Thursday, July 30, 2009

First health care worker fatality in New Zealand

Deaths of health care workers is something we watch closely as they are usually a healthly group that has high exposure to illnesses like pandemic influenza. Seeing an increase in death or hospitalization in health care workers might be a trigger indicator that we're seeing more severe outbreaks, changes in the virus, etc.

So, even though we have not seen any clusters of deaths in health care workers, it is important to take note of stories such as this one of the first health care worker death in New Zealand.

"The 39-year-old woman who died of swine flu in Wellington Hospital this week was a front-line health worker at Hutt Hospital, officials have confirmed.

The woman understood to have been a nurse in the children's ward is believed to be the first health worker to die from the virus in New Zealand.

Her death from a rare complication on Monday, after 11 days in intensive care, is the 13th to be officially recorded.

The woman had suffered a miscarriage within the previous two months. Pregnancy is a known risk factor for viral complications. However, it is not known whether she had the virus at the time she miscarried."

For the full story, go here:

ECDC posts the UK planning assumptions for pandemic flu

The European Centre for Disease Prevention and Control posted the UK planning assumptions for pandemic waves in the fall and winter.

Clinical attack rate 30%
Peak clinical attack rate 6.5% (local planning assumptions 4.5% to 8%) per week
Complication rate
15% of clinical cases
Hospitalisation rate 2% of clinical cases
Case fatality rate 0.1% to 0.2% (cannot exclude up to 0.35%) of clinical cases
Peak Absence Rate 12% of workforce

"UK parameters and their broader applicability

The UK paper is based on a model using parameter estimates from the UK and abroad on the 2009 strain and fitted using real data on UK cases over the period when the majority of cases were confirmed and reported daily.

Clinical attack rate
This is 30 % (The UK clinical attack rate is based on an assumption that half of the infected become symptomatic so this would imply a total infection attack rate of about 60 %). WHO assumptions are that two thirds become symptomatic [5]. Whether the UK or WHO is correct will be determined later when the results from serology become available. The UK assumptions imply a basic reproductive number Ro in the interval 1.4 – 1.5 which seems to be the case at present in the UK. A Ro of value 1.4 implies a total infection attack rate of about 50 % (which would imply a clinical attack rate of 25 % in the UK planning assumptions). A higher value of Ro of 2.0 implies a total infection attack rate of about 80 % (hence a clinical attack rate of 40% in the UK planning assumptions).

Peak clinical attack rate
This can depend on a number of factors such as seasonality, immunity in the population and interventions that might prolong the epidemic but also reduce the peak attack rate [6]. A particularly important point to note is that local epidemics are often shorter and sharper in a pandemic than national rates and so there is a higher value for the peak clinical attack rates for local application [1,3].

Case fatality rate
This is one of the most eagerly sought parameters but it is also amongst the hardest to determine with any accuracy. The earliest studies of this pandemic gave a high CFR of about 0.4 % [7] compared to lower rates for the 1957 and 1968 pandemics but higher rates for 1918 [8]. The UK estimates are of a CFR of 0.1-0.2 though values of up 0.35% cannot be ruled out as impossible [3]. The CFR number reported in the UK are thus as stated the reasonable worst case scenario unless the virus changes its characteristics in terms of lethality while the Norwegian figure is more based on what has been directly observed, adjusted for assumed underreporting."

For the full discussion, see:

Monday, July 27, 2009

Potential "mismatch" for the seasonal flu vaccine

Seasonal influenza vaccines are actually created to fight off several virus strains. Experts gather in late winter/early spring to select what they think will be the predominant strains next fall and winter. Then vaccine production begins.

Sometimes experts get it right, sometimes there's a "mismatch" and another virus strain begins to dominate.

Reporting from Helen Branswell and the ProMed network are raising the possibility that in addition to pandemic strain (novel H1N1), for which we will have limited vaccine supplies, there may be a mismatch for the seasonal flu vaccine as well.

"A component of the seasonal flu shot may not be well matched to the circulating viruses, potentially setting up what's known as a vaccine mismatch.

Some samples of the emerging new strain of H3N2 viruses show a substantially reduced response to antibodies generated by the corresponding virus in the seasonal vaccine, raising the possibility of significantly reduced protection in some cases.

