ECDC Influenza Virus Characterization

# 6784

 

The only constant with influenza viruses is their ability to change over time. Since immune systems can learn to recognize and defeat previously seen viral infections, they would soon run out of susceptible hosts if they could not continually evolve.

 

Most of the time, these changes are incremental, and are due to a process called Antigenic drift. Drift comes about due to replication errors that are common with single-strand RNA viruses.

 

Over time these minor changes can accumulate to the point that previously infected immune systems will fail to recognize it, giving the virus a fresh supply of hosts. 

 

NIAID has a nice 3-minute video illustrating the process, which you can view on their Youtube Channel or in the box below.

 

 

 

So, while we talk about seasonal A/H3N2 or A/H1N109 as if they are single entities, in truth, there are a good many minor variations on each theme circulating around the world.

 

Within each strain, we can see numerous `clades’, or genetically distinct groups.  We watch the formation, and progress of these clades carefully, since they may eventually require a change in the flu vaccine’s formulation.

 

Roughly once a month the ECDC releases an influenza virus characterization report, providing laboratory analysis of recently collected flu virus samples across Europe. Collection dates only extend through week 39, but this latest ECDC report indicates continued diversity among the viruses in circulation.

 

The vast majority of flu viruses identified (68%) were of the type A/H3N2. Relatively few A/H1N1 viruses were collected.

 

Among the influenza B viruses received, samples were pretty evenly divided between the Victoria lineage (included in last year’s vaccine) and the Yamagata lineage (part of this year’s vaccine).

 

 

Here’s the link to their report, and the abstract.

 

Influenza virus characterisation - Summary Europe, November 2012

Surveillance reports - 14 Dec 2012

Available as PDF in the following languages:

 

ABSTRACT

During the 2011/2012 season, A(H1N1)pdm09, A(H3N2) and B/Victoria and B/Yamagata lineage influenza viruses, with collection dates between 1 January and 30 September 2012 (weeks 1–39), have been detected in ECDC-affiliated countries.

• Type A viruses predominated over type B.
• A(H3N2) viruses predominated over A(H1N1)pdm09 viruses.
• A(H1N1)pdm09 viruses continued to show genetic drift from the vaccine virus, A/California/07/2009, but the vast majority remained antigenically similar to it.
• Antigenic drift of A(H3N2) viruses compared to the A/Perth/16/2209 vaccine virus resulted in a recommendation to change to an A/Victoria/361/2011-like component for the 2012/2013 influenza season.
• B/Victoria lineage viruses fell within the B/Brisbane/60/2008 genetic clade and were antigenically similar to reference cell-propagated viruses of the B/Brisbane/60/2008 genetic clade.
• Recent B/Yamagata-lineage viruses fell into two genetic clades in approximately equal proportions: clade 3 represented by the recommended vaccine component for the 2012/2013 influenza season, B/Wisconsin/1/2010, and clade 2 represented by B/Estonia/55669/2012. Viruses in each clade are antigenically distinguishable.

 

 

The split between clade 2 and clade 3 of the Yamagata B virus lineage bears watching, and A/H3N2 shows the most variety with samples falling into 5 distinct genetic groups.

 

The good news, despite this growing diversity among flu viruses, is that the majority of those collected in Europe through week 39 still appear antigenically similar to this year’s vaccine strains.

»» Read More

Barnstorming Avian Flu Viruses?

Photo Credit – FAO

 

# 6782

 

 

My thanks to Helen Branswell this morning for tweeting the link to a new study that suggests that avian influenza viruses can be spread over considerable distance by the wind.  

Long time readers will recall we’ve visited this question a couple of times before. We’ll review those, but first, the new study which looked at the extensive outbreak of H7N7 in the Netherlands in 2003.

 

From the Journal of Infectious Diseases (the full study is behind a pay wall), we get a fair idea of their findings via the Abstract.

