From 4f78618f0bd5f3542d5b7f2e03aaae3b691ebd29 Mon Sep 17 00:00:00 2001 From: Steve Lauer Date: Fri, 31 Jan 2020 11:35:31 -0500 Subject: [PATCH] saved data version for use in manuscript (in case other data get updated); added all active monitoring figures to manuscript doc --- data/backer-params.csv | 2 +- data/nCoV-IDD-traveler-data-manuscript.csv | 102 ++++++++++++++++++ manuscript/nCoV_Incubation.Rmd | 119 +++++++++++++-------- 3 files changed, 180 insertions(+), 43 deletions(-) create mode 100644 data/nCoV-IDD-traveler-data-manuscript.csv diff --git a/data/backer-params.csv b/data/backer-params.csv index b05441c..e76e16d 100644 --- a/data/backer-params.csv +++ b/data/backer-params.csv @@ -1,5 +1,5 @@ study,type,obs,par1,par2 -Backer 2020,weibull,34,2.373476,6.543997 +Backer 2020,Weibull,34,2.373476,6.543997 Backer 2020,gamma,34,4.96,1.15 Backer 2020,log-normal,34,1.63,0.55 Li 2020,log-normal,10,1.42,0.67 \ No newline at end of file diff --git a/data/nCoV-IDD-traveler-data-manuscript.csv b/data/nCoV-IDD-traveler-data-manuscript.csv new file mode 100644 index 0000000..6666db1 --- /dev/null +++ b/data/nCoV-IDD-traveler-data-manuscript.csv @@ -0,0 +1,102 @@ +REVIEWER1,REVIEWER2,REFID1,REFID2,REFID3,UID,COUNTRY.ORIGIN,PROVINCE.ORIGIN,MUNIP.ORIGIN,COUNTRY.DEST,PROVINCE.DEST,MUNIP.DEST,EL,ER,SL,SR,SL_fever,SR_fever,PL,PR,EXP.TYPE,AGEL,AGER,SEX,WUHAN_RESIDENT,WUHAN_VISITED,CONTACTS,NOTES,NOTES2 +FJ,SL/HM,r0002,r0001,r0113,U0001,China,Hubei,Wuhan,USA,Washington,Snohomish County,2019-11-01 00:00:00,2020-01-15 23:59:00,2020-01-19 00:00:00,2020-01-19 23:59:00,,,,,,30,39,Male,No,Yes,,"Case was in Wuhan starting November, flew out of wuhan on jan 15, had symptoms on January 19, nationality unknown.", +FJ,HM,r0004,r0003,,U0002,China,Hubei,Wuhan,USA,Illinois,Chicago,2019-12-15 00:00:00,2020-01-13 23:59:00,2020-01-14 00:00:00,2020-01-24 23:59:00,,,,,,60,69,Female,No,Yes,,"Case was in Wuhan starting in ""late December"", flew out on Jan 13. Had symptoms after arriving in USA, had symptoms a ""few days later"", case announced on 24th", +FJ,HM,r0005,r0012,,U0003,China,Hubei,Wuhan,Australia,Victoria,Melbourne,2020-01-09 00:00:00,2020-01-19 09:00:00,2020-01-23 00:00:00,2020-01-23 12:00:00,,,2020-01-23 00:00:00,2020-01-23 12:00:00,,50,59,Male,No,Yes,,"Chinese National, left Wuhan on January 19th, was in wuhan the two weeks prior to symptom onset. Went to see GP on morning of the 23rd. arrive at 9am in melbourne.", +SL,HM,r0006,r0007,,U0004,China,Hubei,Wuhan,Thailand,Bangkok,Bangkok,,2020-01-05 23:59:00,2020-01-05 00:00:00,2020-01-05 23:59:00,2020-01-05 00:00:00,2020-01-05 23:59:00,2020-01-08 00:00:00,2020-01-08 23:59:00,,61,61,Female,Yes,,,Wuhan woman traveling to Thailand on Jan 5 who presented a fever and was detected at the Suvarnabhumi Airport on Jan 8,"Symptoms reported: fever, chills, sore throat, and headache." +SL,HM,r0008,r0021,,U0005,China,Hubei,Wuhan,Thailand,Bangkok,Bangkok,,2020-01-13 23:59:00,,2020-01-13 23:59:00,,2020-01-13 23:59:00,2020-01-13 00:00:00,2020-01-13 23:59:00,,74,74,Female,Yes,,,Wuhan woman traveling to Thailand on Jan 13 who presented a fever and was detected at the Suvarnabhumi Airport, +SL,HM,r0009,r0015,,U0006,China,Hubei,Wuhan,Japan,Kanto,Kanagawa,2019-12-15 00:00:00,2020-01-03 23:59:00,2020-01-03 00:00:00,2020-01-03 23:59:00,2020-01-03 00:00:00,2020-01-03 23:59:00,2020-01-10 00:00:00,2020-01-10 23:59:00,3,30,39,Male,No,Yes,,"Japanese man traveling to Wuhan in late December, had symptoms January 3rd, returned to Japan January 6th and went to hospital and tested negative for influenza, returned to hospital on January 10th and confirmed as nCoV",Reported being in close contact with person with pneumonia +FJ,HM,r0010,,,U0007,China,Hubei,Wuhan,Australia,New South Wales,Sydney,,2020-01-20 17:00:00,2020-01-20 17:00:00,2020-01-20 23:59:00,,,2020-01-20 17:00:00,2020-01-21 23:59:00,,50,59,Male,No,Yes,,"3rd confirmed imported case of CoV to Australia. Male in his 50s taveled to Wuhan ""in recent weeks"", returned to Sydney Jan 20, developed symptoms that evening and sought care soon after. The arrival flight and symptom onset given.", +FJ,HM,r0010,,,U0008,China,,,Australia,New South Wales,Sydney,,2020-01-06 23:59:00,2020-01-15 00:00:00,2020-01-15 23:59:00,,,2020-01-15 00:00:00,2020-01-15 23:59:00,3,30,39,Male,No,No,,"2nd confirmed imported CoV Case to Australia. Had contact with a known case while in China, DID NOT VISIT WUHAN. Symptoms and presentation on January 15. Arrive in Sydney on January 6.", +FJ,HM,r0010,,,U0009,China,Hubei,Wuhan,Australia,New South Wales,Sydney,,2020-01-18 23:59:00,2020-01-24 00:00:00,2020-01-24 23:59:00,,,2020-01-24 00:00:00,2020-01-24 23:59:00,,40,49,Male,No,Yes,,"4th confirmed imported case to Australia. Traveled to Wuhan ""in recent weeks"", arrival flight and symptom onset given.", +SL,HM,r0011,,,U0010,China,Hubei,Wuhan,Thailand,Bangkok,Bangkok,,2020-01-21 23:59:00,2020-01-21 00:00:00,2020-01-21 23:59:00,2020-01-21 00:00:00,2020-01-21 23:59:00,2020-01-23 00:00:00,2020-01-23 23:59:00,,33,33,Female,Yes,,,Wuhan woman traveled to Thailand on Jan 21. She visited a private hospital complaining of cough and fever before being transfered to a government hospital on Jan 23. Wording makes it hard to determine when symptoms started/when she visited private hospital, +FJ,HM,r0014,r0018,,U0012,China,Hubei,Wuhan,France,Île-de-France,Paris,,2020-01-18 23:59:00,2020-01-19 00:00:00,2020-01-19 23:59:00,,,,,,31,31,Male,,,U0013,"In a couple with U0013, chinese national. Arrived in France without symptoms", +FJ,HM,r0014,r0018,,U0013,China,Hubei,Wuhan,France,Île-de-France,Paris,,2020-01-18 23:59:00,2020-01-23 00:00:00,2020-01-23 23:59:00,,,,,,30,30,Female,,,U0012,"In a couple with U0012, chinese national. Arrived in France without symptoms",** There is a disagreement between r0014 and r0018 regarding onset of symptoms. r0014 says Jan 23 and r0018 says Jan 20 +FJ,HM,r0014,,,U0014,China,Hubei,Wuhan,France,Aquitaine,Bordeaux,,2020-01-22 23:59:00,2020-01-23 00:00:00,2020-01-23 23:59:00,,,2020-01-24 00:00:00,2020-01-24 00:00:00,,48,48,Male,,,,"Chinese national, traveled from Wuhan to netherlands, to bordeaux", +SL,HM,r0011,r0013,r0022,U0011,China,Hubei,Wuhan,Thailand,Nakohm Pathom,,,2020-01-15 23:59:00,,2020-01-15 23:59:00,,,2020-01-15 00:00:00,2020-01-15 23:59:00,,73,73,Female,No,Yes,,Thai woman who spent New Years in Wuhan (or perhaps left before?). She was admitted to hospital on Jan 15 and cleared of virus