Swine influenza 2009/Early time course

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Confirmed data on 2009 H1N1 outbreak initiated in Mexico

  • Base line situation: Phase 3 for both Avian and Swine flu strains, with more serious avian cases worldwide.
  • 10 March Symptom onset of earliest (retrospective) proven human case [1].
  • 18 March Surge of influenza like illness in Mexico, starting around La Gloria, most in retrospect another strain but 5 cases confirmed (later).
  • 1 April First specimen that turns out to be of new flu subtype taken as as part of a clinical trial in San Diego County[2]. First (spanish) media reports of outbreak.
  • 12 April First extra territorial notification by Mexico of a respiratory illness outbreak in Veracruz
  • 13 April First possible flu death in Oaxaca state
  • 15 April CDC identifies novel flu type: A/California/04/2009[2].
  • 17 April Second specimen of novel flu type received by CDC from Imperial County, California and same day notification to WHO[2].
  • 21 April CDC reports 2 isolated cases of novel swine flu in California
  • 23 April Mexico City has had 854 cases of pneumonia with 59 deaths
  • 24 April 12 of Mexico outbreak cases found to be identical
  • 25 April WHO declares public health emergency of international concern as result of 7 cases of Swine Influenza A/H1N1 in USA
  • 26 April 20 cases to date confirmed in USA, 18 cases to date Mexico. Many more cases suspected but there is a lag of several days for full confirmatory tests to be done and Mexican confirmations have to be done in Canada due to USA biosecurity rules.
  • 27 April WHO phase 4, new cases confirmed to date: Mexico (26 - 7 deaths), USA (40), Canada (6), Spain (1)
  • 28 April New cases confirmed to date: Mexico (26 - 7 deaths), USA (64), Spain (2), NZ (3), UK (2), Israel (2)
  • 29 April WHO phase 5, 148 cases, new confirmed to date: Mexico (26 - 7 deaths), USA (91 - 1 death), Canada (13), Spain (4), Germany (3), Austria (1).
  • 30 April 257 cases, new confirmed to date: Mexico (97 - 7 deaths), USA (109 - 1 death), Canada(19), Spain(13), UK (8), Switzerland (1), Netherlands (1)
  • 1 May 367 cases, new confirmed to date: Mexico (156 - 9 deaths), USA (141 - 1 death), Canada (34), NZ (4), Germany (4), China-Hong Kong (1), Denmark (1)
  • 2 May 658 cases, new confirmed to date: Mexico (397 - 16 deaths), USA (160 - 1 death), Canada (51), UK (15), Germany (6), Republic of Korea (1), Italy (1), France (2), Costa Rica (1). Also found in swine herd in Alberta as a result of human transmission from Mexico.
  • 3 May 898 cases, new confirmed to date: Mexico (506 - 19 deaths), USA (226 - 1 death), Canada (85), Spain (40), Germany (8)
  • 4 May 1085 cases, new confirmed to date: Mexico (590 - 25 deaths), USA (286 - 1 death), Canada (101), Spain (54), NZ (5), UK (18), Israel (4), France (4), Colombia (1), El Salvador (2)
  • 5 May 1490 cases, new confirmed to date: Mexico (822 - 29 deaths), USA (403 - 1 death), Canada (140), Spain (57), UK (27), Germany (9), Republic of Korea (2), Italy (5), Ireland (1), Portugal (1)
  • 6 May 1893 cases, new confirmed to date: Mexico (942 - 29 deaths), USA (642 - 2 deaths), Canada (165), Spain (73), UK (28), Denmark (1), France (5), Sweden (1), Guatemala (1)
  • 7 May 2371 cases, new confirmed to date: Mexico (1112 - 42 deaths), USA (896 - 2 deaths), Canada (201), Spain (81), UK (32), Israel (6), Germany (10), Republic of Korea (3), Poland (1).
  • 8 May 2500 cases with 46 deaths, new confirmed to date: Mexico (1204 - 44 deaths), USA (896 - 2 deaths), Canada (214), Spain (88), UK (34), Israel (7), Germany (11), Netherlands (3), France (12), Brazil (4).
  • 9 May 3440 cases with 49 deaths, new reported to 06:00 with 48 deaths. Mexico (1364 - 45 deaths), USA (1639 - 2 deaths), Canada (242 - 1 death), NZ (7), Italy (6), Brazil (6), Panama (2), Japan (3)
  • 10 May 4379 cases, new reported to 07:30: Mexico (1626 - 45 deaths), USA (2254 - 2 deaths), Canada (280 - 1 death), Spain(93), UK (39), Israel (7), Italy (9), Costa Rica (8 - 1 death), Panama (3), Japan (4), Australia (1), Argentina (1).
  • 11 May 4694 cases with 53 deaths, new reported to 06:00: Mexico (1626 - 48 deaths), USA (2532 - 3 deaths), Canada (284 - 1 death), Spain (95), UK (47), China (2), Italy (9), France (13), Colombia (3), El Salvador (4), Sweden (2), Brazil (8), Panama (15), Norway(2).
  • 12 May 5251 cases with 61 deaths, new reported to 06:00. Mexico (2059 - 56 deaths), USA (2600 - 3 deaths), Canada (330 - 1 death), UK (55), Germany (12), Panama (16)
