Appendix of “Epidemiological Characteristics and Incubation Period of SARS-Cov-2 During the 2020-2021 Winter Pandemic Wave in North China: an Observational Study”

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Appendix of “Epidemiological characteristics and incubation period of SARS-CoV-2 during the 2020-2021 winter pandemic wave in north China: an observational study”

Tiantian Liua,b , Zijian Chena, Jin Xua,c

a. School of Statistics, East China Normal University, Shanghai, China b. Faculty of Industrial Engineering and Management, Technion – Israel Institute of Technology, Haifa, Israel c. Key Laboratory of Advanced Theory and Application in Statistics and Data Science – MOE, East China Normal University, Shanghai, China

Corresponding Author: Jin Xu, School of Statistics, East China Normal University, Shanghai 200062, China, Tel: +86-21-6223-3223, E-mail address: [email protected]

A. List of data source of individual patient narratives ...... 2 B. Examples of data extraction from four types of data ...... 4 C. Summary of 20 publications about median incubation period ...... 6 D. Details of the meta-analysis about median incubation period...... 8 E. Details of analyzing covariate effects ...... 10 References: ...... 11

A. List of data source of individual patient narratives

Date Province City N Source webpage (YYYY/MM/DD) 2021/01/02 Hebei Shijiazhuang 1 https://news.sina.com.cn/c/2021-01-03/doc-iizne zxt0358165.shtml 2021/01/03 Hebei Shijiazhuang 2 https://news.sina.com.cn/c/2021-01-04/doc-iiznc tkf0094732.shtml 2021/01/03 Hebei Xingtai 2 https://new.qq.com/omn/20210104/ 20210104A02GQ700.html 2021/01/04 Hebei Shijiazhuang 11 wsjkw.hebei.gov.cn/syyctplj/375192.jhtml 2021/01/04 Hebei Xingtai 3 wsjkw.hebei.gov.cn/syyctplj/375191.jhtml 2021/01/05 Hebei Shijiazhuang 19 wsjkw.hebei.gov.cn/syyctplj/375221.jhtml 2021/01/05 Hebei Xingtai 1 wsjkw.hebei.gov.cn/syyctplj/375219.jhtml 2021/01/06 Hebei Shijiazhuang 50 wsjkw.hebei.gov.cn/syyctplj/375261.jhtml 2021/01/06 Hebei Xingtai 1 wsjkw.hebei.gov.cn/syyctplj/375260.jhtml 2021/01/07 Hebei Shijiazhuang 31 wsjkw.hebei.gov.cn/syyctplj/375294.jhtml 2021/01/07 Hebei Xingtai 2 wsjkw.hebei.gov.cn/syyctplj/375293.jhtml 2021/01/08 Hebei Shijiazhuang 14 wsjkw.hebei.gov.cn/syyctplj/375333.jhtml 2021/01/09 Hebei Shijiazhuang 44 wsjkw.hebei.gov.cn/syyctplj/375370.jhtml 2021/01/09 Hebei Xingtai 2 wsjkw.hebei.gov.cn/syyctplj/375369.jhtml 2021/01/10 Hebei Shijiazhuang 77 wsjkw.hebei.gov.cn/syyctplj/375391.jhtml 2021/01/10 Hebei Xingtai 5 wsjkw.hebei.gov.cn/syyctplj/375390.jhtml 2021/01/11 Hebei Shijiazhuang 39 wsjkw.hebei.gov.cn/syyctplj/375429.jhtml 2021/01/11 Hebei Langfang 1 wsjkw.hebei.gov.cn/syyctplj/375428.jhtml 2021/01/12 Hebei Shijiazhuang 84 wsjkw.hebei.gov.cn/syyctplj/375478.jhtml 2021/01/12 Hebei Xingtai 6 wsjkw.hebei.gov.cn/syyctplj/375477.jhtml 2021/01/13 Hebei Shijiazhuang 75 wsjkw.hebei.gov.cn/syyctplj/375501.jhtml 2021/01/13 Hebei Xingtai 6 wsjkw.hebei.gov.cn/syyctplj/375500.jhtml 2021/01/14 Hebei Shijiazhuang 84 wsjkw.hebei.gov.cn/syyctplj/375548.jhtml 2021/01/14 Hebei Xingtai 6 wsjkw.hebei.gov.cn/syyctplj/375547.jhtml 2021/01/15 Hebei Shijiazhuang 83 wsjkw.hebei.gov.cn/syyctplj/375547.jhtml 2021/01/15 Hebei Xingtai 7 wsjkw.hebei.gov.cn/syyctplj/375582.jhtml 2021/01/16 Hebei Shijiazhuang 65 wsjkw.hebei.gov.cn/syyctplj/375582.jhtml 2021/01/16 Hebei Xingtai 7 wsjkw.hebei.gov.cn/syyctplj/375618.jhtml 2021/01/17 Hebei Shijiazhuang 52 wsjkw.hebei.gov.cn/syyctplj/375644.jhtml 2021/01/17 Hebei Xingtai 2 wsjkw.hebei.gov.cn/syyctplj/375643.jhtml 2021/01/18 Hebei Shijiazhuang 35 wsjkw.hebei.gov.cn/syyctplj/375680.jhtml 2021/01/19 Hebei Shijiazhuang 13 wsjkw.hebei.gov.cn/syyctplj/375719.jhtml 2021/01/19 Hebei Xingtai 6 wsjkw.hebei.gov.cn/syyctplj/375718.jhtml 2021/01/20 Hebei Shijiazhuang 20 wsjkw.hebei.gov.cn/syyctplj/375757.jhtml

