Influenza Virus Mashup

Via Canoe.ca, a report from The Canadian Press by Helen Branswell: Feds expecting millions of unused H1N1 vaccines. Excerpt:

Up until now, Canadian authorities have steadfastly refused to discuss what they might do with the excess vaccine, saying they wanted to ensure Canada’s needs were being met before crossing that bridge. 

That left the country in the unusual position of being odd-man-out of an international agreement brokered by U.S. President Barack Obama’s White House to donate vaccine to the World Health Organization. 

The U.S. and the governments of 10 other vaccine-purchasing countries promised to give the WHO 10 per cent of their supplies on an ongoing basis for redistribution to developing countries that have been unable to buy pandemic vaccine. 

However, vaccine production problems have kept at least some of those countries from fulfilling their promises to date. 

The WHO, which has also been promised more than 150 million doses by four vaccine manufacturers, hopes to start shipping vaccine to recipient countries soon. 

The Canadian spokesperson said it’s not yet clear what form Canada’s donation would take. 

“We’re looking at our options currently,” the source said. “Within a couple of weeks we should come to some sort of resolution of where we’re going with our international … contributions.” 

There are a couple of options. The federal government could give the WHO a financial contribution, something the agency needs to cover the costs of distributing the vaccine. Or it could divert some of the country’s unneeded vaccine doses to the Geneva-based agency.

Via La Prensa.com.ni: Minsa debe ser cuidadoso en aplicación de vacuna. [Ministry of Health should be careful in application of vaccine] Excerpt, with my translation:

Expertos en epidemiología señalaron que es un logro que la vacuna contra la influenza humana pueda llegar al país en diciembre, pero a la vez indicaron que el Ministerio de Salud (Minsa) debe tener una clara estrategia, de cómo aplicarla, para evitar gastar el biológico en personas que pueden esperar por su inmunización o crear falsas expectativas en la población de que todos necesitan la vacuna.
  

Epidemiologists have said it’s good that the H1N1 vaccine could arrive in December, but they warn that the Ministry of Health must have a clear strategy on how to apply it, to avoid wasting the vqccine on persons who can wait for their immunization, or creating false expectations in the public that everyone needs it.

El epidemiólogo Leonel Argüello indicó, por ejemplo, que es correcto priorizar al personal de Salud, pero en particular a los doctores y personal de enfermería en contacto directo con los pacientes.
  

Epidemiologist Leonel Argüello said, for example, that it’s correct to make Health personnel a priority, but in particular the doctors and infirmary staff in direct contact with patients.

El personal médico administrativo o quienes laboren en otras áreas pueden esperar el próximo lote de vacuna. El miércoles pasado el titular del Minsa, Guillermo González, informó que están a la espera de 110 mil dosis.

Administrative medical personnel, or those working in other areas, can wait for the next shipment of vaccine. On Wednesday, Health Minister Guillermo González said he is expecting 110,000 doses.

Via Ukrainian Journal.com: Rada fails to override veto of flu bill. Evidently the outbreak has become even more political. Excerpt:

Parliament on Thursday failed to override a presidential veto of a bill that would have forced the National Bank of Ukraine to print one billion hryvnias to fight the current flu epidemic. 

The Regions Party, the largest opposition group, rejected it. 

The development is a major setback for Prime Minister Yulia Tymoshenko, whose government has been facing a major shortage of funds, and comes despite her personal appeal to lawmakers. 

It may be signaling Tymoshenko’s weakening political clout less than two months before the next presidential election as rivals accuse her government of poor budget management. 

“The attempt to force the National bank to spend non-existing resources is a gross violation of fundamental basics of the country’s financial system,” Oleksandr Shlapak, the top economic advisor of President Viktor Yushchenko, said. 

“It is turning the National bank into a money-printing tool and threatens all people with inflation hikes.” 

Tymoshenko argued the money was needed to prepare for the second wave of flu after many Ukrainian regions have gone through a flu epidemic earlier this month. 

She complained on Thursday that the government’s anti-flu effort will now come to a standstill. 