  • 13 May 5728 cases with 61 deaths, new reported to 06:00: USA (3009 - 3 deaths), Canada (358 - 1 death), Spain (98), UK (68), China (3), Colombia (6), Panama (29), Finland (2), Thailand (2), Cuba (1).
  • 14 May 6497 cases with 65 deaths, new reported to 06:00: USA ( 3352 - 3 deaths), Canada (389 - 1 death), Spain (100), UK (71), China (4), France (14), Colombia (7).
  • 15 May 7520 cases with 65 deaths, new reported to 06:00: Mexico (2446 - 60 deaths), USA ( 4298 - 3 deaths), Canada (449 - 1 death), France (14), Colombia (10), Panama (40), Cuba (3), Belgium (1).
  • 16 May 8451 cases with 72 deaths, new reported to 07:00: Mexico (2895 - 66 deaths), USA ( 4714 - 4 deaths), Canada (496 - 1 death), NZ (9), UK (78), Germany (14), Colombia (11), Costa Rica (9 - 1 death), Guatemala (3), Panama (43), Ecuador (1), Peru (1).
  • 17 May 8480 cases with 72 deaths, new reported to 06:00: Spain (103), UK (82), China (5), Sweden (3), Panama (54), Japan (7), Belgium (4), India (1), Malaysia (2), Turkey (1).
  • 18 May 8829 cases with 74 deaths, new reported to 06:00: Mexico (3103 - 68 deaths), UK (101), China (6), Japan (125), Belgium (5), Turkey (2), Chile (1).
  • 19 May 9830 cases with 79 deaths, new reported to 06:00: Mexico (3648 - 72 deaths), USA (5123 - 5 deaths), UK (102), China (7), El Salvador (6), Panama (59), Japan (159), Peru (2), Chile (4).
  • 20 May 10243 cases with 80 deaths, new reported to 06:00: USA (5469 - 6 deaths), Spain (107), France (15), Colombia (12), Poland (2), Panama (65), Japan (210), Peru (3), Chile (5), Greece (1).
  • 21 May 11034 cases with 85 deaths, new reported to 06:00: Mexico (3892 - 75 deaths), USA (5710 - 8 deaths), Canada (719 - 1 death), Spain (111), UK (109), China (8), Italy (10), France (16), Costa Rica (20 - 1 death), Guatemala (4), Panama (69), Japan (259), Australia (3), Norway (3), Cuba (4).
  • 22 May 11168 cases with 86 deaths, new reported to 06:00: USA (5764 - 9 deaths), Spain (113), UK (112), China (11), Panama (73), Japan (294), Australia (7), Ecuador (8), Peru (5), Chile (24).
  • 23 May 12022 cases with 86 deaths, new reported to 06:00: USA (6552 - 9 deaths), Spain (126), UK (117), Germany (17), Switzerland (2), Italy (14), Panama (76), Japan (321), Australia (12), Norway (4), Belgium (7), Taiwan (1), Russia (1).
  • 24 May No WHO update
  • 25 May 12515 cases with 91 deaths, new reported to 06:00 (no report 24 May): Mexico (4174 - 90 deaths), Canada (805 - 1 death), Spain (133), UK (122), Israel (8), Switzerland (3), China (15), Italy (19), Colombia (13), Costa Rica (28 - 1 death), Poland (3), Brazil (9), Japan (345), Australia (16), Argentina (2), Ecuador (10), Peru (25), Chile (44), Honduras (1), Iceland (1), Kuwait (18).
  • 26 May 12954 cases with 92 deaths, new reported to 06:00: USA (6764 - 10 deaths), Canada (921 - 1 death), Spain (136), UK (137), China (20), Republic of Korea (21), Colombia (16), Costa Rica (33 - 1 death), Japan (350), Australia (19), Argentina (5), Ecuador (24), Peru (27), Chile (74), Philippines (2), Russia (2)
  • 27 May 13398 cases with 95 deaths, new reported to 06:00: Mexico (4541 - 83 deaths), Spain (138), Israel (9), China (22), Italy (23), El Salvador (11), Guatemala (5), Japan (360), Australia (39), Argentina (19), Ecuador (28), Chile (86), Taiwan (4), Bahrain (1), Singapore (1).
  • 28 May No WHO update
  • 29 May 15510 cases with 99 deaths, new reported to 06:00: Mexico (4910 - 85 deaths), USA (7927 - 11 deaths), Canada (1118 - 2 deaths), Spain (143), UK (203), Israel (11), Germany (19), Switzerland (4), China (30), Republic of Korea (33), Italy (26), France (21), Colombia (17), Ireland (3), Sweden (4), Poland (4), Brazil (10), Panama (107), Japan (364 ), Australia (147), Argentina (37), Finland (3), Belgium (8), Ecuador (32), Peru (31), Chile (165), Greece (3), Philippines (6), Taiwan (9), Singapore (4), Romania (3), Czech Republic (1), Dominican Republic (2), Uruguay (2), Slovakia (1).
  • 30 May No report from WHO although ECDC reports 17232 cases with 115 deaths and fair number new cases in Australia and Europe
  • 31 May No report from WHO although ECDC reports 17395 cases with 115 deaths
  • 1 June 17410 cases with 115 deaths, new reported to 06:00: Mexico (5029 - 97 deaths), USA (8975 - 15 deaths), Canada (1336 - 2 deaths), Spain (178), UK (229), Israel (19), Germany (28), Switzerland (8), China (52), Italy (29), France (24), Colombia (20), Costa Rica (37 - 1 death), El Salvador (27), Ireland (4), Guatemala (12), Brazil (18), Japan (370 ), Australia (297), Argentina (100), Belgium (12), Ecuador (39), Peru (36), Turkey (4), Chile (250), Greece (4), Philippines (16), Taiwan (12), Russia (3), Honduras (2), Singapore (5), Uruguay (11), Slovakia (2), Bahamas (1), Hungary (1), Cyprus (1), Bolivia (3), Estonia (1), Jamaica (2), Paraguay (5), Venezuela (2), Viet Nam (1).
