Friday flu shot

Yesterday many US newspapers carried front-page stories on the severity of influenza so far this season. The New York Times story began with “It is not your imagination — more people you know are sick this winter, even people who have had flu shots.” Is this really a bad flu season?

Before we answer that question, I would like to complain about what the Times wrote: ‘more people you know are sick this winter, even people who have had flu shots”.  A similar sentiment appeared in a recent Forbes column “Influenza-like-illness is sweeping the country with the Centers for Disease Control & Prevention reporting that most areas of the country experiencing high rates. I should know, my family is in the midst of it despite having been vaccinated.”

Remember that having a respiratory illness does not mean that you have influenza – it could be caused by a number of other viruses which of course would not be blocked by influenza vaccine. Furthermore, the influenza vaccine is not 100% effective – it’s about 60-70% effective in individuals younger than 65 years. That’s not great, but it is better than having no vaccine. The point that I want to make is that it is not useful for anyone to relay anecdotal information about immunization and infection unless you know for sure that you had influenza virus. It only further discourages widespread immunization, which is already isn’t where it should be (~40%).

To answer my question  – is this a bad flu season? – I looked at data from the Centers for Disease Control and Prevention, which receives thousands of respiratory specimens from laboratories throughout the US and determines if they contain influenza virus, and if so, which subtype. Here are the results through week 1 of January 2013:

influenza 2013 week 1

According to these data, there was a peak of influenza activity in week 51 (December 2012). This is early compared with recent influenza seasons. In the 2011-12 season, influenza activity peaked in week 11 (March) of 2012:

influenza 2011-12

During the 2010-11 season, the peak of influenza activity was week 8 (February) of 2011:

influenza 2010-11

During the 2009-10 season, the peak of influenza activity was quite early, in week 42 (October) 2009:

influenza 2009-10

The number of diagnosed infections each year is also indicative of the extent of the influenza season. So far in the 2012-12 season there have been 28,747 influenza positive specimens. Numbers in the previous years: 157,449 in the 2009-10 season, and 55,403 in the 2010-11 season (I was not able to locate totals for 2011-12).

Pneumonia and influenza mortality has so far not substantially exceeded the epidemic threshold as it has in previous years:

pneumonia and influenza mortality

Pediatric deaths from influenza are on track to exceed last year’s total but not the previous two years:

influenza pediatric deaths

The percentage of outpatient visits for influenza-like illness (based on symptoms, not virus isolation) is following a pattern that resembles recent moderately severe influenza seasons:

influenza like illness

The New York City Department of Health and Mental Hygiene also monitors influenza and produces weekly summaries during the season. One metric they report is the percentage of visits for outpatient influenza-like illness. The curve resembles that for 2010-11:

NYC influenza-like illness

New York City also identifies what type of respiratory virus is associated with influenza-like illness, including influenza viruses, adenovirus, respiratory syncytial virus, parainfluenza virus, and metapneumovirus. For week 1 of 2013 all isolates (n=45) were either influenza A/H3N2 or B, although analysis of about a third of them is pending. In previous weeks a mix of other viruses were found in addition to influenza.

Note also the prevalence of influenza H3N2 this season, which has largely displaced the 2009 pandemic H1N1 strain. The H3N2 subtype is generally associated with more severe influenza seasons.

In summary: the data so far suggest that influenza activity is peaking early than in the past two years, but not at an unprecedented time. Numbers of infections, pneumonia, and mortality, are not off the charts. I would agree with Jean Weinberg, a city health department spokeswoman, who said “This is not a season that is out of the ordinary, though H3 seasons tend to be worse than H1 seasons”.

Influenza is on the rise

flu week 47December 2-8 is National Influenza Vaccination Week. It was established in 2005 by the Centers for Disease Control and Prevention to highlight the importance of continuing immunization throughout the holiday season. This year the push to immunize against flu comes as the disease has begun to increase substantially throughout the United States, as shown in the figure (click the figure for a larger version).