2021/01/21 Hebei Shijiazhuang 15 wsjkw.hebei.gov.cn/syyctplj/375796.jhtml 2021/01/21 Hebei Xingtai 3 wsjkw.hebei.gov.cn/syyctplj/375795.jhtml 2021/01/22 Hebei Shijiazhuang 11 wsjkw.hebei.gov.cn/syyctplj/375795.jhtml 2021/01/22 Hebei Xingtai 4 wsjkw.hebei.gov.cn/syyctplj/375834.jhtml 2021/01/23 Hebei Shijiazhuang 17 wsjkw.hebei.gov.cn/syyctplj/375834.jhtml 2021/01/23 Hebei Xingtai 2 wsjkw.hebei.gov.cn/syyctplj/375834.jhtml 2021/01/24 Hebei Shijiazhuang 7 wsjkw.hebei.gov.cn/syyctplj/375834.jhtml 2021/01/24 Hebei Xingtai 4 wsjkw.hebei.gov.cn/syyctplj/375834.jhtml 2021/01/25 Hebei Shijiazhuang 5 wsjkw.hebei.gov.cn/syyctplj/375834.jhtml 2021/01/26 Hebei Shijiazhuang 5 wsjkw.hebei.gov.cn/syyctplj/375834.jhtml 2021/01/26 Hebei Dingzhou 1 wsjkw.hebei.gov.cn/syyctplj/375834.jhtml 2021/01/26 Hebei Xingtai 1 wsjkw.hebei.gov.cn/syyctplj/375834.jhtml 2021/01/27 Hebei Shijiazhuang 2 wsjkw.hebei.gov.cn/syyctplj/375834.jhtml 2021/01/27 Hebei Xingtai 1 wsjkw.hebei.gov.cn/syyctplj/375834.jhtml 2021/01/28 Hebei Shijiazhuang 1 wsjkw.hebei.gov.cn/syyctplj/375834.jhtml 2021/01/29 Hebei Shijiazhuang 1 wsjkw.hebei.gov.cn/syyctplj/375834.jhtml 2021/01/30 Hebei Shijiazhuang 1 wsjkw.hebei.gov.cn/syyctplj/376102.jhtml 2021/01/31 Hebei Shijiazhuang 1 wsjkw.hebei.gov.cn/syyctplj/376102.jhtml 2021/02/02 Hebei Shijiazhuang 1 wsjkw.hebei.gov.cn/syyctplj/376194.jhtml 2021/02/03 Hebei Shijiazhuang 2 wsjkw.hebei.gov.cn/syyctplj/376231.jhtml 941 Table A.1: List of data source of individual patient narratives published from 2nd January 2021 to 3rd February 2021 by Health Commission of Hebei Province

B. Examples of data extraction from four types of data

We provided one example for each of the four types of data to show extraction of relevant transmission timeline (in MM/DD/YYYY format) and covariates.