“Today Parliament has disarmed me as the premier in the fight for preparing Ukraine for next waves of the flu epidemic,” Tymoshenko said, adding that she was surprised the Regions Party had rejected the bill. 

“I was completely confused when they had failed to vote,” Tymoshenko said. 

Yushchenko vetoed the bill on November 16, suggesting the government must cut other spending or borrow money from commercial banks instead of demanding the cash from the NBU. 

Meanwhile, there were also speculations of alleged corruption with the way the government has been spending the money that had been aimed at fighting flu. 

Tymoshenko claimed the government had spent 500 million hryvnias to fight the epidemic since over the past three weeks and said more money – at least one billion hryvnias – was required to continue the effort. 

But new data cited by the presidential office and by the opposition Regions Party show only 60 million hryvnias has been actually spent with the rest of 440 million hryvnias being unaccounted for. 

“Where is the rest of the money? No one knows,” Hanna Herman, a senior member of the Regions Party, said.

Via CTV Olympics.ca: Extra cops, volunteers on hand should flu hit Games. Excerpt:

An extra 750 police officers will be standing by for the 2010 Winter Games in case the H1N1 flu pandemic thins their ranks. The officers are in addition to the 6,000 being deployed at the Games. 

They’ll remain at home but be ready to go at a moment’s notice, said RCMP Assistant Commissioner Bud Mercer, the head of security for the Games. 

“We would bring them in on short notice for a couple of reasons,” he said in an interview Thursday. 

“If the threat level changes and if we had a requirement because of illness to bring in extra staff, so that’s all part of our contingency planning.” 

Mercer said the RCMP-led Integrated Security Unit has always had concerns about flu, given the close quarters their officers will be keeping during the Games, including on cruise ships. 

“We have medical professionals (and) we have isolation areas that are planned in both the accommodation vessels and up in Whistler,” he said. 

All of their officers will also get an educational package when they arrive for the Games on flu prevention tips and when to seek help. 

Given that the Games are being held during regular flu season, the possibility for seasonal flu to have an impact has always been on the minds of Olympics planners. 

The emergence of the H1N1 pandemic this year just made the potential risk from flu more apparent, said Dr. Mike Wilkinson, the director of medical services for the Olympic organizing committee.

Via France 24, an AFP report: Mutated strain of virus claims two lives in France. Excerpt:

Swine flu virus mutations are spreading in Europe, French health officials said Friday as the World Health Organisation reported a leap in deaths from the disease by more than 1,000 in a week.
   

Two patients who were infected by a mutation that was also recently detected in Norway have died in France, the government’s Health Surveillance Institute (InVS) said in a statement.
   

“This mutation could increase the ability of the virus to affect the respiratory tracts and, in particular, the lung tissue,” said a statement from InVS.  

“For one of these patients, this mutation was accompanied by another mutation known to confer resistance to oseltamivir,” it added, referring to the main drug being used to treat swine flu, under the brand name Tamiflu.
   

The case was the first drug-resistant strain found in France among the 1,200 strains experts have analysed here, the InVS said, adding that “the effectiveness of vaccines currently available is not being questioned.”
   

The two patients were not related and had been hospitalised in two different cities in France, it said.

In this connection, Dr. Vincent Racaniello at virology blog recently posted a discussion of this mutation. But he’s not too worried: the mutation seems to inhibit transmission. 

(Fri, 27 Nov 2009 17:22:00 +0000)

# 4089

Although the numbers reported to, and by the WHO (World Health Organization) are - by their own admission - incomplete and represent a significant undercount of cases, this week the WHO is reporting an increase of more than 1000 deaths from the H1N1 virus.

This makes the largest single-week uptick thus far in the pandemic and has garnered a good deal of press attention this morning. 

Here is how the BBC is reporting the story, including a quote from the WHO’s Keiji Fukuda on the `Norwegian’ mutations.

Jump in number of global swine flu deaths

 

The global number of swine flu deaths has jumped by more than 1,000 in a week, latest figures from the World Health Organization (WHO) show.