Vaccine mismatches are bad at the best of times. More people get sick during flu seasons with mismatches. But a seasonal flu vaccine mismatch coinciding with a flu pandemic? That is no one's idea of a good time."

We don't know yet, however, how much of the seasonal flu we will see in the Northern Hemisphere or if it will be crowded out by H1N1. Also, worlwide we haven't be able to track the varriant of H3N2 because of the flood of pandemic virus reporting and analysis:

"The new variant has been seen on a number of continents, though it still remains a minority member of the H3N2 family, according to experts at the World Health Organization and the U.S. Centers for Disease Control in Atlanta.

With the demands the ongoing pandemic is placing on the WHO's laboratory network, researchers haven't yet had time to study whether the new variant is making up a growing percentage of H3N2 viruses, said Dr. Nancy Cox, director of the CDC's influenza division.

If they were, that would suggest the variant was on its way to becoming the dominant H3N2 virus and a vaccine mismatch would be on the cards.

Further clouding the issue is the fact that labs around the world haven't been submitting as many H3N2 viruses to the WHO network. There are simply fewer of them around.

"We haven't had that many H3N2 viruses to analyze because we've had such a flood of the novel H1N1 viruses because they're predominating," Cox said."

To read the whole story, visit:


Preliminary estimate of the reproduction number from New Zealand

Estimating the reproduction number, sometimes shown or referred to as "R", is very important because it tells us how well a particular influenza virus will spread. Reproduction number refers to the average number of secondary influenza cases caused by one primary case. In other words, if we have an influenza virus with a reproductive number of 3, then each person infected will likely spread the virus to three other people, on average.

Of course, the true reproduction number is difficult to know since we can't be certain of the total number of influenza cases, etc. However, scientists have pretty good methods for estimating it.

A study just out from New Zealand puts the reproduction number at 1.96. The study notes that estimates from Mexico were ranged from 1.4–1.6 and in Japan, for the current wave, 2.0–2.6.

What does this mean? Seasonal flu has a reproduction number of 1.3 - 1.5, so if estimates in New Zealand and Japan are correct, then it would mean that H1N1 is transmitting more efficiently (and will spread more quickly) than seasonal flu. However, these estimates contradict some preliminary studies of H1N1 in ferrets. We'll have to keep an eye on the evidence as it accumulates.

To read the study, visit:

Wednesday, July 22, 2009

Novel H1N1 vaccine trials begin today in Australia

From ABC News in Australia, pandemic vaccine trials start in Adelaide today.

"Rachel David from vaccine makers CSL says the Royal Adelaide Hospital trials will take about seven months, but there will be enough data by September for the Government to start planning distribution in October.

"I think what the chief medical officer in Canberra has been saying in terms of October is quite reasonable," she said.

There will be 240 volunteers between 18 and 64 split into two groups.

Dr David says one group of volunteers will get a single dose of the vaccine.

"The other group is going to receive a double dose," she said, adding that the company is not concerned about the risk of side effects.

"Three weeks after today, they're going to have their blood tested to see what sort of response, or immune response, they've had to that vaccine.

"Sometimes with these brand new strains that start circulating, you need a higher dose to get a decent immune response."

A trial on children aged from six months to nine years will start at Adelaide's Women's and Children's Hospital next month."

Religious rites adapted to prevent the spread of flu

A short but interesting article from Reuters on how religious communities in Britain are adapting rites to prevent the spread of flu.

A great learning piece from this article is that decisions are being made locally on measures that will be taken. It's important that local religious leaders, who are often leaders in their community, are able to understand flu prevention measures and make adaptations to their particular service.

Friday, July 17, 2009

New perspective article from NEJM: "The Persistant Legacy of the 1918 Influenza Virus"P

NEJM just published a great perspectives article on recent findings/thinking about the 1918 virus with an easy to understand analogy of the gene segments of the virus:

"To understand what has been happening since 1918, it is helpful to think of influenza viruses not as distinct entities but as eight-member "gene teams" that work together and must sometimes trade away one or more team members to make way for new gene "players" with unique skills. In nature, avian influenza A viruses seem to exist as transient complexes of eight genes that assemble and reassemble promiscuously, if not randomly, in an enormous global avian reservoir. Within this reservoir, avian viruses remain stably adapted to the enteric tracts of hundreds of avian species, single members of which are often simultaneously infected by multiple viruses that engage in prolific gene reassortment. Because of this continual reassortment, a seemingly endless variety of new viruses with potentially new properties are continually being engineered. Indeed, thousands of unique gene constellations making up avian influenza viruses have already been identified; as research continues, the number will undoubtedly grow."