Type Patient narratives Data extracted

I Confirmed case 6: Female, 55 years old, currently living in W0= NA th Xiaoguozhuang Village, Gaocheng District. From December 20 to W1= NA th December 26 , 2020, the patient stayed at home and did not go out of T0=12/28/2020 th the town. On December 27 , the patient walked to the village to T1=01/01/2021

participate in some activity, stayed there for about one hour, and then T2=01/02/2021 returned home by foot. On the morning of December 28th, she rode an electric bike to a hotel near North Airport Road to attend a wedding, Sex= female but did not go out in the afternoon. The patient stayed at home and Age= 55 did not go out of the town from December 29th to 31th. After the Living with a supper on January 1st, 2021, due to headache and cough, she rode an case= no electric bike to the village clinic to get some medicine from the Symptomatic= doctor. Nucleic acid test was done on January 2nd. And she started yes home-isolation on January 2nd. The nucleic acid test result showed # of false positive on January 3rd. On the same day, she was transferred to the negative= 0 Fifth Hospital of Shijiazhuang City by a negative pressure ambulance. She was diagnosed as a confirmed case on January 4th with grade of “moderate”.

webpage of the original text in Chinese: http://wsjkw.hebei.gov.cn/syyctplj/375192.jhtml

II Confirmed case 14: Female, 24 years old, currently lives in Area A, W0= NA

District 4, Zhongmei Bridge community, Yuhua District. At 10 am on W1= NA th December 28 , 2020, she drove to Oujing Ecological Park, North T0=12/28/2020

Airport Road, Zhengding County to attend a wedding banquet. After T1= censored

that, she went to the hometown of Xiaoguozhuang Village, Zengcun T2=01/04/2021 Town, Gaocheng District, and then drove back home at 4 pm. From December 29th to January 31th, she rode an electric bicycle to the Sex= female kindergarten in Area A of Anyuan Community to pick up and drop off Age= 24 her child. From January 1st to 2nd, 2021, except for some walks in the Living with a community, she did not visit any other public places. On January 3rd, case= no she drove to the first affiliated hospital of Hebei Medical University Symptomatic= of Hebei Province to take a nucleic acid test. The result was negative. no On January 4th, the nucleic acid test showed positive. Then, she was # of false transferred to the Fifth Hospital of Shijiazhuang City by the negative negative= 1 pressure ambulance on the same day. On January 9th, she was transferred to Hebei Chest Hospital by the negative pressure ambulance. She was diagnosed as a confirmed case on January 10th.

webpage of the original text in Chinese: http://wsjkw.hebei.gov.cn/syyctplj/375391.jhtml

III Confirmed case 18: Male, 51 years old, lives in Nanqiaozhai Village, W0=12/29/2020

Zengcun Town, Gaocheng District. He was self-employed for house W1=01/02/2021

decoration work in Changping, Beijing. He returned home from T0=NA th Beijing on December 29 , 2020. He did not go out of the village from T1=01/03/2021 th nd rd December 30 , 2020 to January 2 , 2021. On January 3 , he had T2=01/05/2021 fever and took a nucleic acid test on the same day. The result showed positive on January 4th. On January 5th, he was transferred to the Fifth Sex= male Hospital of Shijiazhuang City by a negative pressure ambulance. He Age= 51 was diagnosed as confirmed case on the same day. Living with a case= no webpage of the original text in Chinese: Symptomatic= http://wsjkw.hebei.gov.cn/syyctplj/375221.jhtml no # of false negative= 0

IV Confirmed case 7: female, 49 years old, currently lives in Ruida Rose W0= NA

Garden community, Changshou street, Xinle City, the mother of the W1=01/04/2021 th st th 25th confirmed case on January 17 . From January 1 to January 4 , T0=NA

2021, she rode an electric bike to work at the cloth shop in Xianyu T1= censored

market, Xinle City every day at 9am, returned home at 4pm. She was T2=01/15/2021 transferred to a designated isolation place in Xinle City for medical observation on January 5th. The nucleic acid tests on January 5th, 7th, Sex= female 9th, and 13th were all negative. On January 15th, the nucleic acid test Age=49 showed positive. On January 16th, she was transferred by a negative Living with a pressure ambulance to Shijiazhuang People’s Hospital of Jianhua case= yes District and she was diagnosed as asymptomatic case. On January Symptomatic= 19th, she was diagnosed as confirmed case. no # of false webpage of the original text in Chinese: negative= 4 http:// wsjkw.hebei.gov.cn/syyctplj/375719.jhtml