 

At least 7,826 people are now known to have died following infection with the H1N1 virus since it first emerged in Mexico in April.

 

Europe saw an 85% increase in the week, with the total number of deaths rising from at least 350 to at least 650.

 

<SNIP>

 

Keiji Fukuda, WHO’s special adviser on pandemic influenza, said: “The question is whether these mutations suggest that there is a fundamental change going on in viruses out there - whether there’s a turn for the worse in terms of severity.

 

“The answer right now is that we are not sure.”

Some excerpts from WHO today’s update, including the latest on the mutations in their virological update.

Pandemic (H1N1) 2009 - update 76

Weekly update

27 November 2009 — As of 22 November 2009, worldwide more than 207 countries and overseas territories or communities have reported laboratory confirmed cases of pandemic influenza H1N1 2009, including over 7820 deaths.

 

As many countries have stopped counting individual cases, particularly of milder illness, the case count is likely to be significantly lower than the actual number of cases that have occurred.

 

<SNIP>

 

 

Situation update:

In temperate regions* of the northern hemisphere, the early arriving winter influenza season continues to be intense across parts of North America and much of Europe. In North America, the Caribbean islands and a limited number of European countries there are signs that disease activity peaked.

 

In the United States and Canada, influenza transmission remains very active and geographically widespread. In the United States, disease activity appears to have peaked in all areas of the country. In Canada, influenza activity remains similar but number of hospitalisations and deaths is increasing. Most countries in the Caribbean have ILI and SARI levels coming down.

 

In Europe, widespread and increasing transmission of pandemic influenza virus was observed across much of the continent and most countries that were not yet experiencing elevated ILI activity in the last few weeks, have seen a rapid increase in ILI. Very high activity is seen in Sweden, Norway, Moldova and Italy. Over 99% of subtyped influenza A viruses in Europe were pandemic H1N1 2009. Impact on health care services is severe in Albania and Moldova. Some countries seem to have peaked already: Belgium, Bulgaria, Belarus, Ireland, Luxemburg, Norway, Serbia, Ukraine and Iceland.

 

(Continue . . . )

 

 

Pandemic (H1N1) 2009 - update 76

Weekly update (more data on virological surveillance)

27 November 2009 — The Global Influenza Surveillance Network (GISN) continues monitoring the global circulation of influenza viruses, including pandemic, seasonal and other influenza viruses infecting, or with the potential to infect, humans including seasonal influenza.

 

<SNIP>

 

A virus mutation at position 222 of the amino acid sequence of the haemagglutinin protein of the pandemic virus was recently reported in a few viruses from Norway. The mutation is D222G (aspartic acid to glycine), which, according to a public accessible gene sequence database “GenBank”, has also been detected sporadically in viruses from several other countries since April 2009.

 

This change in the virus has been found in mild as well as severe cases. WHO, through its Global Influenza Surveillance Network (GISN) is monitoring virus mutations that are of potential public health importance.

 

Systematic surveillance conducted by the Global Influenza Surveillance Network (GISN) including WHO Collaborating Centres (WHOCCs) for reference and research on influenza, continues to detect sporadic incidents of H1N1 pandemic viruses that show resistance to the antiviral oseltamivir. To date, 75 oseltamivir resistant pandemic H1N1 influenza viruses have been detected and characterized worldwide. All of these viruses show the same H275Y mutation. All these viruses remain sensitive to zanamivir. Worldwide, more than 10,000 clinical specimens (samples and isolates) of the pandemic H1N1 virus have been tested and found to be sensitive to oseltamivir.

 

All pandemic H1N1 2009 influenza viruses analysed to date were antigenically and genetically closely related to the vaccine virus A/California/7/2009.

Virology data update

Download update (.pdf)

(Fri, 27 Nov 2009 16:42:00 +0000)

# 4088

Although FluTrackers had word of an 89th confirmed human H5N1 infection out of Egypt a couple of days ago, the WHO has posted an official update today, along with a new table of cases by country.

It should be noted that Indonesia stopped reporting H5N1 cases nearly a year ago, after a couple of years of less than stellar reporting. 