Most interesting to me was this article seems to continue some of the thinking from this weeks PNAS article in challenging some previously held notions,

"But the long-held belief that shifts always cause severe pandemics, whereas drifts lead to more modest increases in seasonal mortality, has been called into question. The effects on mortality of new influenza viruses created by the several genetic mechanisms mentioned above are not easily characterized"

Conclusion was interesting as well:

"If there is good news, it is that successive pandemics and pandemic-like events generally appear to be decreasing in severity over time. This diminution is surely due in part to advances in medicine and public health, but it may also reflect viral evolutionary "choices" that favor optimal transmissibility with minimal pathogenicity — a virus that kills its hosts or sends them to bed is not optimally transmissible. Although we must be prepared to deal with the possibility of a new and clinically severe influenza pandemic caused by an entirely new virus, we must also understand in greater depth, and continue to explore, the determinants and dynamics of the pandemic era in which we live."

Highly recommend the quick read:

Update from WHO: Changes in reporting requirements for pandemic (H1N1) 2009 virus infection

This is an update to the news we reported last week that WHO was no longer asking countries to keep track of individual cases of novel H1N1

"16 JULY 2009 | GENEVA -- As the 2009 pandemic evolves, the data needed for risk assessment, both within affected countries and at the global level, are also changing.

At this point, further spread of the pandemic, within affected countries and to new countries, is considered inevitable.

This assumption is fully backed by experience. The 2009 influenza pandemic has spread internationally with unprecedented speed. 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.

The increasing number of cases in many countries with sustained community transmission is making it extremely difficult, if not impossible, for countries to try and confirm them through laboratory testing. Moreover, the counting of individual cases is now no longer essential in such countries for monitoring either the level or nature of the risk posed by the pandemic virus or to guide implementation of the most appropriate response measures.

Monitoring still needed

This pandemic has been characterized, to date, by the mildness of symptoms in the overwhelming majority of patients, who usually recover, even without medical treatment, within a week of the onset of symptoms. However, there is still an ongoing need in all countries to closely monitor unusual events, such as clusters of cases of severe or fatal pandemic (H1N1) 2009 virus infection, clusters of respiratory illness requiring hospitalization, or unexplained or unusual clinical patterns associated with serious or fatal cases.

Other potential signals of change in the currently prevailing pattern include unexpected, unusual or notable changes in patterns of transmission. Signals to be vigilant for include spikes in rates of absenteeism from schools or workplaces, or a more severe disease pattern, as suggested by, for example, a surge in emergency department visits.

In general, indications that health services are having difficulty coping with cases mean that such systems are under stress but they may also be a signal of increasing cases or a more severe clinical picture.

A strategy that concentrates on the detection, laboratory confirmation and investigation of all cases, including those with mild illness, is extremely resource-intensive. In some countries, this strategy is absorbing most national laboratory and response capacity, leaving little capacity for the monitoring and investigation of severe cases and other exceptional events.

Regular updates on newly affected countries

For all of these reasons, WHO will no longer issue the global tables showing the numbers of confirmed cases for all countries. However, as part of continued efforts to document the global spread of the H1N1 pandemic, regular updates will be provided describing the situation in the newly affected countries. WHO will continue to request that these countries report the first confirmed cases and, as far as feasible, provide weekly aggregated case numbers and descriptive epidemiology of the early cases.

For countries already experiencing community-wide transmission, the focus of surveillance activities will shift to reporting against the established indicators for the monitoring of seasonal influenza activity. Those countries are no longer required to submit regular reports of individual laboratory-confirmed cases to WHO.

Monitoring the virological characteristics of the pandemic virus will be important throughout the pandemic and some countries have well-established laboratory-based surveillance systems in place already for seasonal influenza virus monitoring. Even in countries with limited laboratory capacity, WHO recommends that the initial virological assessment is followed by the testing of at least 10 samples per week in order to confirm that disease activity is due to the pandemic virus and to monitor changes in the virus that may be important for case management and vaccine development.