by Jan 17, +FJ,HM,r0016,r0017,r0070,U0015,China,Hubei,Wuhan,Nepal,No. 3,Kathmandu,,2020-01-09 23:59:00,2020-01-09 00:00:00,2020-01-13 23:59:00,2020-01-09 00:00:00,2020-01-13 23:59:00,2020-01-13 00:00:00,2020-01-13 23:59:00,,32,32,Male,Yes,,,"""The student, in his early 30s, arrived in Nepal on January 9. He went to Sukraraj Tropical and Infectious Disease Hospital in Kathmandu four days later, after running a fever and having breathing problems"". He was released from hospital on Jan 17","Assumes that detection was on day of article release (Jan 24). Symptoms started 4 days prior, so assume SR to be Jan 20" +FJ,HM,r0019,,,U0016,China,Hubei,Wuhan,Singapore,Singapore,Singapore,,2020-01-20 23:59:00,2020-01-20 00:00:00,2020-01-20 23:59:00,2020-01-21 00:00:00,2020-01-21 23:59:00,2020-01-22 00:00:00,2020-01-22 22:00:00,,66,66,Male,Yes,,"U0054, U0055, U0056, U0074","Chinese National, arrived on 20th, had a soar throat on the flight, had fever on 21st. Admitted to hospital on Jan 22 and ID'd as suspect case by 10pm. Confirmed positive by 6pm on Jan 23", +QZ,HM,r0020,r0023,r0025,U0017,China,Hubei,Wuhan,China,HongKong,West Kowloon,,2020-01-21 13:40:00,2020-01-21 00:00:00,2020-01-21 19:54:00,2020-01-21 00:00:00,2020-01-21 19:54:00,2020-01-21 19:54:00,2020-01-21 19:54:00,,39,39,Male,Yes,,,"This man was originally from Wuhan, traveling from Wuhan to Shenzhen(G1015 train) and from ShenZheng to HongKong (G5607 train) with his four families (no symptoms at that time) who flew (flight 5J111) to Manlia, Philippines on 22nd, Jan. He was found to be suffering from a fever on his arrival at the rail terminus in West Kowloon and was confirmed on 21st and underwent another test that confirmed the infection on 22nd. He said he had fever and stuffy nose on 21st. No market history. SR is the time when he arrived at HongKong and ER is the departure time from ShenZhen).", +SL,HM,r0022,r0024,,U0018,China,Hubei,Wuhan,Thailand,Bangkok,Bangkok,,2020-01-19 23:59:00,,2020-01-19 23:59:00,,2020-01-19 23:59:00,2020-01-19 00:00:00,2020-01-19 23:59:00,,68,68,Male,Yes,,,"Wuhan man traveled to Thailand on Jan 19, detected with fever at Suvarnabhumi airport on arrival", +SL,HM,r0026,r0028,,U0019,China,Hubei,Wuhan,Korea,Seoul Capital Area,Incheon,,2020-01-18 23:59:00,2020-01-18 00:00:00,2020-01-18 23:59:00,2020-01-18 00:00:00,2020-01-18 23:59:00,2020-01-19 00:00:00,2020-01-19 23:59:00,4,35,35,Female,Yes,,,"Wuhan woman traveling to Korea Jan 19, detected at airport with fever; symptoms developed on Jan 18 in Wuhan where she was diagnosed with a cold", +QZ,HM,r0025,r0031,,U0021,China,Hubei,Wuhan,China,HongKong,,2020-01-10 00:00:00,2020-01-18 23:59:00,2020-01-18 00:00:00,2020-01-18 23:59:00,2020-01-18 00:00:00,2020-01-18 23:59:00,2020-01-21 00:00:00,2020-01-21 23:59:00,,56,56,Male,No,Yes,,"HongKong man went to Wuhan on January 10 and returned to HongKong on January 19 transtteed at Shenzhen (CA8279). He developed a fever on January 18 without any respiratory symptoms and went to hispital on January 19 but no hospitalization was required at that time. On January 21, he went back to hospital again and was confirmed. No market history and contact with any other suspected cases. ", +SL,HM,r0027,r0029,,U0020,China,,Wuhan,Korea,Seoul Capital Area,Seoul,,2020-01-10 23:59:00,2020-01-10 00:00:00,2020-01-10 23:59:00,2020-01-20 00:00:00,2020-01-22 23:59:00,2020-01-19 00:00:00,2020-01-19 23:59:00,4,55,55,Male,Yes,,,"Korean man who worked in Wuhan developed symptoms on Jan 10, went to a Chinese clinic on Jan 19 but was not diagnosed, arrived in Seoul and had a fever at the Gimpo International airport (western Seoul) Jan 22 and put under active monitoring, case confirmed positive Jan 24", +QZ,HM,r0030,r0033,,U0022,China,Hubei,Wuhan,China,HongKong,Hubei,,2020-01-19 12:07:00,2020-01-20 00:00:00,2020-01-20 23:59:00,2020-01-20 00:00:00,2020-01-20 23:59:00,2020-01-23 00:00:00,2020-01-23 23:59:00,"1,2",62,62,Female,Yes,,,"Wuhan women who lives in Wuhan, travelling from Wuhan to North Railway station in Shenzhen (G1013) , and then from Wuhan to HongKong (G6543) on Jan 19th. She developed a fever and cough on Jan 20th and was admitted to hospital on Jan 23. She had visited a wet market in Wuhan and a relative with cough in a hospital in Wuhan. No wild animal exposure history. ER is the departure time of G1013.", +SL,HM,r0032,,,U0023,China,Hubei,Wuhan,Japan,Kanto,Tokyo,,2020-01-14 23:59:00,2020-01-14 00:00:00,2020-01-14 23:59:00,2020-01-14 00:00:00,2020-01-14 23:59:00,2020-01-15 00:00:00,2020-01-15 23:59:00,4,40,49,Male,Yes,,,"Tourist from Wuhan had a fever on Jan 14, saw doctors in China on Jan 15 and 17, traveled to Japan, saw a doctor there on Jan 20 and 22 before finally being diagnosed", +QZ,HM,r0033,r0036,r0057,U0024,China,Hubei,Wuhan,China,HongKong,,,2020-01-22 14:20:00,2020-01-23 00:00:00,2020-01-23 23:59:00,2020-01-23 00:00:00,2020-01-23 23:59:00,2020-01-23 00:00:00,2020-01-23 23:59:00,,62,62,Female,Yes,,U0025,"Wuhan woman (and her husband, who is the 5th case in HongKong) visited her daughter in HonKong by taking High-speed rail from Wuhan to Hong Kong West Kowloon Station of the Guangzhou-Shenzhen-HongKong Express Rail Link on January 22. She developed fever on January 23. ER is the time when they left Wuhan. According to Government of HongKong, their daughter also developed fever and has been under observation in hospital. ", +QZ,HM,r0033,r0036,r0057,U0025,China,Hubei,Wuhan,China,HongKong,,,2020-01-22 14:20:00,2020-01-23 00:00:00,2020-01-23 23:59:00,2020-01-24 00:00:00,2020-01-24 23:59:00,2020-01-23 00:00:00,2020-01-23 23:59:00,,63,63,Male,Yes,,U0024,"Wuhan man (and his wife, who is the 4th case in HongKong) visited his daughter in HonKong by taking High-speed rail from Wuhan to Hong Kong West Kowloon Station of the Guangzhou-Shenzhen-HongKong Express Rail Link on January 22. He developed cough on Jan 22 and fever on January 23. ER is the time when they left Wuhan. ", +HM,SL,r0037,r0079,,U0026,China,Hubei,Wuhan,USA,California,Orange County,,,,,,,,2020-01-26 01:47:00,,50,59,Male,Yes,,,Man in 50s who traveled from Wuhan tested positive and is in isolation in Orange County. He presented to medical center with symptoms (date?) and CoV status was confirmed by Jan 24, +HM,QZ,r0038,,,U0027,China,Hubei,Wuhan,Taiwan,,,,2020-01-20 23:59:00,,2020-01-20 23:59:00,,2020-01-20 23:59:00,2020-01-21 00:00:00,2020-01-21 23:59:00,,50,59,Female,No,Yes,,over-50-year old female who resides in Southern