  • 2 June 19159 cases with 117 deaths reported to ECDC
  • 3 June 19273 cases with 117 deaths new reported to 06:00: USA (10053 - 17 deaths), Canada (1530 - 2 deaths), Spain (180), NZ (10), UK (339), Israel (33), Switzerland (10), Netherlands (4), China (69), Republic of Korea (41), Italy (30), France (26), Costa Rica (50 - 1 death), El Salvador (41), Portugal (2), Guatemala (14), Sweden (7), Brazil (20), Panama (155), Japan (385), Australia (501), Argentina (131), Finland (4), Belgium (13), Peru (40), Chile (313), Greece (5), Taiwan (14), Singapore (9), Romania (5), Dominican Republic (11), Uruguay (15), Venezuela (3), Viet Nam (3), Bulgaria (1), Egypt (1), Lebanon (3), Nicaragua (1).
  • 4 June 21823 cases with 125 deaths reported to ECDC
  • 5 June 21940 cases with 125 deaths reported to 06:00: Mexico (5563 - 103 deaths), USA (11054 - 17 deaths), Canada (1795 - 3 deaths), Spain (218), NZ (11), UK (428), Israel (39), Germany (43), Austria (2), Switzerland (10), Netherlands (4), China (89), Denmark (4), Republic of Korea (41), Italy (38), France (47), Colombia (24), Costa Rica (68 - 1 death), El Salvador (49), Ireland (8), Portugal (2), Guatemala (23), Sweden (13), Poland (4), Brazil (28), Panama (173), Japan (410), Australia (876), Argentina (147), Norway (9), Finland (4), Thailand (8), Cuba (4), Belgium (13), Ecuador (43), Peru (47), India (4), Malaysia (2), Turkey (8), Chile (369 - 1 death), Greece (5), Philippines (29), Taiwan (16), Russia (3), Honduras (34), Iceland (1), Kuwait (18), Bahrain (1), Singapore (12), Romania (8), Czech Republic (2), Dominican Republic (33), Uruguay (15), Slovakia (3), Bahamas (1), Hungary (3), Cyprus (1), Bolivia (3), Estonia (3), Jamaica (2), Paraguay (5), Venezuela (3), Viet Nam (3), Bulgaria (1), Egypt (1), Lebanon (3), Nicaragua (5), Barbados (1), Luxembourg (1), Saudi Arabia (1).
  • 6 June 25026 cases with 139 deaths reported to ECDC
  • 7 June 25643 cases with 139 deaths reported to ECDC
  • 8 June 26035 cases with 139 deaths reported to ECDC
  • 9 June 26744 cases with 140 deaths reported to ECDC
  • 10 June 27737 cases with 141 deaths reported to 06:00 to WHO
  • 11 June WHO phase 6 (Pandemic). 29254 cases with 144 deaths reported to ECDC
  • 12 June 29837 cases with 145 deaths reported to ECDC
  • 13 June 36389 cases with 164 deaths reported to ECDC
  • 14 June 36864 cases with 165 deaths (1st UK death) reported to ECDC
  • 15 June 37479 cases with 165 deaths reported to ECDC
  • 16 June 39260 cases with 168 deaths reported to ECDC
  • 17 June 41586 cases with 176 deaths reported to ECDC
  • 18 June 42224 cases with 175 deaths reported to ECDC (one US notification withdrawn)
  • 19 June 44287 cases with 180 deaths reported to WHO or 44605 cases with 181 deaths reported to ECDC
  • 20 June 50914 cases with 228 deaths reported to ECDC
  • 21 June 51702 cases with 230 deaths reported to ECDC
  • 22 June 52160 cases with 231 deaths reported to WHO or 52962 cases with 232 deaths reported to ECDC
  • 23 June 54934 cases with 239 deaths reported to ECDC
  • 24 June 55867 cases with 238 deaths reported to WHO or 56129 cases with 249 deaths reported to ECDC
  • 25 June 59179 cases with 258 deaths reported to ECDC
  • 26 June 59814 cases with 263 deaths reported to WHO or 68096 cases with 306 deaths reported to ECDC
  • 27 June 69839 cases with 312 deaths reported to ECDC
  • 28 June 71578 cases with 320 deaths reported to ECDC
  • 29 June 70893 cases with 311 deaths reported to WHO or 73153 cases with 324 deaths reported to ECDC
  • 30 June 76229 cases with 330 deaths reported to ECDC
  • 1 July 77201 cases with 332 deaths reported to WHO
  • 2 July 81700 cases with 339 deaths reported to ECDC. UK moves to mitigation & treatment phase
  • 3 July 89921 cases with 382 deaths reported to WHO or 90852 cases with 384 deaths reported to ECDC
  • 16 July WHO reports "In past pandemics, influenza viruses have needed more than six months to spread as widely as the new H1N1 virus has spread in less than six weeks". 128,273 cases with 679 deaths reported to ECDC. However in one reporting country with good community surveillance, the UK, 55,000 new cases estimated in last week when only 10,649 confirmed including 29 deaths in that week (and only 17 of those deaths in the report to ECDC figure)
  • 6 August 2010 WHO reports 18,449 deaths had been notified worldwide with 491,382 cases notified as serology positive[3] The pandemic phase ended officially on 10th August 2010[4].

