Estimation of transmission dynamics parameters for Omicron BA.5.2 variant—based on real-world data
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摘要:
目的 利用湖北省荆州市2起由奥密克戎BA.5.2变异株引起的局部疫情数据，估算奥密克戎BA.5.2变异株的传播动力学参数，为认识奥密克戎BA.5.2变异株传播能力提供科学依据。 方法 采用自行设计表格收集2起疫情中感染关系明确的感染者与被感染者的感染时间、发病时间及首次核酸阳性采样时间等数据。 对获得数据分别拟合对数正态分布、伽马分布和伽马分布计算潜伏期、世代间隔（GT）、代际间隔（SI）。 分别采用指数增长模型（EG）和极大似然估计法（ML）计算基本再生数（R0），取R2较大者作为R0估算值。 结果 荆州市2起疫情中，疫情A为外市来荆人员在荆州市进行社交活动引起，主要通过同住、同餐、同娱乐和同工作传播，为常见社交传播情形；疫情B涉及人群聚集的批发市场，首发病例进入后停留3 h后随即离开，在农贸市场快速传播并外溢至同住人员，为人群密集场所传播情形。 2起疫情共计纳入感染者与被感染者39对52例的数据用于潜伏期、GT和SI估算。 潜伏期中位数为2.52 d（44例，1.32～4.84 d），SI中位数为2.13 d（37例，1.63～2.64 d），GT中位数为1.91 d（21例，1.05～3.15 d）。 疫情A、疫情B最优拟合模型均为EG模型，对应R2分别为0.62、0.88。疫情A、疫情B拟合的R0分别为5.33（95%CI：2.08～13.44）、22.58（95%CI：7.23～91.36）。 单次暴露感染者观察到暴露至检出最短时间为20～21 h。 结论 奥密克戎BA.5.2变异株具有潜伏期短、传播速度快、传染性强的特点。 在人群密集场所，奥密克戎BA.5.2变异株传播能力极强。 Abstract:Objective To estimate the transmission dynamics parameters of Omicron BA.5.2 variant and provide a scientific evidence for understanding the infectivity of Omicron BA.5.2. Methods The data of infection time, onset time and first positive sampling time of the infection cases with clear infection relationship in two outbreaks in Jingzhou were collected by using self-designed forms. The obtained data were fitted with log-normal distribution, gamma distribution and gamma distribution to calculate incubation period, generation time (GT), and serial interval (SI). The exponential growth model (EG) and the maximum likelihood estimation method (ML) were used to calculate R0, respectively. The fitted value with the larger R2 was used as the R0 estimate. Results In the 2 outbreaks in Jingzhou, outbreak A was caused by the imported virus spread in local population mainly through people's living, dining, amusing and working together, showing a common social transmission pattern. Outbreak B occurred in a wholesale market, which was caused by an infection case who had stay in the market for 3 hours and subsequent rapid transmission in market workers and their close contacts, showing a clustered transmission pattern. A total of 52 cases in 39 pairs of primary and secondary cases in the 2 outbreaks were included for the estimations of incubation period, GT and SI. The median of incubation period was 2.52 days (44 cases, 1.32−4.84 days), the median of SI was 2.13 days (37 cases, 1.63−2.64 days), and the median of GT was 1.91 days (21 cases, 1.05–3.15 days). The optimal fitting models of outbreak A and outbreak B were all EG models, and the corresponding R2 were 0.62 and 0.88, respectively. The fitted R0s of outbreak A and outbreak B were 5.33 (95%CI: 2.08–13.44) and 22.58 (95%CI: 7.23–91.36), respectively. In some cases, the shortest interval (20−21 hours) between exposure and detection was observed. Conclusion Omicron BA.5.2 variant has the characteristics of short incubation period, rapid transmission speed and strong infectivity. In crowded places, Omicron BA.5.2 variant has very strong transmission ability. -
图 1 2022年荆州市奥密克戎BA.5.2变异株疫情A和疫情B的有效再生数估计
Figure 1. Estimated effective reproduction number of Omicron BA.5.2 variant in outbreaks A and B in Jingzhou, 2022
表 1 奥密克戎BA.5.2变异株潜伏期、世代间隔和代际间隔计算结果
