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  • Jon is a contributing correspondent for Science.
 

Swine Flu Outbreak, Day by Day

9 June 2009 4:09 pm
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This chronology of the pandemic will be updated regularly as news breaks and past events come to light. And follow ScienceInsider’s full coverage on the swine flu outbreak here.

9 June
With Australia reporting more than 1000 confirmed cases, WHO's flu chief Keiji Fukuda says the agency is now "really very close" to calling the epidemic a pandemic.  WHO is still working to inform countries exactly what phase  6 means and to avoid a "blossoming of anxiety" once a pandemic is declared. Fukuda also weighed in on what the virus—or the pandemic—should be called, admitting that the current name, influenza A (H1N1), is creating confusion.

8 June
Egypt becomes the first country in Africa to report a confirmed case of swine flu to WHO. Pan-African News Agency reports that six sub-Saharan countries have suspected cases. In all, says WHO, 73 countries to date have reported 25,288 confirmed cases and 139 deaths.

4 June
Trust for America’s Health, a D.C.-based advocacy group, issues “Pandemic Flu Preparedness: Lessons from the Frontlines.” The detailed critique praises U.S. federal, state, and local governments for having invested in pandemic planning, including the stockpiling of drugs and training public health officials to respond appropriately. But the report says public health departments are underfunded and “stretched too thin,” leading to delays in identifying and containing infections.

The 23-page report further warns that the country’s “current vaccine development and production capacity is severely lacking,” adding that “the country has not developed or adequately tested a system that will ensure that all Americans would be able to be inoculated in a short period of time.” WHO’s pandemic alert system, it says, has caused much confusion; the report also criticized some countries for instituting travel restrictions and bans on pork products.

2 June
Australia reports 501 confirmed cases, up from 17 a week before, making the island nation the hardest-hit country outside of North America. With increasing fears about the spread of H1N1 in the Southern Hemisphere, Asia, and Europe,  WHO announces that it’s moving closer to declaring a phase 6 alert, but says it likely will include a severity index tailored for each locale based on both viral characteristics and ability to respond. U.S. President Barack Obama sends a letter to Nancy Pelosi, speaker of the House of Representatives, asking Congress to set aside nearly $10 billion new dollars for swine flu. This would add to the $2 billion a House bill already in the works. Obama made the request out of “an abundance of caution” and the funds would only be tapped if a full-scale pandemic hit the United States.

26 May
Swine flu begins to spike in the Southern Hemisphere, with 74 confirmed cases in Chile alone. The CDC suggests that the disease may have peaked in the United States, as reports of influenza-like illness declined in seven of nine regions. But this does not directly measure the actual prevalence of the novel H1N1 virus, and some epidemiologists caution against undue optimism. CDC also warns that even if the drop is real in the United States—which accounts for just over half of the world’s 12,954 confirmed cases—the virus has not left and may well come roaring back with the cooler weather in the fall.

22 May
Following complaints from member countries at the World Health Assembly meeting held in Geneva this week, WHO announces that it needs to rethink its phasing system and the definition of the word “pandemic.” Despite mounting cases outside of the Americas, the member countries urged WHO not to declare a phase 6 alert, contending that the swine flu does not cause severe enough disease to warrant the label of a full-scale pandemic. Meanwhile, the U.S. Department of Health and Human Services announces that it will dish out $1 billion to several pharmaceutical companies to make a vaccine against the novel H1N1 virus. But the money will only purchase vaccine ingredients, not a final product, and it’s only enough material to vaccinate 20 million people. ScienceExpress publishes the first detailed study of the new virus’s genetic makeup, explaining the twisted histories of its closest relatives.

21 May
MMWR dispatch offers the first concrete evidence that the elderly population may have some immunity to the new virus, which could explain why they largely have been spared from severe disease in this outbreak. According to the study, antibodies from this group worked against the novel H1N1 virus in test tube experiments. The cross-reactive antibody response may reflect their exposure to the H1N1 virus that circulated until 1957, MMWR suggests.

20 May
Confirmed world cases top 10,000. CDC clarifies that no delays expected for vaccine production as many processes are done in parallel, which wasn’t clear from the WHO report the day before. Still, concerns remain about whether a vaccine can actually be manufactured and approved in time for traditional flu season in the Northern Hemisphere.