The plot above starts on 15th April 2009 and from July shows increasingly incomplete data as reporting changed. UK suspected data was not published from 15/6/09 and from 17/6/09 clinically presumed cases presumably diagnosed in retrospect by resolved symptoms were reported. From 25/6/09 Scotland stopped reporting clinically presumed cases. UK data was no longer issued on a daily basis on from 2/7/09 but case ascertainment was probably fair up until the second week of June at least and is likely to be as good data as any other nation could offer at close to real time. Issues such as case ascertainment policies, resources to do this and use of virus detection verus antibody detection mean that this data simply gives a feel for what was really happening. For example UK and Australia by the beginning of July were reporting very similar numbers of confirmed cases but the Australian number of deaths were 3 times higher from effectively identical start times. The most likely explanation is better initial case ascertainment in the UK due mainly to seasonal factors forcing Australia to move to the mitigation and treatment phase much sooner than the UK. The death rate is probably lower than 1 per 1000 infected with fully functioning health care systems in the first epidemic wave but is more than 0.5 per 1000. While unexceptional death rates for a epidemic it as atypical as it is much more biased towards younger adults than seasonal influenza and is certainly the fastest spreading pandemic in history by an order of magnitude. The excess mortality of the 1918 (second wave) pandemic might only be three times greater assuming only half the population were infected then[5]. There is nothing particularly reassuring in the data to hand compared to say the 1957/58 pandemic as already by July southern hemisphere countries are noting heavier demands on their health systems than normal in recent years for seasonal influenza[6]. In the graph above UK data is additively displayed, but in graph below UK data is shown non-additively to illustrate the problems with suspected cases and publicity bias. WHO stopped consistent daily updates on 30/5/09 and ECDC figures were increasingly used after this date. The ECDC has analysed the early European data by date of onset and there are two distinct phases, the first associated with travelers returning from Mexico peaking about 27th April and almost disappearing in second week of May. The second was associated with travel to the USA which really started in 3rd week of May, and these imported cases peaked in the first few days of June and then internal secondary transmission cases became more dominant.

The plots below show time course from 1st March 2009 to 1st June 2009

The data below shows incident data from Mexico first wave. At the peak of the outbreak, about 27th April there were about 1300 new probable cases a day, never confirmed or excluded known to the authorities and an additional 385 confirmed cases as shown occurred that day (data up to 2nd June, will increase slightly as later tests come in). The data displayed in the last few days of May is definitely incomplete and likely to increase from 2 cases to over ten/day.

References

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