Table 1. Calculation results of incubation period, GT and SI of Omicron BA.5.2 variant
参数 对子数
（对）中位数（d） 第2.5百分位（d） 第97.5百分位（d） 潜伏期 44 2.52 1.32 4.84 世代间隔 21 1.91 1.05 3.15 代际间隔 37 2.13 1.63 2.64 代际间隔标准差 37 1.69 1.15 2.01 
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表 2 疫情A和疫情B的基本再生数和倍增时间估计
Table 2. R0 and doubling time estimates for outbreak A and outbreak B
情形 模型 R0 95%CI 指数增长率r 95%CI 倍增时间（d） 95%CI R2值 疫情A EG 5.33 2.08～13.44 0.73 0.28～1.26 0.95 0.55～2.45 0.62 ML 3.95 1.90～7.12 − − − − 0.30 疫情B EG 22.58 7.23～91.36 1.59 0.90～2.56 0.44 0.27～0.77 0.88 ML 12.32 6.05～21.90 − − − − 0.87 注：EG. 指数增长模型；ML. 极大似然估计法；R0. 基本再生数；CI. 置信区间；−表示无数据
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[1] World Health Organization. WHO coronavirus (COVID-19) dashboard [EB/OL]. (2022-10-25)[2022-10-27]. https://covid19.who.int/. [2] World Health Organization. WHO director-general's opening remarks at the media briefing on COVID-19[EB/OL]. (2020-03-11)[2022/10/27].https://www.who.int/director-general/speeches/detail/who-director-general-s-opening-remarks-at-the-media-briefing-on-covid-19---11-march-2020. [3] Li Q, Guan XH, Wu P, et al. Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia[J]. N Engl J Med, 2020, 382(13): 1199–1207. DOI: 10.1056/NEJMoa2001316. [4] Liu T, Qi L, Yao ML, et al. Serial interval and reproductive number of COVID-19 among 116 infector-infectee Pairs - Jingzhou city, Hubei province, China, 2020[J]. China CDC Wkly, 2020, 2(27): 491–495. DOI: 10.46234/ccdcw2020.118. [5] Singhal T. The emergence of omicron: challenging times are here again![J]. Indian J Pediatr, 2022, 89(5): 490–496. DOI: 10.1007/s12098−022−04077−4. [6] Tian DD, Sun YH, Xu HH, et al. The emergence and epidemic characteristics of the highly mutated SARS-CoV-2 omicron variant[J]. J Med Virol, 2022, 94(6): 2376–2383. DOI: 10.1002/jmv.27643. [7] Shrestha LB, Foster C, Rawlinson W, et al. Evolution of the SARS-CoV-2 omicron variants BA. 1 to BA. 5: implications for immune escape and transmission[J]. Rev Med Virol, 2022, 32(5): e2381. DOI: 10.1002/rmv.2381. [8] Jiang H, Wu CC, Xu WB, et al. First imported case of SARS-CoV-2 omicron subvariant BA. 5 - Shanghai Municipality, China, May 13, 2022[J]. China CDC Wkly, 2022, 4(30): 665–666. DOI: 10.46234/ccdcw2022.104. [9] Feng ZM, Shen Y, Li S, et al. The first outbreak of omicron subvariant BA. 5.2 - Beijing Municipality, China, July 4, 2022[J]. China CDC Wkly, 2022, 4(30): 667–668. DOI: 10.46234/ccdcw2022.136. [10] 国务院应对新型冠状病毒肺炎疫情联防联控机制综合组. 新型冠状病毒肺炎防控方案(第九版)[J]. 中国病毒病杂志,2022,12(5):331–338. DOI:10.16505/j.2095−0136.2022.0049.The Joint Prevention and Control Mechanism Group of the State Council to COVID-19. Guidelines for prevention and control of coronavirus disease 2019 (Ninth Edition)[J]. Chin J Viral Dis, 2022, 12(5): 331–338. DOI: 10.16505/j.2095−0136.2022.0049. [11] Reich NG, Lessler J, Cummings DAT, et al. Estimating incubation period distributions with coarse data[J]. Stat Med, 2009, 28(22): 2769–2784. DOI: 10.1002/sim.3659. [12] Virlogeux V, Fang VJ, Wu JT, et al. Brief report: incubation period duration and severity of clinical disease following severe acute respiratory syndrome coronavirus infection[J]. Epidemiology, 2015, 26(5): 666–669. DOI: 