19 May
WHO releases a report from an ad hoc advisory group looking at making vaccines against the new virus, which suggests the “seed stock” needed to scale-up production of a H1N1 vaccine may not be ready until mid-July. This is two months later than an estimate made by WHO’s Marie-Paul Kieny on 1 May. Given that it takes up to six months to manufacture vaccine, this raises questions about whether it will be ready in time for winter in the Northern Hemisphere. Confirmed cases in Japan climb to 191, mostly among school children, and higher than any country outside of the Americas.

18 May
At the opening of the World Health Assembly in Geneva, several countries urged WHO Director-General Margaret Chan to revise the pandemic alert system, as it reflects geographic spread but not the severity of disease. Chan says the alert level will remain at phase 5, despite Japan reporting 129 cases—up from four a few days earlier. She says, “The virus has given us a grace period” but cautions against complacency. “No one can say whether this is just the calm before the storm.” Cases in Japan continue to climb.

17 May
Japan reports sharp spike in cases. There is increasing pressure on WHO to raise the alert level from phase 5 to 6

15 May
With apathy setting in, CDC’s Daniel Jernigan, deputy director of the influenza division,  stresses that “the H1N1 virus is not going away.” Jernigan estimates that “upwards of maybe 100,000” people in the United States have influenza-like illness—more than 20 times the number of confirmed and probable novel H1N1 cases in the country. But Jernigan says some of the spike in flu cases likely comes from seasonal viruses, not the new strain, as well as the “profound amount of testing that has gone on in the last few weeks.” CDC also changes its recommendations for people who want to travel to Mexico, downgrading the “warning” that advised people to put off “nonessential” trips to a “precaution.” In Europe, which has yet to see sustained transmission in communities, four countries cut deals with GlaxoSmithKline to purchase more than 100 million doses of a vaccine that targets the new H1N1 virus.

14 May
A Texan whose pregnant wife died of swine flu takes legal action against the U.S. co-owner of a Mexican pig farm, Granjas Carroll, which he alleges may have kick-started the outbreak. WHO announces that it no longer will hold daily press briefings.

13 May
With the outbreak still teetering on the brink of phase 6, a full-scale pandemic, WHO’s Sylvie Briand, a project leader in the Global Influenza Programme, acknowledges the limits of the phasing system, which gauges transmission, not severity. But Briand says a “severity index” for flu “is not very helpful” because it depends on several factors that can differ even within one country, including virulence, vulnerability, and community “resilience.” CDC, for the first time since 23 April, will no longer hold daily press briefings.

12 May
WHO and CDC officials suggest that European and Asian countries may have made headway against the virus with aggressive screening of travelers and prompt treatment of infected people and their contacts with antivirals. CDC’s MMWR dispatch advises use of antiviral drugs for any pregnant woman with confirmed disease. Thirty countries report more than 5200 confirmed cases, nearly 90% of which were in Mexico and the United States, but WHO and CDC advise that case counts are underestimates. Story breaks about scientist who suggests that the virus might be an accidental laboratory creation, which immediately is met with deep skepticism.

11 May
Mainland China reports its first case. Science publishes paper that estimates 23,000 people in Mexico were infected by 30 April, and that the virus looks similar in severity to one that caused 1957 pandemic.

9 May
Confirmed cases in the U.S. (1639) outnumber those in Mexico (1364) for the first time, but this might reflect more aggressive surveillance and testing capabilities than actual infections.

7 May
Mexico reports nearly 12,000 suspected cases, more than 1000 confirmed. WHO says community transmission does not appear to be happening outside the Americas. A media backlash begins, accusing scientists and officials of hyping the outbreak. Canadians clarify details about the pig farm outbreak, noting that others on the farm developed influenza-like illness but have tested negative for the virus.

6 May
Canada reports that the worker on the Alberta pig farm tested negative for the virus, although the sample may have been collected too late to detect it. Tests of his blood for antibodies begin.

5 May
First death of a U.S. resident: a 33-year-old schoolteacher who had recently given birth. CDC announces that schools should no longer close if they have a case. Mexico’s Córdova says cases are decreasing in severity and number, and that businesses in Mexico City may reopen. Mexico reports the detection of a Mexico City case with symptoms on 11 March, earliest date yet reported.