 

Genetic data provide evidence for wind-mediated transmission of highly pathogenic avian influenza

Rolf J.F. Ypma1, Marcel Jonges, Arnaud Bataille, Arjan Stegeman3, Guus Koch4, Michiel van Boven1, Marion Koopmans1,W. Marijn van Ballegooijen1 and Jacco Wallinga

Outbreaks of highly pathogenic avian influenza in poultry can cause severe economic damage, and represent a public health threat. Development of efficient containment measures requires an understanding of how these influenza viruses are transmitted from one farm to the next. However, the actual mechanisms of inter-farm transmission are largely unknown.

 

Dispersal of infectious material by wind has been suggested, but never demonstrated, as a possible cause of transmission between farms. Here we provide statistical evidence that the direction of spread of avian influenza A(H7N7) is correlated with the direction of wind at date of infection.

 

We find the direction of spread by reconstructing the transmission tree for a large outbreak in the Netherlands in 2003, using detailed genetic and epidemiological data. We conservatively estimate the contribution of a possible wind-mediated mechanism to the total amount of spread during this outbreak to be around 18%.

 

Although it occurred nearly 10 years ago, this outbreak of H7N7 continues to interest scientists, as it represents the largest cluster of human infection by H7 flu virus we’ve seen. 

 

This report from the December 2005 issue of the Eurosurveillance Journal.

 

Human-to-human transmission of avian influenza A/H7N7, The Netherlands, 2003

M Du Ry van Beest Holle, A Meijer, M Koopmans³ CM de Jager, EEHM van de Kamp, B Wilbrink, MAE. Conyn-van Spaendonck, A Bosman

An outbreak of highly pathogenic avian influenza A virus subtype H7N7 began in poultry farms in the Netherlands in 2003. Virus infection was detected by RT-PCR in 86 poultry workers and three household contacts of PCR-positive poultry workers, mainly associated with conjunctivitis.

 

More than 30 million birds residing on more than 1,000 farms were culled to control the outbreak.

 

One person - a veterinarian who visited an infected farm – died a week later of respiratory failure. The rest of the symptomatic cases were relatively mild.

 

Normally, when avian flu manages to spread among local farms, we think of transport mechanisms like the farm-to-farm movement of infected birds or eggs, or of contaminated or infected personnel or equipment, or even a bird or small mammal vector.

 

The idea that the virus might be blown (likely carried on dust, or some other particulate) – while unproven -  has come up before.

 

Back in January of 2008 I wrote a blog called The Virus My Friend, Is Blowin' In The Wind where I cast a dubious eye upon claims by the Indian Government that the bird flu virus (H5N1) was being blown by the wind across the border from neighboring Bangladesh, and was infecting hapless Indian Poultry.

 

It wasn’t impossible, of course.  And I went into some of the other types of pathogens (mostly fungi and bacteria) that are known to travel in the wind.

 

Then in May of 2010 (see Viruses Blowin’ In The Wind?) we saw a report in the journal Environmental Health Perspectives, that suggested that it was possible for H5N1 (or any Influenza A virus) to be transported across long distances in the air.

 

Although researchers demonstrated influenza RNA could be detected in ambient air samplings, they didn’t establish that the virus remained viable over long distances.

 

But we have seen studies indicating that the H5N1 virus can – under the right environmental conditions – remain viable for hours or even days in the environment (see EID Journal: Persistence Of H5N1 In Soil and H5N1: Hiding In Plain Sight)

 

Lending at least a little credence to the idea that they might survive on the wind long enough to infect downwind farms.

 

It has also been suggested that dried chicken droppings (`poultry dust’) may also serve to spread the virus, and Indonesian authorities have mentioned this as a possible vector (see Indonesian Updates And Vector Concerns).

 

Hong Kong authorities also mentioned the possibility (of at least short-range windborne transmission) in a highly detailed epidemiological report issued by the University of Hong Kong, on the outbreak of H5N1 on a solitary chicken farm in the New Territories in 2008.

 

Epidemiology Report of the Highly Pathogenic Avian Influenza H5N1 Outbreak in December 2008 in a Chicken Farm in Ha Tsuen, New Territories

 

Excerpt

(ii) The strong winds and gust from the north and north-east from 4 to 6 December 2008 could have deposited potentially contaminated dust and leaves from the trees into the nearby shed no. 17 via its north opening. These contaminated materials could then have gathered at the corner of the shed where the initial high mortality in poultry occurred.