Taiwan and works in Wuhan. She took a flight from Wuhan to Taiwon on Jan 20 and was transferred to a hospital by quarantine officer upon arrival. nCoV was confirmed Jan 21,"self-reported and observed symptoms included fever, cough, and shortness of breath" +HM,QZ,r0039,r0089,,U0028,China,Hubei,Wuhan,Taiwan,,,,2020-01-21 23:59:00,2020-01-23 00:00:00,2020-01-23 23:59:00,2020-01-23 00:00:00,2020-01-23 23:59:00,2020-01-23 00:00:00,2020-01-23 23:59:00,,50,59,Female,Yes,,,Chinese woman in her 50s came to Taiwan on Jan 21 in tour group from Wuhan., +HM,QZ,r0039,r0089,,U0029,China,Hubei,Wuhan,Taiwan,,,,2020-01-20 23:59:00,2020-01-20 00:00:00,2020-01-20 23:59:00,,,2020-01-23 00:00:00,2020-01-23 23:59:00,,50,59,Male,Yes,,,"Taiwanese man in his 50s is a businesess man based in Wuhan. He thought he had a cold, and sought medicine on Jan 23 after returning to Taiwan on Jan 21.", +HM,QZ,r0040,,,U0030,China,Hubei,Wuhan,China,Macau,,2020-01-10 00:00:00,2020-01-14 23:59:00,2020-01-10 00:00:00,2020-01-14 23:59:00,2020-01-21 18:00:00,2020-01-21 23:59:00,2020-01-21 18:00:00,2020-01-21 18:00:00,,52,52,Female,Yes,,,"First case reported in Macau. 52- year old Wuhan business woman confirmed nCoV on Wed, Jan 22. She traveled by highspeed rail from Wuhan to Zhuhai and arrived in Macau Sun Jan 19. She has a cough and sore throat a week before arriving in Macau",Did not have a fever at the time of arrival and passed through checks undetected +FJ,HM,r0041,r0042,,U0031,China,Hubei,Wuhan,Canada,Ontario,Toronto,,2020-01-22 23:59:00,2020-01-22 00:00:00,2020-01-23 23:59:00,2020-01-22 00:00:00,2020-01-23 23:59:00,2020-01-23 00:00:00,2020-01-23 23:59:00,,50,59,Male,No,Yes,,"Unidentified man who traveled to Wuhan, arrived in Toronto on Jan 22 and then developed symptoms/got admitted to hospital ""within in a day"" of return", +HM,QZ,r0043,r0091,,U0032,China,Hubei,Wuhan,China,Macau,San Antonio,,2020-01-23 09:00:00,,2020-01-23 23:59:00,,2020-01-23 23:59:00,,2020-01-23 23:59:00,,58,58,Female,Yes,,,58 year old female Wuhan resident. Arrived in Macau Thursday () via jetfoil (that went through Hong Kong). She immediately took a taxi to Hospital (Kiang Wu Hospital) for feeling dizzy,Had a low fever +HM,QZ,r0043,r0091,,U0033,China,Hubei,Wuhan,China,Macau,,,2020-01-22 00:00:00,2020-01-25 12:00:00,2020-01-25 18:00:00,2020-01-25 12:00:00,2020-01-25 23:59:00,2020-01-25 12:00:00,2020-01-25 23:59:00,,39,39,Female,Yes,,,39 year old female Wuhan resident. Arrived in Macau on Jan 22 via Flor de Lotus border. Started having a low fever on Sat (Jan 25) and was sent to hospital where infection was confirmed, +HM,QZ,r0043,,,U0034,China,Hubei,Wuhan,China,Macau,,,2020-01-23 12:00:00,2020-01-25 12:00:00,2020-01-25 18:00:00,,,2020-01-25 12:00:00,2020-01-25 18:00:00,,21,21,Female,Yes,,,21 year old female Wuhan resident. Arrived in Macau on ??? through the Lotus Flower Border. Infection confirmed morning of Jan 26, +KG,HM,r0044,r0051,,U0035,China,Hubei,Wuhan,China,Guangdong,Shenzen,2019-12-29 00:00:00,2020-01-03 23:59:00,2020-01-03 00:00:00,2020-01-03 23:59:00,2020-01-03 00:00:00,2020-01-03 23:59:00,2020-01-11 00:00:00,2020-01-11 23:59:00,,66,66,Male,No,Yes,,"first import into Shenzen, Guandong province. 66 years old. Went to visit relatives in Wuhan Dec 29, developed fever Jan 3, returned to Shenzhen Jan 4, sought treatment Jan 11", +SL,HM,r0034,r0035,,U0036,China,Hubei,Wuhan,Vietnam,Ho Chi Minh City,,,2020-01-13 23:59:00,2020-01-17 00:00:00,2020-01-17 23:59:00,2020-01-17 00:00:00,2020-01-17 23:59:00,2020-01-22 12:00:00,2020-01-22 23:59:00,,66,66,Male,Yes,,U0037,"Chinese man traveled from Wuhan to visit son (U0037) in Vietnam, arrived on Jan 13, symptoms on Jan 17, hospitalized Jan 22", +SL,HM,r0034,r0035,,U0037,Vietnam,Khanh Hoa,Nha Trang,Vietnam,Ho Chi Minh City,,2020-01-13 00:00:00,2020-01-17 23:59:00,2020-01-20 00:00:00,2020-01-20 23:59:00,2020-01-20 00:00:00,2020-01-20 23:59:00,2020-01-22 12:00:00,2020-01-22 23:59:00,2,28,28,Male,No,No,U0036,"Chinese man living in Vietman, visited his father (U0036), had a fever on Jan 20, checked into the hospital on Jan 22", +KG,HM,r0046,r0051,,U0038,China,Hubei,Wuhan,China,Shanghai,Shanghai,,2020-01-12 23:59:00,2020-01-15 00:00:00,2020-01-15 23:59:00,2020-01-15 00:00:00,2020-01-15 23:59:00,2020-01-15 00:00:00,2020-01-15 23:59:00,,56,56,Female,Yes,,,"first import into Shanghai city/province; Wuhan resident, traveled to Shanghai 2020-01-12, visited clinic with symptoms 2020-01-15", +KG,QZ,r0048,r0051,,U0039,China,Hubei,Wuhan,China,Zhejiang,Hangzhou,,2020-01-03 23:59:00,2020-01-04 00:00:00,2020-01-04 23:59:00,2020-01-04 00:00:00,2020-01-04 23:59:00,2020-01-04 00:00:00,2020-01-04 23:59:00,,46,46,Male,Yes,,,"first import to Zhejiang, drove from Wuhan to Hangzhou Jan 3, presented to hospital Jan 4. Isolation treatment performed at hospital on Jan 17", +KG,QZ,r0049,r0051,,U0040,China,Hubei,Wuhan,China,Chongqing,Chongqing,,2020-01-15 23:59:00,2020-01-15 00:00:00,2020-01-15 23:59:00,2020-01-15 00:00:00,2020-01-15 23:59:00,2020-01-15 00:00:00,2020-01-15 23:59:00,,44,44,Female,Yes,,,first import to Chongqing city/province; found with fever/fatigue symptoms on same day as travel back from Wuhan, +KG,QZ,r0050,r0051,,U0041,China,Hubei,Wuhan,China,Sichuan,Chengdu,,2020-01-11 00:00:00,2020-01-11 00:00:00,2020-01-11 23:59:00,2020-01-11 00:00:00,2020-01-11 23:59:00,2020-01-11 00:00:00,2020-01-11 23:59:00,,34,34,Male,Yes,,,"first import to Sichuan; employee in Wuhan, presented Jan 11 with fever to hospital in Chengdu", +KG,QZ,r0052,r0051,,U0042,China,Hubei,Wuhan,China,Shandong,Rizhao,,2020-01-17 23:59:00,,2020-01-17 23:59:00,,2020-01-17 23:59:00,,2020-01-17 23:59:00,,37,37,Male,Yes,,,"First confirmed imported nCov pneumonia patient in Shandong: male, 37, visited clinic on 01/17/2020, travelled to Wuhan within two weeks of symptom onset.", +KG,QZ,r0053,r0051,,U0043,China,Hubei,Wuhan,China,Yunnan,Kunming,,2020-01-15 23:59:00,2020-01-16 00:00:00,2020-01-16 23:59:00,2020-01-16 00:00:00,2020-01-16 23:59:00,2020-01-16 00:00:00,2020-01-16 23:59:00,,51,51,Male,Yes,,,"First confirmed imported nCov pneumonia patient in Yunnan: male, 51, Wuhan resident, visited Yunan on 01/15/2020, symptom onset on 01/16/2020 and hospitalized.", +HM,QB,r0045,,,U0044,China,Hubei,Wuhan,China,Macau,Se,,2020-01-22 16:00:00,,2020-01-22 16:00:00,,2020-01-22 16:00:00,2020-01-22 16:00:00,2020-01-22 16:00:00,,66,66,Male,Yes,,,"Second case imported into Macau - 66 year old man. Arrived 4pm