During week 47, 812 of 5,342 (15.2%) of respiratory samples tested positive for influenza virus. Of those isolates that were subtyped, most were either H3N2 or an influenza B virus strain. The 2009 swine-origin H1N1 strain has only been found in one sample so far. Fortunately the H3N2 component of the influenza vaccine for 2012-13 is a good match for the circulating H3N2 strain.

A substantial rise in the number of influenza cases typically does not occur until the end of December in the US. The last time that the disease incidence rose so early was in 2003-04. That was one of the most lethal seasons in 35 years, with 48,000 deaths. This year two children have already died of influenza in the US.

The good news is that 112 million doses of influenza vaccine have already been administered this year, and there is still time to be immunized. The CDC recommends that everyone over 6 months of age be immunized against influenza. Vaccination is especially important for individuals who are at risk for developing serious influenza-related complications: pregnant women, children younger than 5 years old (but those less than 6 months of age should not be immunized), people with with chronic medical conditions such as asthma, diabetes, and heart disease, and those over 65 years old.

The influenza vaccine is available in two types: an injected, inactivated preparation, and an infectious version that is sprayed in the nose. After immunization, approximately two weeks are required to be fully protected against infection.

Derek Smith on antigenic cartography

Derek Smith, Professor of Infectious Disease Informatics, University of Cambridge, U.K., has developed a method for visualizing antigenic evolution by creating two-dimensional maps in a process called antigenic cartography. These maps are made with data that provide information on the antigenic properties of the pathogen. In the case of influenza virus, the data come from measuring the ability of an antiviral antibody to inhibit hemagglutination – binding of virions to red blood cells. Such maps show how amino acid changes can affect antibody binding to virus particles, which cannot be done by comparing nucleotide sequences of different virus isolates. By charting influenza virus strains in this way, it should be possible to better understand genetic and antigenic evolution.

I discussed antigenic cartography with Dr. Smith during ICAAC Boston 2010, as part of TWiV 99. View the video below, or right click to download the 292 MB .mp4 file.

TWiV 112: Creating a killer poxvirus

dickson despommierHosts: Vincent RacanielloAlan Dove, and Rich Condit

On episode #112 of the podcast This Week in Virology, Vincent, Alan, and Rich review the making of a virulent poxvirus by insertion of the gene encoding IL-4, and severe 2009 H1N1 influenza due to pathogenic immune complexes.

Click the arrow above to play, or right-click to download TWiV #112(71 MB .mp3, 98 minutes).

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Links for this episode:

Weekly Science Picks

Rich – The Scientist’s Top 10 Innovations 2010
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Pandemic influenza vaccine was too late in 2009

Influenza researcher Peter Palese visited yesterday and spoke about “Pandemic influenza: Past and Future”. A key part of his talk was a review of his efforts to produce a universal influenza vaccine which protects against all strains. He used the following graph to make the point that when influenza pandemic strains emerge, there is insufficient time to deliver a vaccine using current technology.

influenza like illness and vaccine distributionImage source: CIDRAP

The graph depicts the percentage of visits for influenza-like illness (ILI – the red line) and distribution of the swine-origin influenza vaccine (blue line) from September 2009 to May 2010 in the US. At the peak of ILI at the end of October 2009, fewer than 20 million doses of vaccine had been shipped. By the time 120 million doses had been distributed, infections with the new H1N1 strain had subsided. Dr. Palese believes that immunization was too late to have a substantial impact on this second wave of influenza. The inability to immunize the population in time to prevent influenza was conceded by the Centers for Disease Control and Prevention in October 2009.

Dr. Palese’s solution to this dilemma is to deploy universal vaccines which would protect against any influenza strain, including future pandemic viruses. He and others have already made impressive progress towards this goal.

The head of Columbia’s Environmental Health & Safety division pointed out to Dr. Palese that despite being delivered too late to prevent the second wave of influenza, the vaccine would be expected to reduce influenza during the 2010-2011 season in the US.