Updated WHO guidelines for global surveillance reflect in greater detail these recommended changes, in line with reporting requirements set out in the International Health Regulations."

Wednesday, July 15, 2009

Community-based surveillance in the news

Just a small break from H1N1 reporting - the AI Daily Digest had two good descriptions of community-based surveillance in Indonesia and Bangladesh (next post)

July 2009 FAO AIDE News - Operational Research in Indonesia for More Effective Control of Avian Influenza? commenced in Indonesia in July 2008. Funded by USAID and the World Bank, the project aims to develop an evidence base for the selection of effective and feasible control alternatives in backyard poultry in Indonesia. These alternatives include mass voluntary
vaccination against avian influenza (AI), and AI plus Newcastle disease and are implemented in the context of ongoing field Participatory Disease Surveillance and Response (PDSR) activities. The Food and Agriculture Organization (FAO) is supporting local government and the Ministry of Agriculture to implement the control strategies, and providing ongoing support for PDSR field activities. The FAO team works in close collaboration with JSI Deliver (responsible for procurement of vaccine, cold chain equipment and vaccination supplies, and providing logistical support for project implementation) and the International Livestock Research Institute (ILRI) (responsible for the design of ORI HPAI, supervision of data collection and analysis of the research results).

FAO has worked with national and local animal health services to train 64 district officers in
16 districts of West Java, Central Java and Yogyakarta provinces as trainers of community
vaccinators and community mobilisers. In collaboration with JSI, FAO has also trained these
district officers in cold chain and logistics management, and continues to provide technical
assistance, logistics support, monitoring and refresher training to these officers and the
vaccinators they have trained.

Community vaccinators play a key role in the project. Under the supervision of the district
livestock authorities, the vaccinators work at local level to organize the vaccination
campaigns which are carried out four times a year.

Before the campaigns, they discuss the benefits of vaccination with members of their communities and encourage poultry owners to vaccinate their birds. They liaise with local animal health authorities to ascertain the disease status of the villages they are to vaccinate and during the campaigns, they ensure that there is sufficient good quality vaccine for the vaccinations through careful planning and cold chain management. After the campaigns they report the results to their supervisors. Since the first vaccination campaign in July 2008, 1,088 vaccinators have administered approximately 20 million doses of AI vaccine and 10 million doses of Newcastle disease vaccine to village poultry.

In Temanggung district, one of the 16 districts participating in the Operational Research Project, several of the persons selected and trained as community vaccinators are also Village Avian Influenza Coordinators (VAIC). VAIC are community level volunteers trained by the USAID-funded Community-Based Avian Influenza Control Project, implemented by Development Alternatives Inc. The VAICs form part of the passive surveillance network that is so important to the PDSR program. As Community Vaccinators, the VAICs receive training about diseases affecting village poultry, disease control measures, the use of vaccination as a tool in disease control, cold chain management and waste disposal, community mobilisation and the practical aspects of vaccination. This complements their knowledge and experience as VAICs and has enabled them to be more effective in working with PDSR officers, poultry owners and helping to raise awareness of HPAI and its effects on poultry and communities. This increased range of activities complements the PDSR program and contributes to the overall HPAI Control Program.

SMS reporting for avian flu in Bangladesh

From the AI Daily Digest...

July 2009 FAO AIDE News--Bangladesh is conducting active Highly Pathogenic Avian Influenza (HPAI) surveillance in 150 out of 487 sub-districts as part of an USAID funded FAO project. A total of 450 Community Animal Health Workers (CAHW), 50 Additional Veterinary Surgeons (AVS) and 150 Upazilla Livestock Officers (ULOs) are using Short Message Service (SMS) gateway (i.e. method of sending and receiving SMS messages between computers and mobile phones) to collect data and report on disease and death in poultry.