Wed (Jan 22), fever detected at border screening and sent to Conde S. Januario Hospital after being tested positive", +KG,QZ,r0054,r0051,,U0045,China,Hubei,Wuhan,China,Jiangxi,Dongxiang,2019-12-20 00:00:00,2020-01-09 23:59:00,2020-01-10 00:00:00,2020-01-10 23:59:00,2020-01-10 00:00:00,2020-01-10 23:59:00,2020-01-10 00:00:00,2020-01-10 23:59:00,,56,56,Male,No,Yes,,"new confirmed imported nCov pneumonia patient in Jiangxi: male, 56, visited Wuhan on 12/20/2019, return to Jiangxi on 01/09/2020, symptoms onset on 01/10/2020.", +KG,QZ,r0054,r0051,,U0046,China,Hubei,Wuhan,China,Jiangxi,Pingxiang,,2020-01-02 23:59:00,,2020-01-10 23:59:00,,2020-01-10 23:59:00,2020-01-10 00:00:00,2020-01-10 23:59:00,,50,50,Male,No,Yes,,"new confirmed imported nCov pneumonia patient in Jiangxi: male, 50, visited Wuhan for poultry trading, return to Jiangxi on 01/02/2020, symptoms onset on 01/10/2020.", +KG,QZ,r0076,r0051,,U0047,China,Hubei,Wuhan,China,Liaoning,Dalian,,2020-01-11 23:59:00,2020-01-11 00:00:00,2020-01-11 23:59:00,2020-01-11 00:00:00,2020-01-11 23:59:00,2020-01-17 00:00:00,2020-01-17 23:59:00,,33,33,Male,No,Yes,,"First confirmed imported nCov pneumonia patient in Liaoning: male, 33, works in Wuhan, symptom onset on 01/11/2020, visit clinic in Liaoning Dalian on 01/17/2020.", +KG,QZ,r0056,r0051,,U0048,China,Hubei,Wuhan,China,Fujian,Lianjiang,,2020-01-17 23:59:00,,2020-01-20 23:59:00,,,2020-01-20 00:00:00,2020-01-20 23:59:00,,70,70,Male,No,Yes,,"First confirmed imported nCov pneumonia patient in Fujian: male, 70, works in Wuhan, return to Fujian on 01/17/2020, visit clinic on 01/20/2020.", +HM,SL,r0058,,,U0049,China,Hubei,Wuhan,Korea,,,,2020-01-20 23:59:00,2020-01-22 00:00:00,2020-01-22 23:59:00,2020-01-22 00:00:00,2020-01-22 23:59:00,2020-01-25 00:00:00,2020-01-25 23:59:00,,54,54,Male,Yes,,,"3rd confirmed imported nCov patient in South Korea. Male 54, South Korean resident of Wuhan who returned to South Korea on Jan 20, had fever and symptoms on Jan 22, and checked into hospital on Jan 25", +QZ,QB,r0059,,,U0050,China,Hubei,Wuhan,China,HongKong,,2020-01-16 00:00:00,2020-01-20 23:59:00,2020-01-20 00:00:00,2020-01-20 23:59:00,2020-01-20 18:00:00,2020-01-20 23:59:00,,2020-01-16 00:00:00,1,47,47,Male,No,Yes,,"HongKong man worked in Wuhan for about a week in the middle of January, as an accountant at a market (not the smae market believed to be the source of the outbreak). He arrived at HongKong on Thursday (2020-01-23) and developed a fever on Jan 20th while in Wuhan. Unsure about the time he presented at the hospital (use the time of his arrival in HongKong as PL and the time when the news was released as PR). No detailed information about when he worked in Wuhan and we only know it;s about one week, so assuming the ER as the time he arrives in HongKong and EL as one week before that time. ", +HM,SL,r0060,,,U0051,China,Hubei,Wuhan,Thailand,,,,,,,,,,2020-01-26 07:39:00,,,,,Yes,,,Wuhan resident visiting Thailand. Case confirmed on Jan 26, +HM,SL,r0060,,,U0052,China,Hubei,Wuhan,Thailand,,,,,,,,,,2020-01-26 07:39:00,,,,,Yes,,,Wuhan resident visiting Thailand. Case confirmed on Jan 26, +HM,SL,r0060,,,U0053,China,Hubei,Wuhan,Thailand,,,,,,,,,,2020-01-26 07:39:00,,,,,Yes,,,Wuhan resident visiting Thailand. Case confirmed on Jan 26, +QZ,SL,r0061,r0062,r0019,U0054,China,GuangDong,GuangZhou,Malaysia,Kuala Lumpur,,2020-01-20 00:00:00,2020-01-22 22:00:00,2020-01-23 00:00:00,2020-01-25 11:57:00,,,2020-01-23 00:00:00,2020-01-25 11:57:00,2,65,65,Female,Yes,,"U0016, U0055, U0056, U0074","They flew from GuangZhou to Singapore on Jan 20 with one of the confirmed cases in Singapore (66 yearsold Wuhan man, U0016) and entered Malaysia on Jan 22. All of the three cases developed light symptoms such as a dry cough. Not sure when they developed the symptoms after they arrived in Malaysia, using the time when they arrive in Malaysia as SL and the earliest time when news was released (which mentioned the light symptoms) as SR. ER was estimated using the PR of U0016 (assuming the time they spent with U0016 was the exposure time) ", +QZ,SL,r0061,r0062,r0019,U0055,China,GuangDong,GuangZhou,Malaysia,Kuala Lumpur,,2020-01-20 00:00:00,2020-01-22 22:00:00,2020-01-23 00:00:00,2020-01-25 11:57:00,,,2020-01-23 00:00:00,2020-01-25 11:57:00,2,11,11,Male,Yes,,"U0016,U0054, U0056, U0074","They flew from GuangZhou to Singapore on Jan 20 with one of the confirmed cases in Singapore (66 yearsold Wuhan man) and entered Malaysia on Jan 22. All of the three cases developed light symptoms such as a dry cough. Not sure when they developed the symptoms after they arrived in Malaysia, using the time when they arrive in Malaysia as SL and the earliest time when news was released (which mentioned the light symptoms) as SR. ER was estimated using the PR of U0016 (assuming the time they spent with U0016 was the exposure time)", +QZ,SL,r0061,r0062,r0019,U0056,China,GuangDong,GuangZhou,Malaysia,Kuala Lumpur,,2020-01-20 00:00:00,2020-01-22 22:00:00,2020-01-23 00:00:00,2020-01-25 11:57:00,,,2020-01-23 00:00:00,2020-01-25 11:57:00,2,2,3,Male,Yes,,"U0016, U0054, U0055, U0074","They flew from GuangZhou to Singapore on Jan 20 with one of the confirmed cases in Singapore (66 yearsold Wuhan man) and entered Malaysia on Jan 22. All of the three cases developed light symptoms such as a dry cough. Not sure when they developed the symptoms after they arrived in Malaysia, using the time when they arrive in Malaysia as SL and the earliest time when news was released (which mentioned the light symptoms) as SR. ER was estimated using the PR of U0016 (assuming the time they spent with U0016 was the exposure time)", +KG,QZ,r0063,r0051,,U0057,China,Hubei,Wuhan,China,Beijing,Beijing,2020-01-03 00:00:00,2020-01-04 23:59:00,2020-01-09 00:00:00,2020-01-09 23:59:00,2020-01-09 00:00:00,2020-01-09 23:59:00,2020-01-14 00:00:00,2020-01-14 23:59:00,,39,39,Male,No,Yes,,"new confirmed imported nCov pneumonia patient in Beijing: male, 39, visited Wuhan on 01/03/2020, return to Beijing on 01/04/2020, symptoms onset on 01/09/2020, hospitalized on 01/14/2020.", +KG,QZ,r0063,r0051,,U0058,China,Hubei,Wuhan,China,Beijing,Beijing,2020-01-08 00:00:00,2020-01-16 23:59:00,2020-01-16 00:00:00,2020-01-16 23:59:00,2020-01-16 00:00:00,2020-01-16 23:59:59,2020-01-20 00:00:00,2020-01-20 23:59:00,,56,56,Male,No,Yes,,"new confirmed imported nCov pneumonia patient in Beijing: male, 56, visited Wuhan on 01/08/2020, return to Beijing on 