An interesting question is whether the additional cost of rushing production and development of the vaccine in 2009 was a worthwhile expenditure. In hindsight it would appear that the answer is no. But had the fall wave of influenza peaked later – December or January, for example – the vaccine might have been more effective in preventing infections. That’s why we’ll have to do the same when the next pandemic strain emerges – unless by then we have a universal influenza vaccine.

Thoughts on this season’s influenza vaccine

After my lecture on influenza pathogenesis and evolution at the Northeast Laboratory Conference 2010 in Portland, Maine, I was asked if it is necessary to receive the influenza vaccine every year. This question was precipitated by my statement that the 2010-11 trivalent influenza vaccine contains the same swine-origin H1N1 strain as last year’s monovalent vaccine. That virus has not undergone sufficient antigenic drift to necessitate the formulation of a new vaccine.

There are two main considerations* when deciding whether to be immunized yearly against influenza: the nature of the vaccine and age of the recipient. Last year’s seasonal influenza vaccine for the northern hemisphere contained the following strains:

  • A/Brisbane/59/2007 (H1N1)
  • A/Brisbane/10/2007 (H3N2)
  • B/Brisbane/60/2008

Also made available last year was a monovalent vaccine comprising the pandemic strain, A/California/7/2009.

Strains included in the 2010-11 vaccine are:

  • A/California/7/2009 (H1N1)
  • A/Perth/16/2009 (H3N2)
  • B/Brisbane/60/2008

The seasonal H1N1 strains of previous years are no longer circulating and have been eliminated from the vaccine. If you received last year’s seasonal vaccine and the monovalent vaccine, is it necessary to receive this year’s vaccine? The answer is yes, because the H3N2 strain is different – last year the vaccine contained a Brisbane strain while this year’s H3N2 isolate is from Perth. The full WHO report on strain selection is available as a pdf document.

What would be the answer if this year’s trivalent vaccine were identical to that used last year? The answer would still be to receive the vaccine, because the duration of immunity provided by the inactivated influenza vaccine has always been an issue. In elderly recipients (>65 years of age) immunity barely lasts for a single influenza season. Younger recipients will likely be protected from disease for one influenza season, and perhaps a second season as well, although in the latter case a milder respiratory disease may result. For these reasons the CDC recommends annual immunization against influenza virus for all individuals 6 months of age and older.

The current inactivated influenza vaccines were developed during World War II, and although they have since been refined and purified, there are still deficiencies, including brief duration of protective immunity. Development of new influenza vaccines that not only overcome this problem, but also provide broader protection, is clearly needed.

*This post, like everything else on virology blog, does not contain medical advice. It comprises scientific information about the vaccines which can be used, together with your health care provider, to reach a decision about immunization.

TWiV 95: Does a virus shift in the woods?

Hosts: Vincent Racaniello, Dickson DespommierAlan Dove, and Rich Condit

On episode #95 of the podcast This Week in Virology, Vincent, Dickson, Alan, and Rich consider the end of the influenza H1N1 pandemic, dengue in Florida, vaccinia virus infection in Brazilian monkeys, and viruses in the faecal microbiota.

Click the arrow above to play, or right-click to download TWiV #95 (68 MB .mp3, 94 minutes)

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Links for this episode:

Weekly Science Picks

Alan – Families Fighting Flu
Rich –
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H1N1 pandemic is over

The World Health Organization has declared the end of the pandemic caused by H1N1 influenza virus. According to Director-General Margaret Chan,

The world is no longer in phase 6 of influenza pandemic alert. We are now moving into the post-pandemic period. The new H1N1 virus has largely run its course.

As we enter the post-pandemic period, this does not mean that the H1N1 virus has gone away. Based on experience with past pandemics, we expect the H1N1 virus to take on the behaviour of a seasonal influenza virus and continue to circulate for some years to come.

According to the Director-General, levels and patterns of H1N1 transmission are now different from those observed during the pandemic. Out-of-season outbreaks are no longer being reported, and their intensity is similar to that seen during seasonal epidemics. In addition, multiple influenza viruses are being isolated in many countries, a pattern typical of many recent seasonal epidemics.