Since October 2008, 21 HPAI outbreaks out of a total of 35 have been detected through
this active surveillance programme. The SMS reporting structure is rather simple: at the end of the working day, each CAHW sends a SMS message with the total number of all investigated poultry (chickens, ducks and other birds) and their health status (the number of sick and dead birds) to the SMS gateway system. This data is used to; A) monitor trends in disease and mortality in poultry, and B) monitor who is working that day. Additionally, CAHWs send flash reports by SMS on suspected outbreaks according to a case definition. The system then automatically contacts the ULO in the same area by SMS, who initiates an investigation by sending an AVS or visits the suspect outbreaks him/herself. After the investigation, the ULOs and AVS send a SMS message to the gateway server to declare the suspect outbreak as negative or report that it may require further (diagnostic) tests. Initially a Gateway server receiving these messages was located at the Department of Livestock Services in Dhaka, the capital. Currently the system is internet based.

Specialised staff monitor the change in mortality and morbidity rates and perform spatial and
temporal analysis against concurrent HPAI outbreaks and monitor the number of suspect cases and the results of the ULOs and AVS investigations. The result of the analysis is submitted to the Chief Veterinary Officer, used in workshops to sensitise staff and farmers, donor meetings as well as in periodic project reporting. This real-time reporting using SMS has been contributing to effective HPAI outbreak response and control. The key to the success may be its simple approach and clearly defined work-sharing by using familiar tools (mobile phones).

Tuesday, July 14, 2009

1918 pandemic flu virus may have circulated in pigs and humans prior to pandemic

Previous research on the 1918 pandemic virus has come to the conclusion that it may have jumped directly from birds to humans.

A new paper published in PNAS this week suggests a different path,

"Our results indicate that genetic components of the 1918 H1N1 pandemic virus circulated in mammalian hosts, i.e., swine and humans, as early as 1911 and was not likely to be a recently
introduced avian virus. Phylogenetic relationships suggest that the A/Brevig Mission/1/1918 virus (BM/1918) was generated by reassortment between mammalian viruses and a previously circulating human strain, either in swine or, possibly, in humans. Furthermore, seasonal and classic swine H1N1 viruses were not derived directly from BM/1918, but their precursors co-circulated during the pandemic. Mean estimates of the time of most recent common ancestor
also suggest that the H2N2 and H3N2 pandemic strains may have been generated through reassortment events in unknown mammalian hosts and involved multiple avian viruses preceding pandemic recognition. The possible generation of pandemic strains through a series of reassortment events in mammals over a period of years before pandemic recognition suggests that appropriate surveillance strategies for detection of precursor viruses may abort
future pandemics."

It's not an easy read, but worth trying:

WHO makes vaccine reccomendations

An advisory group to WHO, Strategic Advisory Group of Experts (SAGE) on Immunization, met last week on recommendations related to vaccine for the pandemic (H1N1).

The groups recommendations included:

Health-care workers should be the first priority for vaccine
2. Because there will be limited vaccine availability, vaccine makers should consider using adjuvants
3. Since there will be limited evaluations of vaccine effectiveness and safety prior to use, countries should prioritize sharing this information so changes to the vaccine can be made rapidly.

Monday, July 13, 2009

Novel H1N1 vaccine production problems

"The World Health Organization says so far the yield for egg-based production is half or less what manufacturers get when they make vaccine to protect against seasonal H1N1 viruses."

That statement is very problematic for novel H1N1 vaccine production. Under the best case scenario the world was likely to see pandemic vaccine available to richer nations that had pre-ordered the vaccine in November. There are a number of uncertainties with production of the pandemic vaccine in order to make projections about availability - How many doses will be required? Can an adjuvant be used?

The article from Helen Branswell outlines a few scenarios:

Best case scenario: if the yield was equal to what we see in seasonal flu, the vaccine is made using the lowest possible effective dose and if countries only order 1 dose per person, then manufacturers might fill vaccine orders by November and could then possibly begin production on vaccine for other countries.

However, if the yield is half that of seasonal flu vaccine production then the best case scenario would be mid-January before all existing orders are filled.

If the yield is low and countries demand two shots per citizen, then it might be next June before orders are filled.

Read the whole article here:

Thursday, July 9, 2009

2009 Flu Prevention PSA Contest!

2009 Flu Prevention PSA Contest Rules

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Buenos Aires tries to shut down for the weekend

One situation we are watching out for is outbreaks of novel H1N1 that seem to be causing more severe disease, higher proportions of death, social unrest, etc. As WHO notes, pandemic severity is not just about the virus itself, but also about the vulnerabilities of the population and how prepared a community is.