Numbers from other countries, where surveillance and reporting may be less than optimal, probably don’t reflect the true picture either.

Egypt has seen 38 human infections this year, a nearly 500% increase over 2008.   Remarkably, however, the fatality rate has dropped to just about 10% in 2009.

The H5N1 virus remains endemic in poultry in Egypt, despite attempts to eradicate the virus through culling, vaccination, and public education.

Avian influenza - situation in Egypt - update 25

27 November 2009 — The Ministry of Health of Egypt has reported a new confirmed human case of avian influenza A(H5N1).

 

The case is a 3 year-old male from Minia Governorate. His symptoms started on 21 November 2009.

 

He was admitted to hospital on 22 November and his condition is stable. Investigations into the source of infection indicated that the case had close contact with dead and/or sick poultry.

 

The cases were confirmed by the Egyptian Central Public Health Laboratories.

 

Of the 89 cases confirmed to date in Egypt, 27 have been fatal.

A few of the recent reports of H5N1 in poultry, carried on the SAIDR website, include:

• RECENT CASES:
• Date of result: 24 November 2009
  Date of sampling: 23 November 2009
  Governorate: Fayoum
  District: Senouris
  Village: Sanhour el Baharia
  Type of rearing: Household
  Species: Chicken
  Number of birds: 40
  Vaccination status: Unvaccinated
  Purpose of sampling: PDS
  Comments: The village is 500 meters from Lake Qaroun, and the domestic poultry has regular contact with migratory ducks. The outbreak started six months ago and was still circulating among the households around the time of sampling.
  Three weeks ago, the household had sudden deaths with 100 percent mortality associated with cyanosis in comb and wattles for 200 layer chickens. After cleaning and decontamination, the household introduced new 40 young grower chickens bought from a nursery farm via peddler: Three days after introducing new chickens, mortalities started again with cyanosis in comb and wattles. The source of the outbreak is unknown. The newly purchased chickens may have been bought infected from the nursery farm, or may have contracted the infection at the household after contact with contaminated matter from the layer chickens that died in the earlier episode.

• ———————————————————-

• Date of result: 24 November 2009
  Date of sampling: 23 November 2009
  Governorate: Fayoum
  District: Etsa
  Village: Ahrit
  Type of rearing: Household
  Species: Mixed (chickens, ducks)
  Number of birds: 14
  Vaccination status: Unvaccinated
  Purpose of sampling: PDS
• ———————————————————-

• Date of result: 18 November 2009
  Date of sampling: 17 November 2009
  Governorate: Dakahlia
  District: Tomay el Amdid
  Village: El Fath el Gedida
  Type of rearing: Household
  Species: Mixed (chickens, ducks, geese)
  Number of birds: 37
  Vaccination status: Unvaccinated
  Purpose of sampling: PDS
  Comments: The outbreak exhibits progressive mortality, clear signs of cyanosis of the head and wattles in chicken, and nervous manifestations in ducks in many households in the village. Signs of an outbreak were first observed two weeks earlier. There was a massive spread of the infection in majority of houses. The source of infection was ducks provided as a gift from Kom el Khalig village, Mansoura district, Dakahlia.

(Fri, 27 Nov 2009 13:35:00 +0000)

# 4087

You don’t have to be an epidemiologist to know that schools are hotbeds of respiratory illness each winter, and that kids are very efficient spreaders of viruses. 

 

It was for that reason that in early pandemic planning – particularly when considering a high mortality virus such as H5N1 – school closures for up to 12 weeks were prominently featured.

Once it was established that the novel H1N1 virus was nowhere near as virulent as bird flu, social policy in most countries was to try to keep schools open as much as possible.

While it has been assumed that closing schools would help curb the spread of a pandemic virus, until now there has been very little research that quantifies the benefit. 

Something that we really ought to know before the next pandemic virus emerges.

Today we get a study, published in the open access journal BMC Infectious Diseases, that finds that forced school closures can reduce secondary infections by roughly 20%.