 

 

So . . . while none of this is a slam dunk proving wind-borne transmission of viable avian (or any other flu) viruses, we have at least some credible evidence that suggests it may have happened.

 

How big of a factor this plays in the spread of viruses remains to be seen.

 

But it does provide investigators another avenue of epidemiological query when multiple farms in close proximity are infected with avian influenza.

 

 

Note: `Barnstorming’ is an Americanism that some of my readers may not be familiar with.  It refers to the early days of aviation when pilots would fly to rural areas, land in farmer’s fields, and sell rides, or put on an air show for the locals.

»» Read More

Uganda MOH: Update On Marburg Outbreak

  Credit Wikipedia

 

 

# 6675

 

The Ugandan Minister of Health, Dr. Christine Ondoa, has issued the following update on the Marburg virus outbreak which has been ongoing in that nation since October 19th.

 

The major points are that there are now 8 deaths confirmed, and that cases have now been confirmed in three districts; Kabale , Ibanda, and Mbarara.

 

This from the Ugandan Media Centre.

 

 

PRESS STATEMENT ON THE UPDATE OF MARBURG OUTBREAK

October 29th 2012

Today on behalf of the Ministry of Health, I take this opportunity to welcome you all to this press briefing organized to update you on the outbreak of Marburg in the country. You will recall that we declared an outbreak of this highly infectious disease on October 19th and since then the Ministry of Health and its partners have undertaken a number of interventions to control the spread of the disease.

 
I wish to inform you that cases are now reported in the neighbouring districts of Ibanda and Mbarara. However, I want to assure you that the Ministry of Health and its partners are on the ground in the mentioned districts to contain the spread and manage the identified cases.

 

To date, the death toll of both the probable and confirmed cases stands at eight, with the latest being a case that died at the isolation facility at Rushoroza Health Centre III on October 27th (Saturday). The case that was referred from Ibanda Hospital – Ibanda to Mbarara Regional Referral Hospital died on October 24th.

 

I wish to clarify that since the onset of the outbreak, we have collected a total of 45 samples of which nine were confirmed positive; five in Kabale, two in Kampala and two from Ibanda.

 

Working closely with the US Center for Disease Control and Prevention (CDC), we have set up a field diagnostic laboratory at Kabale Regional Referral Hospital. All samples from the affected neighbouring districts will hence be taken to this laboratory for quick diagnostics. This will shorten the time when we get results to three hours from the original 24 hours due to distance. Further serological testing will be undertaken at the Uganda Virus Research Institute (UVRI).

 

Due to the presence of cases in other districts, we have established temporary isolation facilities to accommodate the suspected and confirmed cases. In Ibanda, a temporary isolation ward has been created at Ibanda Hospital, while plans are underway to set up a proper isolation facility by tomorrow.

 

At Mbarara Regional Referral Hospital, a separate temporary has been designated for the suspect Marburg cases. A triage has also been set up at the causality ward.

 

We have assembled a team of experts to work in the newly established isolation facilities and they are expected in these districts today.  We also plan to undertake infection control procedures in these facilities as safety measures for the workers and the admitted patients.

 

Today, the total number of cases admitted is 12. Eight are currently admitted at Rushoroza Health Center III in Kabale. Two confirmed cases, a couple (husband and wife) still remain admitted at Mulago National Referral Hospital. Another two suspect cases are currently admitted at Mayanja Memorial Hospital in Mbarara.

 

There are seven suspect cases (student nurses) quarantined at Ibanda. These cases attended to the confirmed case that later died at Mbarara Regional Referral Hospital on October 24th. Other health workers who attended to the patient are closely being monitored.

 

We have line-listed a total of 436 contacts for close observation in four districts of  Kabale, Kam-pala, Ibanda, Mbarara, Fort Portal and Rukungiri. Those being monitored got into contact with either the dead or confirmed cases. The team continues to monitor them on a daily basis for possible signs and symptoms of this highly infectious disease until they have completed 21 days without showing any signs and symptoms.