So, we are watching Argentina carefully, as spread of H1N1 seems to be causing more disruption and strain on health services as the virus spreads in the densely populated urban slums surrounding Buenos Aires. Also, underlying vulnerabilities could possibly be causing more deaths as Argentina now is third behind US and Mexico in number of deaths. Too soon to tell, but these are the events we want to keep an eye on to get an idea of how H1N1 might play out in certain communities.

The government has closed theaters since last Monday and now they are encouraging a people to stay home for a long weekend. Thursday is a national holiday, and many government institutions will close Friday and Monday (

We are likely to continue to see governments respond with sporadic social distancing measures in areas where the spread novel H1N1 doesn't feel like a moderate pandemic in the local community.

WHO asks infected countries to stop testing for H1N1

"GENEVA (AFP) — The World Health Organisation said Tuesday it would ask countries with large caseloads of swine flu to move away from laboratory testing of individual cases towards collecting more macro-trends of the disease.

"In the next few days, the WHO will be issuing updated surveillance recommendations to countries," said Keiji Fukuda, interim assistant director-general of the WHO.
With some 137 countries and territories having reported over 98,000 cases including over 440 deaths, Fukuda said "we are now at a place in which changing the surveillance approach makes a lot of sense for many countries".

In countries where many cases have been reported, it is now necessary to move towards looking for "larger national indicators of the disease" including following influenza-like illnesses or pneumonia cases.

In countries where cases have yet to be reported, Fukuda said the WHO would still recommend that individual suspect cases be tested.

He added that all countries would also be asked to test cases that appear to be unusual, in order for changes in epidemiology of the virus, which has been renamed pandemic (H1N1) 2009 by the WHO, to be recorded.

"Because the number of cases have increased in so many countries it is very hard to keep up and so we need to move towards these kinds of indicators to keep following on with the trend of the pandemic," said Fukuda, noting that a shift would also ease pressure on laboratories."

WHO statement on Tamiflu resistance

"Viruses resistant to oseltamivir (Tamiflu) identified

8 JULY 2009 | GENEVA -- WHO has been informed by health authorities in Denmark, Japan and the Special Administrative Region of Hong Kong, China of the appearance of H1N1 viruses which are resistant to the antiviral drug oseltamivir (known as Tamiflu) based on laboratory testing.

These viruses were found in three patients who did not have severe disease and all have recovered. Investigations have not found the resistant virus in the close contacts of these three people. The viruses, while resistant to oseltamivir, remain sensitive to zanamivir.

Close to 1000 pandemic H1N1 viruses have been evaluated by the laboratories in the Global Influenza Surveillance Network for antiviral drug resistance. All other viruses have been shown sensitive to both oseltamivir and zanamivir. WHO and its partners will continue to conduct ongoing monitoring of influenza viruses for antiviral drug resistance.

Therefore, based on current information, these instances of drug resistance appear to represent sporadic cases of resistance. At this time, there is no evidence to indicate the development of widespread antiviral resistance among pandemic H1N1 viruses. Based on this risk assessment, there are no changes in WHO's clinical treatment guidance. Antiviral drugs remain a key component of the public health response when used as recommended."

Monday, July 6, 2009

New Materials Added to the H2P website

The WHO/UNICEF Behavioral Interventions for Reducing the Transmission and Impact of Influenza A (H1N1) Virus: A Framework for Communication Strategies - June 2009

Click Here!

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3 instances of tamiflu resistance reported

Three instances of tamiflu resistance has been reported in novel H1N1 cases in the last week.

1) Denmark - 1 case of resistance but the patient recovered and may not have infected anyone else

2) Japan - Also an isolated case of resistance

3) Hong Kong - This cases was slightly different than the first two isolated cases

"Public health authorities in Hong Kong announced Friday they have found a case of Tamiflu resistance in a woman who hadn't taken the drug. That means she was infected with swine flu viruses that were already resistant to Tamiflu"

Though it's slightly more worrying to find a resistant strain spreading, it would be impossible not to see resistance pop up occasionally. So, too early to worry but something to keep an eye on

WHO update

July 6th, 2009 - 94,512 cases in 429 countries