This study makes the assumption that social mixing and interaction during a pandemic induced school closure would mimic social contacts currently seen during routine weekend and holiday school closures.  

Their estimates, therefore, are probably conservative.  Social distancing beyond just the closure of schools would likely be taking place, and large social gatherings probably discouraged. 

School closings have costs, both economic and social, and those have to be taken into account as well.  Forced school closings are not something to be done lightly.

During a severe pandemic wave, however, this study makes a pretty good case for the closing of schools to significantly lower the attack rate.

Estimating the impact of school closure on social mixing behaviour and the transmission of close contact infections in eight European countries

 

Niel Hens , Girma Minalu Ayele , Nele Goeyvaerts , Marc Aerts , Joel Mossong , John W Edmunds  and Philippe Beutels

 

BMC Infectious Diseases 2009, 9:187doi:10.1186/1471-2334-9-187

Published:
27 November 2009

Background

Mathematical modelling of infectious disease is increasingly used to help guide public health policy. As directly transmitted infections, such as influenza and tuberculosis, require contact between individuals, knowledge about contact patterns is a necessary pre-requisite of accurate model predictions. Of particular interest is the potential impact of school closure as a means of controlling pandemic influenza (and potentially other pathogens).

Methods

This paper uses a population-based prospective survey of mixing patterns in eight European countries to study the relative change in the basic reproduction number (R0 - the average number of secondary cases from a typical primary case in a fully susceptible population) on weekdays versus weekends and during regular versus holiday periods. The relative change in R0 during holiday periods and weekends gives an indication of the impact collective school closures (and prophylactic absenteeism) may have during a pandemic.

Results

Social contact patterns differ substantially when comparing weekdays to the weekend and regular to holiday periods mainly due to the reduction in work and/or school contacts. For most countries the basic reproduction number decreases from the week to weekends and regular to holiday periods by about 21% and 17%, respectively. However for other countries no significant decrease was observed.

Conclusions

We use a large-scale social contact survey in eight different European countries to gain insights in the relative change in the basic reproduction number on weekdays versus weekends and during regular versus holiday periods. The resulting estimates indicate that school closure can have a substantial impact on the spread of a newly emerging infectious disease that is transmitted via close (non sexual) contacts.

The complete article is available as a provisional PDF. The fully formatted PDF and HTML versions are in production.

(Fri, 27 Nov 2009 12:44:00 +0000)

# 4086

Fergus Walsh, the BBC’s medical correspondent, has been doing a terrific job for months covering the H1N pandemic in his blog, Fergus on Flu.  

Today he addresses the state of the  UK’s pandemic vaccination program, and a call for a more aggressive roll out of the vaccine.  He also updates us on the latest information out of the DOH.

GPs urged to go ‘full throttle’ in accelerating vaccination

 

Fergus Walsh | 08:57 UK time, Friday, 27 November 2009

Around one million people in England are now estimated to have been vaccinated against swine flu.

 

Across the UK, 10 million doses of the vaccine have been distributed to GPs and hospitals.

 

That one million figure refers to those in the initial priority groups, such as those with chronic asthma, heart and other organ disease, immune problems and pregnant women.

 

Clearly there is still a long way to go. There are nine million people in the priority groups in England, and around 11.5 million across the UK. Then add to that the three million or more under fives who will be offered the jab after that.

 

Professor David Salisbury, Director of Immunisation at the Department of Health said he hoped GPs would now be able to accelerate the vaccination process:

 

(Continue . . . )

Fergus has a variety of graphs today showing the pandemic’s impact on the UK.  Among them is this one, showing the weekly `laboratory confirmed’ H1N1 fatalities.  

These numbers are, no doubt, a serious undercount. 

And as Fergus explains in his blog, the official estimate of cases in the UK may be off by a factor of 10 or more.

The latest weekly estimate for England was 46,000 cases of swine flu with a cumulative total of 760,000. But since the Health Protection Agency now reckons that one in five children may have had swine flu, that cumulative figure maybe just a tenth of the real total (and that’s just my guess).

Follow the link to read the blog in its entirety.