10.1097/EDE.0000000000000339. [13] Lauer SA, Grantz KH, Bi QF, et al. The incubation period of coronavirus disease 2019 (COVID-19) from publicly reported confirmed cases: estimation and application[J]. Ann Intern Med, 2020, 172(9): 577–582. DOI: 10.7326/M20−0504. [14] Lau YC, Tsang TK, Kennedy-Shaffer L, et al. Joint estimation of generation time and incubation period for coronavirus disease 2019[J]. J Infect Dis, 2021, 224(10): 1664–1671. DOI: 10.1093/infdis/jiab424. [15] Ganyani T, Kremer C, Chen DX, et al. Estimating the generation interval for coronavirus disease (COVID-19) based on symptom onset data, March 2020[J]. Euro Surveill, 2020, 25(17): 2000257. DOI: 10.2807/1560−7917.ES.2020.25.17.2000257. [16] 刘天, 侯清波, 姚梦雷, 等. 传染病暴发疫情中传播动力学参数计算及疫情规模预测实现——基于R[J]. 疾病监测,2022,37(9):1211–1215. DOI: 10.3784/jbjc.202111170600.Liu T, Hou QB, Yao ML, et al. Calculation of transmission dynamics parameters and prediction of epidemic size in infectious disease outbreak—based on software R[J]. Dis Surveill, 2022, 37(9): 1211–1215. DOI: 10.3784/jbjc.202111170600. [17] Obadia T, Haneef R, Boëlle PY. The R0 package: a toolbox to estimate reproduction numbers for epidemic outbreaks[J]. BMC Med Inform Decis Mak, 2012, 12: 147. DOI: 10.1186/1472−6947−12−147. [18] Ferretti L, Wymant C, Kendall M, et al. Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing[J]. Science, 2020, 368(6491). DOI: 10.1126/science.abb6936. [19] Du ZW, Hong HP, Wang SQ, et al. Reproduction number of the omicron variant triples that of the delta variant[J]. Viruses, 2022, 14(4): 821. DOI: 10.3390/v14040821. [20] Liu Y, Rocklöv J. The effective reproductive number of the omicron variant of SARS-CoV-2 is several times relative to delta[J]. J Travel Med, 2022, 29(3): taac037. DOI: 10.1093/jtm/taac037. [21] Nishiura H, Ito K, Anzai A, et al. Relative reproduction number of SARS-CoV-2 omicron (B. 1.1. 529) compared with delta variant in South Africa[J]. J Clin Med, 2021, 11(1): 30. DOI: 10.3390/jcm11010030. [22] Niu Y, Luo L, Yang ST, et al. Comparison of epidemiological characteristics and transmissibility of different strains of COVID-19 based on the incidence data of all local outbreaks in China as of March 1, 2022[J]. Front Public Health, 2022, 10: 949594. DOI: 10.3389/fpubh.2022.949594. [23] Delamater PL, Street EJ, Leslie TF, et al. Complexity of the basic reproduction number (R0)[J]. Emerg Infect Dis, 2019, 25(1): 1–4. DOI: 10.3201/eid2501.171901. [24] 黄森忠, 魏凤英, 彭志行, 等. 常态化防控下新型冠状病毒肺炎新发疫情研判方法[J]. 疾病监测,2020,35(8):679–686. DOI:10.3784/j.issn.1003−9961.2020.08.004.Huang SZ, Wei FY, Peng ZX, et al. Assessment method of coronavirus disease 2019 outbreaks under normal prevention and control[J]. Dis Surveill, 2020, 35(8): 679–686. DOI: 10.3784/j.issn.1003−9961.2020.08.004. [25] Cao YL, Yisimayi A, Jian FC, et al. BA. 2.12. 1, BA. 4 and BA. 5 escape antibodies elicited by omicron infection[J]. Nature, 2022, 608(7923): 593–602. DOI: 10.1038/s41586−022−04980−y. [26] Ruan F, Zhang XB, Xiao SJ, et al. An outbreak of the SARS-CoV-2 omicron variant BA. 1 - Zhuhai city, Guangdong province, China, January 13, 2022[J]. China CDC Wkly, 2022, 4(30): 669–671. DOI: 10.46234/ccdcw2022.032. -
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