4 May
Official case count tops 1000 for first time. Virus found in 20 countries.

3 May
WHO reports 18 countries with 898 confirmed cases. Phase 6, full-scale pandemic, remains imminent but not declared.

2 May
Canada reports the first isolation of the virus from pigs. A farm worker who traveled to Mexicali, Mexico, returned to Canada on 12 April and apparently infected a herd in Alberta. Mexican Health Minister José Ángel Córdova says he believes the outbreak in his country is stabilizing. Mexico still has a backlog of untested samples but has confirmed 506 cases and 19 deaths. U.S. cases climb to 226 and 30 hospitalizations.

1 May
Thirteen countries report cases, taking the total to 367. Between 1billion and 2 billion doses of a pandemic vaccine may be available within a year, says WHO’s Marie-Paule Kieny. Ensuring access for the world’s poorest is a WHO priority, she says.

30 April
The backlog of untested cases is in the thousands, as few labs other than CDC and PHAC can confirm cases. MMWR publishes detailed reports about outbreaks in Mexico and a New York City school. In London, the European Medicines Agency meets with E.U. member countries, vaccine producers, WHO, and the European Centre for Disease Prevention and Control to discuss the criteria a pandemic vaccine will have to meet.

29 April
WHO raises the threat level from phase 4 to 5, indicating sustained community transmission in two countries (Mexico and the United States) in the same region. Ten countries report confirmed cases, including South Korea, the first in Asia. The first related death is reported in the United States: a toddler from Mexico visiting relatives. WHO’s Chan holds a teleconference with vaccine manufacturers around the globe to discuss the production of a pandemic vaccine.

28 April
Seven countries report cases to WHO. CDC reports five new hospitalized cases in the United States, and acting CDC Director Richard Besser says he expects to see deaths. The Mexican government bans dining in Mexico City restaurants. Cuba suspends flights to and from Mexico, becoming the first of several countries to do so.

27 April
Canada and Spain report confirmed cases to WHO. After an Emergency Committee meeting, WHO raises the pandemic threat level from phase 3 to phase 4, indicating sustained human-to-human transmission in a community. Mexico suspends schools nationwide.

26 April
CDC confirms cases in five states, none severe. The mystery deepens about why Mexico appears to have many related hospitalizations and deaths. Other countries, including New Zealand and France, report suspect cases. Churches in Mexico City do not hold mass

25 April
WHO convenes an Emergency Committee to evaluate evidence. Chan declares the outbreak a Public Health Emergency of International Concern 24 April

CDC publishes MMWR dispatch about six new U.S. cases with increasing evidence of human-to-human transmission and publicly links same strain of H1N1 to the Mexican outbreak. WHO receives reports from Mexico of 884 suspected cases, most in Mexico City, and 62 deaths. Most cases are in otherwise healthy young adults. The Mexican government closes schools in Mexico City.

23 April
Samples from Mexico arrive at CDC. PHAC and CDC confirm Mexico cases are the same  A(H1N1) of swine origin.

There is a teleconference between PHAC, CDC, and Mexican officials. Genetic analysis shows that the virus is a mix of avian and swine viruses from North America, a swine flu strain usually seen in Asia, and a human influenza strain. Margaret Chan, WHO’s director general, learns details upon arrival in Washington, D.C., for World Malaria Day and quickly returns to Geneva. In a press conference, CDC says it’s producing a “seed strain” for the production of a pandemic vaccine.

22 April
Samples from Mexico arrive at PHAC. 21 April

CDC publishes first dispatch in the Morbidity and Mortality Weekly Report (MMWR) about two cases in California. Mexico reports atypical influenza behavior associated with severe pneumonia in various cities. InDRE ships samples to PHAC’s National Microbiology Laboratory in Winnipeg and CDC.

