0.00 0 0.00 5 1.51 324 97.59 3 0.90 合计 947 81 8.55 90 9.50 29 3.06 730 77.09 17 1.80 注：a 包括BQ.1及其分支、CH.1.1及其分支、XAP、CJ.1、XAY.1.1、DZ.2、XBL、GD.1、CM.8.1、EN.1。 
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表 2 2023年1 — 6月上海市浦东新区XBB及其亚分支分布
Table 2. Month-specific subtype ratios of SARS-CoV-2 Omicron variant XBB among 947 infections in Pudong New Area, Shanghai during January – June 2023 based on whole-genome sequencing
月份 有效测序病例数 XBB.1.16型别 a XBB.1.9型别 b XBB.1.5型别 c XBB.1.22型别 d XBB.2.3型别 e 其他XBB型别 f 例数 构成比（%） 例数 构成比（%） 例数 构成比（%） 例数 构成比（%） 例数 构成比（%） 例数 构成比（%） 1 62 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 2 10 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 0 0.00 3 70 0 0.00 12 17.14 13 18.57 0 0.00 0 0.00 1 1.43 4 188 31 16.49 34 18.09 30 15.96 1 0.53 5 2.66 5 2.66 5 285 101 35.44 81 28.42 63 22.11 14 4.91 8 2.81 7 2.46 6 332 126 37.95 107 32.23 36 10.84 38 11.45 8 2.41 9 2.71 合计 947 258 27.24 234 24.71 142 14.99 53 5.60 21 2.22 22 2.32 注：a 包括FU.1、FU.2、XBB.1.16、XBB.1.16.1、XBB.1.16.2；b 包括EG.2、EG.5.1、EG.5.1.1、FL.1、FL.2、FL.3、FL.4、FL.12、XBB.1.9及其分支；c 包括EU.1.1、XBB.1.5及其分支；d 包括FY.1、FY.3、FY.3.1、XBB.1.22及其分支；e 包括GE.1、XBB.2.3及其分支；f 包括XBB.1、XBB.1.17.1、XBB.1.11.1、、XBB.1.24.3、XBB.2.9、XBB.1.18及其分支、XBB.1.19及其分支。
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表 3 XBB感染者临床症状影响因素多因素非条件logistic回归分析
Table 3. Associations of gender, age, COVID-19 vaccination, and previous COVID-19 infection with clinical symptoms of Omicron variant XBB infection: multivariate logistic regression analysis on data from 381 laboratory-confirmed infectees
因素 比较组 参照组 β $ S_{\bar x}$ Wald χ2 值 P 值 OR 值 95%CI 性别 女性 男性 – 0.564 0.328 2.966 0.085 0.569 0.299～1.081 年龄（岁） 21～40 ≤ 20 – 0.263 0.509 0.266 0.606 0.769 0.283～2.087 41～60 0.205 0.491 0.174 0.676 1.227 0.469～3.211 > 60 1.259 0.844 2.227 0.136 3.523 0.674～18.418 疫苗接种 1剂次 未接种 0.402 0.385 1.090 0.296 1.495 0.703～3.179 2剂次 – 0.610 0.644 0.897 0.344 0.543 0.154～1.920 ≥ 3剂次 0.303 0.524 0.335 0.563 1.354 0.485～3.778 既往感染 否 是 0.873 0.351 6.175 0.013 2.395 1.203～4.769
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