01/16/2020, symptoms onset on 01/16/2020, hospitalized on 01/20/2020.", +QZ,QB,r0063,,,U0092,China,Hubei,Wuhan,China,Beijing,Beijing,2020-01-10 00:00:00,2020-01-11 23:59:00,2020-01-14 00:00:00,2020-01-14 23:59:00,2020-01-14 00:00:00,2020-01-14 23:59:00,2020-01-20 00:00:00,2020-01-20 23:59:00,,37,37,Male,No,Yes,,"new confirmed imported nCov pneumonia patient in Beijing: male, 37 visited Wuhan on Jan 10, retured to Beijing on Jan 11", +QZ,QB,r0063,,,U0093,China,Hubei,Wuhan,China,Beijing,Beijing,2020-01-12 00:00:00,2020-01-17 23:59:00,2020-01-19 00:00:00,2020-01-19 23:59:00,2020-01-19 00:00:00,2020-01-19 23:59:00,2020-01-20 00:00:00,2020-01-20 23:59:00,,18,18,Female,No,Yes,,"new confirmed imported nCov pneumonia patient in Beijing: female, 18 visited Wuhan on Jan 12, retured to Beijing on Jan 17", +QZ,QB,r0063,,,U0094,China,Hubei,Wuhan,China,Beijing,Beijing,2020-01-13 00:00:00,2020-01-17 23:59:00,2020-01-13 00:00:00,2020-01-17 23:59:00,,,2020-01-20 00:00:00,2020-01-20 23:59:00,,32,32,Female,No,Yes,,"new confirmed imported nCov pneumonia patient in Beijing: female, 32 visited Wuhan on Jan 13, retured to Beijing on Jan 17", +KG,QZ,r0064,r0051,,U0059,China,Hubei,Wuhan,China,Guizhou,Guiyang,,2020-01-14 23:59:00,2020-01-14 00:00:00,2020-01-14 23:59:00,2020-01-14 00:00:00,2020-01-14 23:59:00,2020-01-14 00:00:00,2020-01-14 23:59:00,,51,51,Male,No,Yes,,"First confirmed imported nCov pneumonia patient in Guizhou: male, 51, lived in Wuhan ""week before onset"", symptom onset on 01/14/2020, visit clinic on 01/14/2020.", +KG,QZ,r0065,r0051,,U0060,China,Hubei,Wuhan,China,Shanxi,Taiyuan,2020-01-12 00:00:00,2020-01-15 23:59:00,2020-01-19 00:00:00,2020-01-19 23:59:00,2020-01-19 00:00:00,2020-01-19 23:59:00,2020-01-20 00:00:00,2020-01-20 23:59:00,,,,Male,No,Yes,,"First confirmed imported nCov pneumonia patient in Shanxi: male, visited Wuhan from 01/12/2020 to 01/15/2020, symptom onset on 01/19/2020, visit clinic on 01/20/2020, 6 contacts traced.", +KG,QZ,r0066,r0051,,U0061,China,Hubei,Wuhan,China,Ningxia,Yinchuan,,2020-01-19 23:59:00,,,,,2020-01-19 00:00:00,2020-01-19 23:59:00,,29,29,Male,No,Yes,,"First confirmed imported nCov pneumonia patient in Ningxia: male, 29, works in Wuhan. Ningxia and visit clinic on 01/19/2020.", +KG,QZ,r0067,r0051,,U0062,China,Hubei,Wuhan,China,Guangxi,Beihai,,2020-01-12 23:59:00,2020-01-16 12:00:00,2020-01-16 18:00:00,,,2020-01-17 00:00:00,2020-01-17 23:59:00,,66,66,Female,Yes,,,"First confirmed imported nCov pneumonia patient in Guangxi: female, 66, lives in Wuhan. arrived in Beihai, Guangxi on 01/16/2020, and visited clinic on 01/17/2020 due to symptoms.", +KG,QZ,r0068,r0051,,U0063,China,Hubei,Wuhan,China,Hebei,Shijiazhuang,,2020-01-18 23:59:00,,2020-01-19 23:59:00,,2020-01-19 23:59:00,2020-01-19 00:00:00,2020-01-19 23:59:00,,72,72,Male,Yes,,,"First confirmed imported nCov pneumonia patient in Hebei: male, 72, Wuhan resident. visited relative in Shijiazhuang, Hebei on 01/18/2020, symptom onset on 01/19/2020 and hospitalized, 6 contacts traced.", +KG,QZ,r0069,r0051,,U0064,China,Hubei,Wuhan,China,Jiangsu,Suzhou,,2020-01-10 23:59:00,,2020-01-10 23:59:00,,2020-01-10 23:59:00,2020-01-10 00:00:00,2020-01-10 23:59:00,,37,37,Male,No,Yes,,"First confirmed imported nCov pneumonia patient in Jiangsu: male,37, returned to Jiangsu from Wuhan on 01/10/2020.", +KG,QZ,r0071,r0051,,U0065,China,Hubei,Wuhan,China,Heilongjiang,Mudanjiang,,2020-01-12 23:59:00,,2020-01-12 23:59:00,,2020-01-12 23:59:00,2020-01-12 00:00:00,2020-01-12 23:59:00,,69,69,Male,No,Yes,,"First confirmed imported nCov pneumonia patient in Heilongjiang: male, 69, returned to Mudanjiang, Heilongjiang from Wuhan on 01/12/2020, symptom onset after return and has been hospitalized", +KG,QZ,r0072,r0051,,U0066,China,Hubei,Wuhan,China,Jilin,Changchun,,2020-01-19 23:59:00,,2020-01-19 23:59:00,,2020-01-19 23:59:00,2020-01-19 23:59:00,2020-01-19 23:59:00,,42,42,Female,No,Yes,,"First confirmed imported nCov pneumonia patient in Jilin: female, 36, return to Changchun, Jilin from Wuhan on 01/19/2020 and visit clinic due to symptom onset.", +KG,QB,r0073,r0051,,U0067,China,Hubei,Wuhan,China,Gansu,Lanzhou,2020-01-11 00:00:00,2020-01-17 23:59:00,2020-01-18 00:00:00,2020-01-18 23:59:00,2020-01-18 00:00:00,2020-01-18 23:59:00,2020-01-21 00:00:00,2020-01-21 23:59:00,,43,43,Male,No,No,,"First confirmed nCov pneumonia patient in Gansu: male, 43, lives in Lanzhou, Gansu, visited Hunan, Jiangxi since 01/11/2020, met with individual from Wuhan during the visit, return to Lanzhou Gansu on 01/17/2020, symptom onset on 01/18/2020, visit clinic on 01/21/2020, tested positive on 01/23/2020.", +KG,QZ,r0074,r0051,,U0069,China,Hubei,Wuhan,China,Inner Mongolia,Manzhouli,,2020-01-21 23:59:00,,2020-01-21 23:59:00,,,2020-01-21 00:00:00,2020-01-21 23:59:00,,30,30,Male,Yes,,,"First confirmed imported nCov pneumonia patient in Inner Mongolia: male, 30, Wuhan resident, arrived in Inner Mongolia from Wuhan on 01/21/2020, hospitalized on 01/21/2020.", +QZ,SL,r0061,r0075,,U0068,China,Hubei,Wuhan,Malaysia,Johor,,,2020-01-22 23:59:00,2020-01-23 00:00:00,2020-01-23 23:59:00,2020-01-23 00:00:00,2020-01-23 23:59:00,2020-01-23 00:00:00,2020-01-23 23:59:00,,40,40,Male,Yes,,,"4th confirmed patient in Malaysia who traveled by bus in Singapore on Wed (Jan 22th) and developed fever next day. On the same day (Jan 23), he sought care. ", +QZ,QB,r0076,r0051,,U0070,China,Hubei,Xiantao,China,Liaoning,Fushun,,2020-01-13 23:59:00,2020-01-14 00:00:00,2020-01-14 23:59:00,2020-01-19 00:00:00,2020-01-19 23:59:00,2020-01-19 00:00:00,2020-01-19 23:59:00,,40,40,Male,No,Yes,,"2nd confirmed patient in Liaoning Province who worked in Xiaotao, Hubei province and flew back to Liaoning province on Jan 13th, during which he transitted at Wuhan for two hours. On Jan 14th, he felt body ache and developed fever+cough on Jan 19th, so he wen to fever clinic and got confirmed. ", +QZ,QB,r0077,,,U0071,China,Hubei,Wuhan,China,HongKong,,,2020-01-24 23:59:00,2020-01-25 00:00:00,2020-01-25 23:59:00,2020-01-25 00:00:00,2020-01-25 23:59:00,2020-01-24 00:00:00,2020-01-24 23:59:00,,64,64,Male,Yes,,U0022,8th confirmed patient in HongKong. He is from Wuhan and traveled with his wife on Jan 19 who is the 3rd confirmed case in HongKong from Wuhan to Shenzhen to HongKong. No age or other information were released now. , +QZ,QB,r0077,r0104,,U0072,China ,Hubei,Wuhan,China,HongKong,Fanling,2020-01-09 00:00:00,2020-01-18 23:59:00,,2020-01-25 23:59:00,,2020-01-25 