 

We have completed an orientation of the Kabale district taskforce on Marburg case presentation and prevention, barrier nursing and infection control. Plans are underway to conduct the orien-tation at Ibanda and at Mbarara Regional Referral Hospital.
We have trained a total of 42 volunteers from the Uganda Red Cross Society and deployed them to conduct house to house community sensitization and active case tracing.

 

We plan to set up burial committees in Ibanda district to manage burials of people suspected to have died of the disease. The committee will be oriented on burial procedures and infection prevention and control. This is one of the control measures to curb the spread of the highly con-tiguous disease.

The Ministry of Health would also wish to clarify on media reports that one of its officers, Dr. Sheila Ndyanabangi, the head of the Mental Health Unit Division, had contracted Marburg and had been isolated. Dr. Ndyanabangi has not been isolated but has been advised to exercise social distancing. She is one of the contacts who are being monitored. She has not developed any signs or symptoms of the disease and therefore cannot be isolated from the community. She is due to complete the 21 days of observation.

 

I once again urge the public to take the following measures to avert the spread of the disease.

• Report immediately any suspected patient to a nearby health unit
• Avoid direct contact with body fluids of a person suspected to be suffering from Marburg by using protective materials like gloves and masks
• Persons who have died of Marburg must be handled with strong protective wear and buried immediately
• Avoid eating dead animals
• Avoid unnecessary public gathering especially in the affected district
• Burial of suspicious community deaths should be done under close supervision of well trained burial teams
• Report all suspicious deaths to a nearby health facility 

Once again the Ministry of Health calls upon the public to stay calm as all possible measures are being undertaken to control the situation. 

 

For a history of the Marburg virus, you may wish to revisit Marburg Virus Reported In Western Uganda.

»» Read More

Pathogens At the Gate

Thermal Scanner – Credit Wikipedia

 

# 6593

 

While there are no indications that the coronavirus detected recently in the Middle East has spread beyond the first two cases, some places around the world are taking this threat very seriously.

 

For example, local media is reporting that thermal scanners have been deployed at the Ninoy Aquino International Airport in the Philippines in an attempt to screen arrivals from the Middle East for possible infection.

 

Whenever a novel virus appears, people’s thoughts understandably turn to a pandemic scenario, even though experience has shown that most emerging viruses don’t have the `legs’ to spark a global epidemic (see Novel Viruses & Chekhov’s Gun).

 

Nevertheless, history tells us that pandemics come along several times each century, and another pandemic is all but inevitable.

 

And so the world’s attention this week has quite naturally focused on the novel coronavirus that killed one man in Saudi Arabia last July and has a Qatari man currently hospitalized in London.

 

Memories of the SARS outbreak in 2002 and 2003 remain vivid, particularly in Asia, where the virus hit hardest.

 

Fortunately, while there is still much we don’t know about this emerging pathogen, there are no immediate signs that this virus poses a pandemic threat.

 

While we may not know when - or which virus - will spark the next global health crisis, we have pretty good idea how it will arrive in most countries.

 

Scheduled airline traffic around the world, circa June 2009 – Credit Wikipedia

 

The world’s airlines carry 2.6 billion passengers each year, on more than 17 million flights.  And as the map above indicates, millions of them are international flights.

 

With most viral diseases having an incubation period of several days or longer, someone who is newly infected with a virus could change planes and continents several times before showing their first signs of illness.

 

Last July, in MIT: Contagion Dynamics Of International Air Travel we looked at a study appearing in PloS One, that simulated the early spread of a pandemic virus via air travel and ranked U.S. airports based on how much they contributed to the spread of the illness.

 

An excerpt from a report that appeared in MIT News.

 

New model of disease contagion ranks U.S. airports in terms of their spreading influence

Airports in New York, Los Angeles and Honolulu are judged likeliest to play a significant role in the growth of a pandemic.