20 April
Teleconference with CDC, PAHO, and PHAC. Cooperation established between Mexico, the United States, and Canada.

18 April
The U.S. focal point publishes confirmed California cases of A(H1N1) in WHO’s EIS. Mexico acknowledges receipt of information and responds that in March and April the country had an unusual increase in seasonal influenza with predominance of B strain; some cases presented with severe pneumonia in adults of reproductive age. Mexico notes that the case of a severe pneumonia in patient who died in Oaxaca could be related. PHAC and InDRE have teleconference and conclude it may be a novel agent, unrelated to influenza17 April
Mexican focal point asks local officials in Mexico to verify news reports of a cluster of cases of acute respiratory illness in Oaxaca hospital. Officials reply there is no such outbreak, but there is one patient with diabetes who has a severe case, presumably viral. InDRE Director Celia Alpuche sends an e-mail asking for help to Francis Plummer, head of the National Microbiology Laboratory in Winnipeg, part of the Public Health Agency of Canada (PHAC).

16 April
CDC notifies San Diego County Health & Human Services Agency of a local case of a novel swine influenza. PAHO receives a news story alert from Veratect about a supposed coronavirus outbreak in a hospital in Oaxaca state. 14 April
CDC tests the San Diego boy’s sample and determines the virus is A(H1N1) of swine origin. The boy had no contact with pigs.

13 April
Wisconsin’s State Laboratory of Hygiene tests specimen, confirms that it’s untypable, and sends to CDC. NHRC also sends CDC a sample of isolated virus. PAHO asks Mexico’s focal point if it can post a notice about the outbreak in WHO’s surveillance network’s Event Information System (EIS). Mexico’s focal point doesn’t respond.

12 April
Mexico’s director general of epidemiology, Hugo López-Gatell Ramírez, confirms to PAHO the existence of acute respiratory infections but says there is no link to fecal contamination of pig farms. Studies continue. Mexico’s focal point considers outbreak to be a “potential public health event of international importance” because it meets IHR criteria: severe public health impact and an unusual event.

11 April
As per the International Health Regulations (IHR), the World Health Organization (WHO) has a pandemic alert and response network, which relies on designated people or institutions in each member country to report unusual disease patterns. PAHO, a regional office of WHO, asks the Mexican IHR “focal point” to verify the outbreak reported in the news.

10 April
The Pan American Health Organization (PAHO) accesses Veratect database and notes news stories reporting an outbreak of acute respiratory infections in La Gloria, Veracruz. Wisconsin State Laboratory of Hygiene in Madison receives sample of San Diego boy from Marshfield Labs.

7 April
Instituto Nacional de Diagnóstico y Referencia Epidemiológicos (InDRE), the main influenza diagnostic lab in the country, located in Mexico City, learns of unusual severe respiratory diseases in young adults seen at the National Institute of Respiratory Diseases and begins investigating the cluster.

6 April
Veratect, a Kirkland, Washington-based company that scours news reports for emerging threats, reports in its subscription-only database that local Mexican health officials have declared an alert because of respiratory disease outbreak in La Gloria, Veracruz state, Mexico. Residents believe it is caused by pig breeding farms in the area. Local officials launch a spraying campaign that targets flies, an influenza vaccination campaign, and an epidemiological investigation back to 10 March. A Mexican news story reports 60% of inhabitants infected and three deaths.

1 April
NHRC researchers determine that the boy is likely infected with influenza A, but they cannot subtype the strain. As per protocol, the sample is sent to Marshfield Labs in Wisconsin. HealthMap, a global disease alert system run by academics, flags a news story from Mexico about a strange respiratory outbreak in the state of Veracruz that has claimed two lives.

30 March
A 10-year-old boy with fever, cold, and vomiting goes to the Naval Medical Center San Diego in California. As part of a clinical study, a nasopharyngeal swab is sent across town to the Naval Health Research Center (NHRC).

18 March
Mexican surveillance begins noting cases of influenza-like illness in the Distrito Federal, which includes Mexico City.

11 March
First documented symptoms (as of 5 May) in a Mexico City resident who later would be found to have confirmed infection with A(H1N1) swine flu.

 

 

  
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Sources: Mirta Roses Periago and Daniel Epstein, PAHO; Celia Alpuche, InDRE; Mauricio Hernandez-Avilia, Mexican Ministry of Health; Francis Plummer, PHAC; CDC, WHO, and Mexican government press conferences; Veratect; Michele Ginsberg, San Diego County Health & Human Services Agency; U.S. Naval Health Research Center, HealthMap.

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