23:59:00,2020-01-25 00:00:00,2020-01-25 23:59:00,3,68,68,Female,No,Yes,,7th confirmed patient in HongKong who had a close contact with a confirmed case at a hospital in Wuhan. She was stopped and developed a fever with cough and sore throat at the border of Lo Wu. No detailed information about her date of symptom onset and age., +QZ,SL,r0078,r0094,,U0073,China,Hubei,Wuhan,Singapore,Singapore,Singapore,,2020-01-21 00:40:00,2020-01-21 12:00:00,2020-01-21 18:59:00,2020-01-21 12:00:00,2020-01-21 18:59:00,2020-01-22 21:00:00,2020-01-22 21:00:00,,53,53,Female,Yes,,,"2nd confirmed patient in Singapore who traveled from Wuhan to Singapore on Jan 21 and developed fever, cough and chills in the afternoon of her arrival on Jan 21, went to hospital on Jan 22 21:00. Flight TR121 left at 00:40 and landed at 05:30", +QZ,SL,r0078,r0019,r0094,U0074,China,Hubei,Wuhan,Singapore,Singapore,Singapore,,2020-01-20 23:59:00,,2020-01-23 18:30:00,,,2020-01-22 00:00:00,2020-01-23 18:30:00,2,37,37,Male,Yes,,"U0016, U0054, U0055, U0056",3rd confirmed patient in Singapore who is also the son of the first Singapore confirmed patient (U0016). He was treated as a suspect case and was tested as positive on Jan 24. Singapore MOH reports he was symptomatic on Jan 23 at 18:30, +QZ,SL,r0081,r0092,,U0075,China,Hubei,Wuhan,Singapore,Singapore,Singapore,,2020-01-22 23:59:00,2020-01-23 00:00:00,2020-01-23 23:59:00,,,2020-01-24 00:00:00,2020-01-24 23:59:00,,36,36,Male,Yes,,,"Wuhan man flew to Singapore (4th confirmed patient in Singapore), developed a cough on Jan 23, checked into the hospital on Jan 24, and confirmed on Jan 25", +HM,SL,r0080,r0112,,U0076,China,Hubei,Wuhan,USA,California,LA,,,,,,,2020-01-22 00:00:00,2020-01-22 23:59:00,,,,Male,Yes,,,4th confirmed case of CoV imported into USA. Wuhan resident who was flying through LAX on Jan 22 on his way back to China. Presented themselves for care at LAX airport when noticed he wasn't feeling well, +HM,SL,r0080,,,U0077,China,Hubei,Wuhan,USA,Arizona,Maricopa County,,,,,,,,2020-01-26 11:07:00,,,,,No,Yes,,5th confirmed case of CoV imprted into USA. Waiting for more details. Statements put out at Jan 26 11:07AM., +QZ,QB,r0082,r0083,,U0078,China,Hubei,Wuhan,Taiwan,,,2020-01-13 00:00:00,2020-01-22 23:59:00,2020-01-22 00:00:00,2020-01-22 23:59:00,,,2020-01-25 00:00:00,2020-01-26 23::59:00,4,50,59,Female,No,Yes,,"4th confirmed case in Taiwan. She was in Wuhan between Jan 13-15 and traveled to Europe since Jan 16. She started to cough on Jan 22 and became worse on Jan 25. On the same day (Jan 25), she flied back to Taiwan and reported to local government. She was confirmed on Jan 26.. ", +QZ,QB,r0084,r0085,,U0079,China,Hubei,Wuhan,Japan,,,,2020-01-18 23:59:00,2020-01-21 18:00:00,2020-01-21 23:59:00,2020-01-21 18:00:00,2020-01-21 23:59:00,2020-01-23 00:00:00,2020-01-23 23:59:00,,30,39,Female,Yes,,,3rd confirmed patient in Japan who lives in Wuhan and arrived at Japan with three of her families on Jan 18. She didn't have any symptoms upon her arrival and developed a fever+cough on Jan 21 night. She was not hospitalized, +QZ,SL,r0086,,,U0080,China,Hubei,Wuhan,Japan,,,,2020-01-22 23:59:00,2020-01-23 00:00:00,2020-01-23 23:59:00,2020-01-23 00:00:00,2020-01-23 23:59:00,2020-01-24 00:00:00,2020-01-24 23:59:00,,40,49,Male,Yes,,,4th confirmed patient in Japan who is from Wuhan. He didn't have symptoms upon his arrival in Japan on Jan 22 and developed a fever Jan 23. He went to hospital Jan 24 for pain in the joints and was hospitalized. , +QZ,QB,r0087,,,U0081,China,Hubei,Wuhan,China,Guangxi,Hechi,,2020-01-15 00:00:00,2020-01-21 00:00:00,2020-01-21 15:00:00,,,2020-01-21 15:00:00,2020-01-21 15:00:00,,49,49,Female,Yes,,,"2nd confirmed patient in Hechi, Guangxi and she has been living in Wuhan for 20 years", +QZ,QB,r0087,,,U0082,China,Hubei,Wuhan,China,Guangxi,Hechi,,2020-01-21 00:00:00,2020-01-22 15:30:00,2020-01-22 16:30:00,2020-01-22 15:30:00,2020-01-22 16:30:00,2020-01-23 01:00:00,2020-01-23 01:00:00,,2,2,Female,Yes,,,"3rd confirmed patient in Hechi, Guangxi and she lives in Wuhan before this.", +SL,HM,r0088,r0090,,U0083,China,Hubei,Wuhan,Korea,,,,2020-01-20 23:59:00,2020-01-21 00:00:00,2020-01-21 23:59:00,2020-01-25 00:00:00,2020-01-25 23:59:00,2020-01-21 00:00:00,2020-01-21 23:59:00,,55,55,Male,No,Yes,,"55 year old Korean man who visited Wuhan and returned on Jan 20 with no symptoms, developed cold-like symptoms on Jan 21 and received treatment, then developed a fever on Jan 25 and was isolated", +FJ,SL,r0093,r0097,,U0084,Germany,Bavaria,Starnberg,Germany,Bavaria,Starnberg,2020-01-21 00:00:00,2020-01-21 23:59:00,2020-01-25 00:00:00,2020-01-26 23:59:00,,,2020-01-27 00:00:00,2020-01-27 23:59:00,3,33,33,Male,No,No,,"33 year old German man, had contact with a colleague visiting from Shanghai ""last week"" (article published on January 28). The colleague left germany to fly back to china on the 23rd. Man began to have symptoms ""over the weekend"" (25&26). Was tested positive on Monday the 27th. MOH report says exposed at event on Jan 21.", +SL,HM,r0095,,,U0085,China,Hubei,Wuhan,Singapore,Singapore,Singapore,,2020-01-18 23:59:00,2020-01-24 00:00:00,2020-01-24 23:59:00,,,2020-01-26 00:00:00,2020-01-26 23:59:00,,56,56,Female,Yes,,,"5th case confirmed in Singapore: Wuhan woman arrived in Singapore Jan 18 asymptomatic, symptoms on Jan 24, ambulance required to take her to hospital on Jan 26, coronavirus confirmed Jan 27", +SL,HM,r0096,,,U0086,China,Hubei,Wuhan,Singapore,Singapore,Singapore,,2020-01-19 23:59:00,2020-01-25 00:00:00,2020-01-25 23:59:00,,,2020-01-26 00:00:00,2020-01-26 23:59:00,,56,56,Male,Yes,,,"6th case confirmed in Singapore: Wuhan man arrived in Singapore Jan 19 asymptomatic, symptoms on Jan 25, and presented to hospital on Jan 26, nCoV confirmed on Jan 27", +SL,HM,r0096,,,U0087,China,Hubei,Wuhan,Singapore,Singapore,Singapore,,2020-01-23 23:59:00,2020-01-24 00:00:00,2020-01-24 23:59:00,,,2020-01-24 00:00:00,2020-01-24 23:59:00,,35,35,Male,Yes,,,"7th case confirmed in Singapore: Wuhan man arrived in Singapore Jan 23 asymptomatic, symptoms on Jan 24, hospitalized Jan 24, nCoV confirmed Jan 27", +SL,KG,r0098,,,U0088,Japan,Kanto,Tokyo,Japan,Nara,,2020-01-08 00:00:00,2020-01-14 23:59:00,2020-01-14 00:00:00,2020-01-14 23:59:00,,,2020-01-17 00:00:00,2020-01-17 23:59:00,3,60,69,Male,No,No,,"Japanese bus driver drove Wuhan tourists roundtrip Osaka-Tokyo with a stop in Nara from Jan 8-16, developed symptoms on Jan 14, went to medical facility in Nara on Jan 17, returned to hospital on Jan 25", +KG,HM,r0099,,,U0089,China,Hubei,,Sri Lanka,Colombo,Colombo,,2020-01-19 23:59:00,2020-01-25 00:00:00,2020-01-25 23:59:00,2020-01-25 00:00:00,2020-01-25 23:59:00,2020-01-25 00:00:00,2020-01-25 23:59:00,,40,49,Female,Hubei,,,"first case in Sri Lanka; Chinese tourist from Hubei province arrived Jan 19, presented with fever to hospital in Colombo Jan 25", +KG,HM,r0100,r0101,,U0090,China,Hubei,Wuhan,Cambodia,Sihanoukville,Sihanoukville,,2020-01-23 03:57:00,2020-01-25 00:00:00,2020-01-25 23:59:00,2020-01-25 00:00:00,2020-01-25 23:59:00,2020-01-26 00:00:00,2020-01-26 23:59:00,,60,60,Male,Yes,,,"Chinese national; male 60 YO traveling with family; first case in Cambodia; left Wuhan on flight LQ809 23 Jan, reported symptoms 25 Jan", +HM,SL,r0080,r0114,,U0091,China,Hubei,,France,Paris,,,,,,,,,2020-01-28 19:14:00,,80,80,Male,Hubei,,,Elderly Chinese tourist visiting Paris from Hubei. 