Kennedy Airport is ranked first by the model, followed by airports in Los Angeles, Honolulu, San Francisco, Newark, Chicago (O'Hare) and Washington (Dulles). Atlanta's Hartsfield-Jackson International Airport, which is first in number of flights, ranks eighth in contagion influence. Boston's Logan International Airport ranks 15th.

 

 

All of which begs the question, can we really screen, identify, and isolate infectious airline passengers before they can spread a pandemic virus?

 

 

Sadly, the evidence to date has not been very encouraging.

 

Last April, in EID Journal: Airport Screening For Pandemic Flu In New Zealand, we examined a study that found the screening methods used at New Zealand’s airport were inadequate to slow the entry of the 2009 pandemic flu into their country, detecting less than 6% of those infected.

 

New Zealand did not employ thermal scanners, although countries that did, didn’t fare much better.

  

Proving that `there’s no place like home’ during a global crisis, in Vietnam Discovers Passengers Beating Thermal Scanners, we saw evidence of passengers taking fever-reducers to beat the airport scanners in a desperate attempt to get home.

 

In December of 2009, in Travel-Associated H1N1 Influenza in Singapore, I blogged on a NEJM Journal Watch article on of a new study that has been published, ahead of print, in the CDC’s  EID Journal  entitled:

 

Epidemiology of travel-associated pandemic (H1N1) 2009 infection in 116 patients, Singapore. Emerg Infect Dis 2010 Jan; [e-pub ahead of print]. Mukherjee P et al

Travel-Associated H1N1 Influenza in Singapore

Airport thermal scanners detected only 12% of travel-associated flu cases; many travelers boarded flights despite symptoms.

 

 

In June of 2010  CIDRAP carried this piece on a study of thermal scanners in New Zealand in 2008 (before the pandemic) presented at 2010’s ICEID.

 

Thermal scanners are poor flu predictors

Thermal scanners for screening travelers do moderately well at detecting fever, but do a poor job at flagging influenza, according to researchers from New Zealand who presented their findings today at the International Conference on Emerging Infectious Diseases (ICEID) in Atlanta.

 

And in early 2009, Helen Branswell penned an article for the Canadian Press, that stated:

 

Studies show little merit in airport temperature screening for disease

Monday, 16 February 2009 - 11:58am.

By Helen Branswell

TORONTO — Using temperature scanners in airports to try to identify and block entry of sick travellers during a disease outbreak is unlikely to achieve the desired goal, a report by French public health officials suggests.

(Continue. . .)

 

 

The evidence is pretty clear.

 

With the technology of today, coupled with likelihood of having many pre-symptomatic and asymptomatic carriers, there isn’t much hope to identify more than a fraction of infected travelers.

 

As far as the risk of catching a pandemic flu virus while a passenger on an airliner, in May of 2010 we saw a study that appeared in the BMJ that looked at that very topic (see BMJ: Flu Transmission Risks On Airplanes)

 

BMJ 2010;340:c2424

Research

Transmission of pandemic A/H1N1 2009 influenza on passenger aircraft: retrospective cohort study

Conclusions

A low but measurable risk of transmission of pandemic A/H1N1 exists during modern commercial air travel. This risk is concentrated close to infected passengers with symptoms. Follow-up and screening of exposed passengers is slow and difficult once they have left the airport.

 

Another study, conducted by researchers at UCLA and published in BMC Medicine in late 2009:

 

Calculating the potential for within-flight transmission of influenza A (H1N1)

Bradley G Wagner, Brian J Coburn and Sally Blower^*

Results

The risk of catching H1N1 will essentially be confined to passengers travelling in the same cabin as the source case. Not surprisingly, we find that the longer the flight the greater the number of infections that can be expected. We calculate that H1N1, even during long flights, poses a low to moderate within-flight transmission risk if the source case travels First Class.

(Continue . . .)

 

 

While there will likely be intense public clamor to try to block the entry of a pandemic virus into this, or any other country, the truth is – it is highly unlikely that it will work.