C. Summary of 20 publications about median incubation period

Article Coverage Data source N Median Distribution Study type period region model (MM/DD/YY (analysis YY) software) Backer et al. (2020)1 01/20/2020-0 China 88 6·4 Weibull meta-analysis 1/28/2020 Bui et al. (2020)2 01/23/2020-0 Vietnam 19 5·6 Weibull independent 4/13/2020 study Cheng et al. (2020)3 Before Taiwan 100 4·1 NA independent 03/18/2020 study Du et al. (2020)4 01/08/2020-0 China 109 5·1 Gamma independent 2/05/2021 study Deng et al. (2020)5 01/19/2020-0 China 1211 8·5 Gamma independent 1/23/2020 study Guan et al. (2020)6 01/12/2019-0 China 1099 4 NA independent 1/29/2020 study Kong et al. (2020)7 01/15/2020-0 China 136 8·3 NA independent 1/22/2020 (CumFreq) study Lauer et al. (2020)8 01/04/2020-0 China, 181 5·1 Lognormal independent 2/24/2020 except study Hubei province Lee et al. (2020)9 02/20/2020-0 Korea 47 3 Lognormal independent 3/03/2020 study Linton et al. (2020)10 01/01/2020-0 China, 158 5·6 Lognormal independent 1/31/2021 except study Wuhan McAloon et al. 12/01/2019-0 Worldwide NA 5·1 Lognormal meta-analysis (2020)11 4/08/2020 Nie et al. (2020)12 01/19/2020-0 China, 7015 5 NA independent 2/08/2020 except study Hubei province Patrikar et al. (2020)13 02/01/2020-0 India 268 6.93 Normal independent 4/19/2020 study Qian et al. (2020)14 01/20/2020-0 Zhejiang, 91 6 NA independent 2/11/2020 China study Qin et al. (2020)15 Before China, 1084 7·76 Weibull independent 02/15/2020 except study Hubei province Sun et al. (2020)16 01/20/2020-0 Beijing, 55 7·5 NA independent 6

2/15/2020 China study Tan et al. (2020)17 01/23/2020-0 Singapore 164 5 NA independent 4/02/2020 study Viego et al. (2020)18 03/20/2020-0 Argentina 18 6·1 Lognormal independent 5/08/2020 study Xiao et al. (2020)19 Before China, 2555 8 Weibull independent 02/21/2020 except study Hubei, Qinghai, Xizang Province Yang et al. (2020)20 01/20/2020-0 Shiye, 178 5·4 Weibull independent 4/01/2020 Hubei (coarseData study province Tools) Table C.1: Summary of 20 publications about median incubation period used in plotting Figure 4 and meta-analysis

D. Details of the meta-analysis about median incubation period

A simple meta-analysis based on seven published articles was conducted to obtain a pooled estimate of the median of incubation period (IP) during the first SARS-CoV-2 pandemic wave (from December 2019 to April 2020) in China. The process was outlined by the flow chart in Figure D.1.

The R package “metamedian” developed by McGrath21 was used to analyze the data. The detail of the source information along with the forest plot was shown in Figure D.2. The estimate of the overall median IP was found to be 5·6 days (95% CI 5·1–8·3).

Figure D.1: Flow chart of processing of source information for the meta-analysis

Figure D.2: Source information used in the meta-analysis and the resulting forest plot for the overall estimate of the median incubation period

E. Details of analyzing covariate effects

We applied the Cox model to test the covariate effects of sex, age and living with a case with respect to IP. The estimated coefficients of covariates and associated p-values were obtained in Table E.1 based on different aggregated types of data. All p-values were greater than 0·05, indicating no significant effect of the considered covariates.

aggregated types sex age living with a case I + II 0·016 (0·10) -0·44 (0·29) -0·42 (0·32) I + II + III 0·016 (0·10) -0·50 (0·22) -0·52 (0·22) I + II + III + IV 0·015 (0·11) -0·49 (0·11) -0·25 (0·56) Table E.1: Estimated coefficients of covariates and associated p-values in parentheses obtained by the Cox model for the different aggregated types of data

We used the traditional log-rank test to test the equality of the distributions of IP between two age groups. Figure E.1 shows Kaplan-Meier estimates of the probability of being asymptomatic of the two age groups based on different aggregated types of data. The p-values of the test were shown in the second column of Table E.2. In the presence of possible crossing survival curves, we also reported the p-values in the third column of Table E.2 of the restricted mean survival time (RMST) based test22 between the two groups. Again, none of the results showed significant difference between the two groups.

Figure E.1: Kaplan-Meier estimates of probability of being asymptomatic of two age groups based different aggregated types of data

aggregated types Log-rank test RMST-based test I + II 0·09 0·16 I + II + III 0·07 0·13 I + II + III + IV 0·20 0·29 Table E.2: P-values of the log-rank test (for equality of the distributions of IP) and p-values of the RMST-based test (for equality of RMSTs of IP)

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