4th case in France, +QZ,HM,r0105,r0106,,U0095,China,Hubei,Wuhan,Taiwan,,,2019-10-20 00:00:00,2020-01-20 23:59:00,2020-01-25 00:00:00,2020-01-25 23:59:00,2020-01-25 00:00:00,2020-01-25 23:59:00,2020-01-25 00:00:00,2020-01-25 23:59:00,,50,59,Female,No,Yes,U0098,"5th confirmed patient in Taiwan. She worked in Wuhan in late october. She took the same flight as the first confirmed patient in Taiwan on Jan 20, but there sat 20 rows apart. SHe's more likely to get infected when she was in Wuhan. She traveled to Europe between staying in Wuhan and returning to Taiwan", +QZ,HM,r0107,,,U0096,China,Hubei,Wuhan,Taiwan,,,,2020-01-22 23:59:00,2020-01-25 00:00:00,2020-01-25 23:59:00,2020-01-25 00:00:00,2020-01-25 23:59:00,2020-01-25 00:00:00,2020-01-25 23:59:00,,70,79,Female,Yes,,U0097,6th confirmed patient in Taiwan who is from Wuhan., +QZ,HM,r0107,,,U0097,China,Hubei,Wuhan,Taiwan,,,,2020-01-22 23:59:00,2020-01-25 00:00:00,2020-01-25 23:59:00,2020-01-25 00:00:00,2020-01-25 23:59:00,2020-01-25 00:00:00,2020-01-25 23:59:00,,70,79,Female,Yes,,U0096,7th confirmed patient in Taiwan who is from Wuhan., +QZ,HM,r0108,r0109,,U0098,Taiwan,,,Taiwan,,,2020-01-20 00:00:00,2020-01-25 23:59:00,2020-01-26 00:00:00,2020-01-26 23:59:00,,,2020-01-26 00:00:00,2020-01-26 23:59:00,,50,59,Male,No,No,U0095,8th confirmed patient in Taiwan and 1st domestic patient in Taiwan who is the husband of U0095. He developed cough (not fever) on Jan 26., +QZ,QB,r0110,,,U0099,China,Hubei,Wuhan,Singapore,,,,2020-01-18 23:59:00,2020-01-24 00:00:00,2020-01-24 23:59:00,,,2020-01-26 00:00:00,2020-01-26 23:59:00,,56,56,Female,Yes,,,5th confirmed patient in Singapore. She is from Wuhan and was asymptomatic during the flight to Singapore. She developed symptoms on Friday and was sent to hospital on Sunday., +QZ,QB,r0111,,,U0100,China,Hubei,Wuhan,Singapore,,,,2020-01-19 23:59:00,2020-01-25 00:00:00,2020-01-25 23:59:00,,,2020-01-26 00:00:00,2020-01-26 23:59:00,,56,56,Male,Yes,,,6rh confiemd patient in Singapore. He arrived at Singapore on Jan 19 and developed a cough on Jan 25., +QZ,QB,r0111,,,U0101,China,Hubei,Wuhan,Singapore,,,,2020-01-23 23:59:00,2020-01-24 00:00:00,2020-01-24 23:59:00,,,2020-01-24 00:00:00,2020-01-24 23:59:00,,35,35,Male,Yes,,,7th confirmed patient in Singapore. He arrived at Singapore on Jan 23 and developed symptoms on Jan 24., \ No newline at end of file diff --git a/manuscript/nCoV_Incubation.Rmd b/manuscript/nCoV_Incubation.Rmd index 551d819..aa65072 100644 --- a/manuscript/nCoV_Incubation.Rmd +++ b/manuscript/nCoV_Incubation.Rmd @@ -1,6 +1,6 @@ --- title: "Estimating incubation period of novel coronavirus 2019 in Wuhan, China" -output: md_document +output: pdf_document editor_options: chunk_output_type: console --- @@ -28,14 +28,15 @@ library(tidyverse) library(lubridate) library(coarseDataTools) library(gridExtra) -# devtools::install_github("reichlab/activemonitr") +library(ggpubr) +# devtools::install_github("salauer/activemonitr") library(activeMonitr) cbbPalette <- c("#000000", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7") set.seed(1) ## read in coronavirus data -ncov_raw <- read_csv("data/nCoV-IDD-traveler-data.csv") %>% +ncov_raw <- read_csv("data/nCoV-IDD-traveler-data-manuscript.csv") %>% rename(EL_date=EL, ER_date=ER, SL_date=SL, SR_date=SR) ## change dates to restrict exposure to after 1 December 2019 @@ -419,13 +420,13 @@ all_est_plot <- ncov_inc_fit_boot@ests[-2, -4] %>% # rename(est_foreign=est, CIlow_foreign=CIlow, # CIhigh_foreign=CIhigh) %>% mutate(qtile=c("mean", 2.5, 5, 25, 50, 75, 95, 97.5), - type="weibull")) %>% + type="Weibull")) %>% bind_rows(ncov_erl_fit@ests[-2, -4] %>% as.data.frame() %>% # rename(est_year=est, CIlow_year=CIlow, # CIhigh_year=CIhigh) %>% mutate(qtile=c("mean", 2.5, 5, 25, 50, 75, 95, 97.5), - type="erlang")) %>% + type="Erlang")) %>% mutate(est=ifelse(qtile=="mean", exp(est), est), CIlow=ifelse(qtile=="mean", exp(CIlow), CIlow), CIhigh=ifelse(qtile=="mean", exp(CIhigh), CIhigh), @@ -475,8 +476,8 @@ Since the winter often brings cold air and other pathogens that can cause sore t Since a plurality of our cases came from mainland China, where assumptions about local transmission may be less firm, we ran an analysis without those cases. Finally, we challenge our assumption that unknown ELs can be assumed to be 2019 December 1 ([Nextstrain estimates that it could have happened as early as September](https://nextstrain.org/ncov?dmax=2019-12-04&m=num_date)), by setting unknown ELs to 2018 December 1. -```{r all-sens-plot, warning=F, message=F} -all_sens_plot <- ncov_inc_fit_boot@ests[-2, -4] %>% +```{r all-sens-plot, warning=F, message=F, eval=F} +all_sens_dat <- ncov_inc_fit_boot@ests[-2, -4] %>% as.data.frame() %>% mutate(qtile=c("mean", 2.5, 5, 25, 50, 75, 95, 97.5), type="all") %>% @@ -508,7 +509,7 @@ all_sens_plot <- ncov_inc_fit_boot@ests[-2, -4] %>% # select(-CIhigh, -CIlow) %>% # spread(qtile, est, sep="_") -all_sens_plot <- ggplot(data=all_sens_plot, +all_sens_plot <- ggplot(data=all_sens_dat, aes(y=est, ymin=CIlow, ymax=CIhigh, x=as.factor(qtile), color=type)) + geom_errorbar(height=0.2, position=position_dodge(0.9)) + geom_point(position=position_dodge(0.9)) + @@ -516,7 +517,6 @@ all_sens_plot <- ggplot(data=all_sens_plot, scale_x_discrete("Estimate quantile") + scale_color_manual("Est\ntype", values=cbbPalette[c(1,6,4,7)]) + - ggtitle("A") + theme_bw() + coord_flip() + theme(axis.text=element_text(color="black")) ``` @@ -539,11 +539,11 @@ backer_comp <- ncov_inc_fit_boot@ests[-2, -4] %>% bind_rows(ncov_wei_fit_boot@ests[-2, -4] %>% as.data.frame() %>% mutate(qtile=c("mean",2.5, 5, 25, 50, 75, 95, 97.5), - type="weibull")) %>% + type="Weibull")) %>% bind_rows(ncov_erl_fit@ests[-2, -4] %>% as.data.frame() %>% mutate(qtile=c("mean",2.5, 5, 25, 50, 75, 95, 97.5), - type="erlang")) %>% + type="Erlang")) %>% mutate(est=ifelse(qtile=="mean", exp(est), est), CIlow=ifelse(qtile=="mean",exp(CIlow), CIlow), CIhigh=ifelse(qtile=="mean",exp(CIhigh), CIhigh), @@ -553,27 +553,27 @@ backer_comp <- ncov_inc_fit_boot@ests[-2, -4] %>% select(-CIhigh, -CIlow) %>% spread(qtile, est, sep="_") %>% bind_rows(backer_params %>% - mutate(`qtile_2.5`=ifelse(type=="weibull", + mutate(`qtile_2.5`=ifelse(type=="Weibull", qweibull(.025, par1, par2), ifelse(type=="gamma", qgamma(.025, par1, scale=par2), qlnorm(.025, par1, par2))), - qtile_25=ifelse(type=="weibull", + qtile_25=ifelse(type=="Weibull", qweibull(.25, par1, par2), ifelse(type=="gamma", qgamma(.25, par1, scale=par2), qlnorm(.25, par1, par2))), - qtile_50=ifelse(type=="weibull", + qtile_50=ifelse(type=="Weibull", qweibull(.5, par1, par2), ifelse(type=="gamma", qgamma(.5, par1, scale=par2), qlnorm(.5, par1, par2))), - qtile_75=ifelse(type=="weibull", + qtile_75=ifelse(type=="Weibull", qweibull(.75, par1, par2), ifelse(type=="gamma", qgamma(.75, par1, scale=par2), qlnorm(.75, par1, par2))), - `qtile_97.5`=ifelse(type=="weibull", + `qtile_97.5`=ifelse(type=="Weibull", qweibull(.975, par1, par2), ifelse(type=="gamma", qgamma(.975, par1, scale=par2), @@ -583,7 +583,7 @@ backer_comp <- ncov_inc_fit_boot@ests[-2, -4] %>% ifelse(study=="Backer 2020", 2, 1)), study=reorder(study, study_order)) -comparison_plot <- ggplot(data=backer_comp, +ggplot(data=backer_comp, aes(middle=qtile_50, ymin=qtile_2.5, ymax=qtile_97.5, lower=qtile_25, upper=qtile_75, x=type, fill=study)) + @@ -595,14 +595,16 @@ comparison_plot <- ggplot(data=backer_comp, scale_fill_manual("Study", breaks=c("JHU-IDD", "Backer 2020", "Li 2020"), values=cbbPalette[c(4,2,3)]) + - ggtitle("B") + + # ggtitle("B") + theme_bw() + coord_flip() + theme(axis.text=element_text(color="black")) -grid.arrange(all_sens_plot, comparison_plot) +# grid.arrange(all_sens_plot, comparison_plot, layout_matrix=cbind(c(1), c(2))) ``` -```{r missed-cases} +```{r missed-cases, fig.height=7} +# saveRDS(ncov_gam_fit_boot, "generated-data/gam-fit-boot.rds") +# ncov_gam_fit_boot <- readRDS("generated-data/gam-fit-boot.rds") ## Figure 1 ## plot with x-axis in days, y axis as cases missed per XX monitored ## (similar to fig 3 of activemonitr manuscript) @@ -614,8 +616,8 @@ ncov_gamma_dat <- tibble(shape=ncov_gam_fit_boot@samples$par1, p95=qgamma(0.95, shape=shape, scale=scale), chain=1) -phis <- c(1/100, 1/1000, 1/10000) -durs <- 1:25 +phis <- c(1, 1/100, 1/1000, 1/10000) +durs <- 0:25 yrange <- c(1e-18, 1e-2) ## determine max u for each disease such that max(u)/2 + m = 90th percentile of T @@ -624,41 +626,74 @@ tmp_ncov <- mean(qgamma(.90, shape=ncov_gamma_dat$shape, maxu_ncov <- 2*(tmp_ncov - mean(ncov_gamma_dat$median)) ## make plots/data -ncov_monitor_probs <- plot_risk_uncertainty(ncov_gamma_dat,# phi=phis, +ncov_monitor_probs <- plot_risk_uncertainty(ncov_gamma_dat, phi=phis, + long_tail_pct=0.99, + nreps=1e3, max_u = maxu_ncov, durations=durs, return_plot=FALSE, return_data=TRUE, - include_xlab = FALSE, yrange=yrange, + include_xlab = FALSE, + yrange=yrange, include_legend=FALSE) ncov_monitor_cases <- ncov_monitor_probs$data %>% mutate( - escaped_cases_per_1k_p05 = p05 * 1000, - escaped_cases_per_1k_p25 = p25 * 1000, - escaped_cases_per_1k_p50 = p50 * 1000, - escaped_cases_per_1k_p75 = p75 * 1000, - escaped_cases_per_1k_p95 = p95 * 1000, + escaped_cases_per_1k_p05 = (p05 * 10000), + escaped_cases_per_1k_p25 = (p25 * 10000), + escaped_cases_per_1k_p50 = (p50 * 10000), + escaped_cases_per_1k_p75 = (p75 * 10000), + escaped_cases_per_1k_p95 = (p95 * 10000), risk_group = factor(phi, levels=phis, - labels=c("high risk (1 in 100)", - "some risk (1 in 1,000)", - "low risk (1 in 10,000)")) + labels=c("Infected (1 in 1)", + "High risk (1 in 100)", + "Some risk (1 in 1,000)", + "Low risk (1 in 10,000)")) ) -ggplot(ncov_monitor_cases, - aes(x=d, y=escaped_cases_per_1k_p50, color=risk_group, +am_plot_dat <- ncov_monitor_cases %>% + mutate(escaped_cases_per_1k_p05 = ifelse(escaped_cases_per_1k_p05>100, + NA,escaped_cases_per_1k_p05), + escaped_cases_per_1k_p50 = ifelse(escaped_cases_per_1k_p50>100, + NA,escaped_cases_per_1k_p50), + escaped_cases_per_1k_p95 = ifelse(escaped_cases_per_1k_p95>100, + NA,escaped_cases_per_1k_p95),) + +am_plot <- ggplot(ncov_monitor_cases, + aes(x=d, y=escaped_cases_per_1k_p50 %>% round, color=risk_group, group=risk_group, fill=risk_group)) + # geom_ribbon(aes(ymin=escaped_cases_per_1k_p25, # ymax=escaped_cases_per_1k_p75), alpha=.5) + - geom_ribbon(aes(ymin=escaped_cases_per_1k_p05, - ymax=escaped_cases_per_1k_p95), alpha=.25) + + geom_ribbon(aes(ymin=escaped_cases_per_1k_p05 %>% round, + ymax=escaped_cases_per_1k_p95 %>% round), alpha=.25) + geom_line(size=2) + - ylab("expected cases missed per 1,000 monitored") + - xlab("duration of monitoring (days)") + - scale_color_brewer(type="qual") + - scale_fill_brewer(type="qual") + + ylab("Expected cases missed\nper 10,000 monitored") + + xlab("Duration of monitoring (days)") + + scale_color_brewer("Risk group", type="qual") + + scale_fill_brewer("Risk group", type="qual") + theme_bw() + - # scale_y_log10()+ - theme(legend.position = c(.8,.8), legend.justification = c(1,1)) + scale_y_sqrt(breaks=c(1,10,25,50,75,100))+ + coord_cartesian(ylim=c(0,100)) + + theme(legend.position = c(.95,.9), legend.justification = c(1,1), + axis.text=element_text(color="black")) + + +am_tbl_dat <- ncov_monitor_cases %>% + mutate(risk_group=reorder(risk_group, phi, mean)) %>% + filter(d %in% c(5, 10, 15, 20)) %>% + transmute(Duration=d, + risk_group=risk_group, + est=paste0(escaped_cases_per_1k_p50 %>% round(), + " (", escaped_cases_per_1k_p05 %>% round(), + ", ", escaped_cases_per_1k_p95 %>% round(), ")")) %>% + spread(risk_group, est) + +colnames(am_tbl_dat) <- gsub("\\(", "\n\\(", colnames(am_tbl_dat)) +# window_tbl <- tableGrob(window_tbl_dat[-1,], theme=ttheme_minimal()) +am_tbl <- ggtexttable(am_tbl_dat, + theme=ttheme("classic", padding=unit(c(8,8), "mm")), + rows=rep("", nrow(am_tbl_dat))) +# grid.arrange(window_fig, window_tbl, nrow=2) +ggarrange(am_plot, am_tbl, nrow=2) ```