Areas that receive a very small number of arrivals might be able to institute a quarantine system (see Can Island Nations Effectively Quarantine Against Pandemic Flu? ), but even then the ability to identify and isolate infected travelers won’t be 100%.

 

Still, even if the success rate is likely to be low, there may be some value in trying to limit the number of infected persons arriving into a country, particularly during the opening days and weeks of an outbreak.

 

The more introductions of a virus into a population, the more points it will have from which to spread.

 

Since it takes months to produce and deploy a vaccine, and time to prepare a society to deal with a pandemic, any delaying action that can reduce the speed and spread of the virus has value.

 

The takeaway from all of this is that we ignore global healthcare and infectious disease outbreaks – even in the remotest areas of the world – at our own peril.

 

Vast oceans and extended travel times no longer offer us protection, and there is no technological shield that we can erect that would keep an emerging pandemic virus out.

 

The place to try to stop the next pandemic is not at the gate, but in the places around the world where they are likely to emerge.

 

Which makes the funding and support of international public health initiatives, animal health initiatives, and disease surveillance ever so important, no matter where on this globe you happen to live.

»» Read More

SciAm: Excerpts From Nathan Wolfe’s `Viral Storm’

 

 

# 5891

 

Nathan Wolfe is a field virologist . . . a virus hunter . . . who hopes his work, and those of his colleagues, will reveal the identity of the next deadly virus to jump species from animals to humans.

 

Dr. Wolfe founded and directs the  Global Viral Forecasting Initiative (GVFI), a collaboration of more than 100 scientists worldwide who work to serve as a pandemic early warning system.

 

I’ve called Wolfe the `Indiana Jones of Virology’ because he spends about half of each year tramping around the jungles of Africa looking for next doomsday virus (see Nathan Wolfe And The Doomsday Strain).

 

In 2008 the New York Times ran a major story (see Deep In The Rain Forest, Stalking the Next Pandemic) on Dr. Wolfe’s work, and you can learn more from his inspiring 2009 TED TALK  Video Link.

 

 

 

Today Scientific American has excerpts from Dr. Wolfe’s new book, The Viral Storm: The Dawn of a New Pandemic Age, published on October 11th.  Follow the link to read:

 

How an Interconnected Planet Is Fueling the Brewing Viral Storm

In his new book, award-winning biologist and author Nathan Wolfe​ examines the origins and spread of viruses around the globe

For more on the book, and an audio interview with Dr. Wolfe, visit:

 

The Viral Storm

The Dawn of a New Pandemic Age

»» Read More

Referral: CIDRAP On Virus-sharing, Pandemic Vaccine Access

 

# 5489

 

 

While it seems hard to believe, the impasse over the sharing of H5N1 influenza samples out of Indonesia has been ongoing since late 2006.  

 

Since avian influenza viruses evolve over time, it is essential that the world have access to fresh samples, particularly from a region where the virus is endemic and the CFR (case fatality ratio) of known cases is above 80%.

 

Many times between 2007 and 2007 there were signs that an arrangement might be brokered between the Indonesian Ministry of Health and the World Health Organization, but every time the deal fell through.

 

Among the many mentions of these negotiations in this blog, in 2008 I wrote  Despite Progress Indonesia Still Unwilling to Share Virus Samples and in 2009, Geneva: No Deal On Virus Sharing.

 

Over the past two years, very little has been said publicly regarding this stalemate, but work has been going on quietly in the background. 

 

While the impasse with Indonesia has been the focus of the discussion, other developing nations have a stake in the outcome of these negotiations as well. 

 

Which brings us to a report by Lisa Schnirring of CIDRAP News, that outlines renewed efforts to strike a deal on virus sharing.

 

WHO group renews push for pact on virus-sharing, pandemic vaccine access

Lisa Schnirring Staff Writer

Apr 12, 2011 (CIDRAP News) – Leaders from a World Health Organization (WHO) working group on virus sharing and vaccine issues related to pandemic preparedness today said they hope to reach an agreement by Friday (Apr 15) so that it could go to the World Health Assembly (WHA) for a vote in May.

(Continue . . . )

 

»» Read More