I take particular interest in what the Director-General believes did not happen:

This time around, we have been aided by pure good luck. The virus did not mutate during the pandemic to a more lethal form. Widespread resistance to oseltamivir did not develop. The vaccine proved to be a good match with circulating viruses and showed an excellent safety profile.

I continue to wonder why the Director-General, and many others, feel that influenza virus must change to a more lethal form. Although the four previous influenza pandemics occurred in multiple waves of increasing lethality, there is no evidence that they are a consequence of viral mutation. For example, the only virus available from the 1918 pandemic was rescued from an Alaskan influenza victim who was buried in permafrost in November of that year, when higher mortality was already evident. This makes it impossible to correlate any genetic changes in the virus with increased virulence. Viruses are available from different stages of the pandemics of 1957 and 1968, which also occurred in waves of increasing lethality, but to my knowledge the virulence studies have not been done.

I believe that a major selective force for viral evolution is the need to maintain efficient transmission among hosts. This may be achieved by any number of phenotypic changes, such as increases in stability and virion production. Changes in lethality might also lead to more effective transmission – for example, by inducing more severe coughing, the virus could be better transmitted among humans. But there is no genetic evidence that such changes have occurred during influenza virus pandemics.

How has the idea that influenza virus mutates to greater lethality permeated our popular culture? I don’t know the answer, but John Barry’s The Great Influenza is a prime suspect.

TWiV 89: Where do viruses vacation?

Hosts: Vincent Racaniello and Alan Dove

On episode #89 of the podcast This Week in Virology, Vincent and Alan review recent findings on the association of the retrovirus XMRV with ME/CFS, reassortment of 2009 pandemic H1N1 influenza virus in swine, and where influenza viruses travel in the off-season.

Click the arrow above to play, or right-click to download TWiV #89 (56 MB .mp3, 78 minutes)

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Secondary changes allow spread of oseltamivir resistant influenza virus

The influenza virus neuraminidase (NA) protein is required for virus release from the cell, a property exploited by the antiviral drugs oseltamivir (Tamiflu) and zanamavir (Relenza). During clinical testing of oseltamivir in 2001, some individuals shed drug-resistant viruses with an amino acid change from histidine to tyrosine (H274Y) in NA. Such viruses are not inhibited by oseltamivir because the amino acid change leads to  decreased binding of the drug. But these viruses replicated less well in cell culture, and had reduced infectivity in ferrets. It was concluded that oseltamivir resistant influenza virus mutants would not spread in the population. Why was this conclusion wrong?

During the 2008-09 flu season oseltamivir resistant influenza H1N1 viruses with the H274Y change began to spread, and within a year they were found in most seasonal isolates. It was hypothesized that these viruses contained other amino acid changes that masked the deleterious effect of H274Y. The H274Y mutation does not affect the catalytic activity of the NA: the ability to cleave sialic acid from glycoproteins. However it does lead to a decease in the amount of NA protein that is transported to the surface of infected cells.

Computational methods were used to identify amino acids in NA that could potentially compensate for the effect of H274Y. A single amino acid change at position 194 of NA, when present with H274Y, restored NA on the cell surface to normal levels.

Did a similar amino acid change in seasonal H1N1 strains allow the spread of oseltamivir resistant viruses with H274Y? Introduction of this amino acid change into the seasonal H1N1 strains A/Texas/91 and A/New Caledonia/99 causes a decrease in surface NA. However the same change has a lesser effect on surface NA in cells infected with A/Solomon Islands/2006. Two amino acid changes were identified in the NA protein of recent oseltamivir-resistant seasonal H1N1 viruses that restore surface levels of NA in the presence of H274Y: V234M and R222Q.

It seems likely that the amino acid changes V234M and R222Q emerged first in the NA of seasonal H1N1 viruses. Why these changes appeared is unknown, but they could be a consequence of random drift, antigenic selection, or a need to balance HA and NA activities. Once these changes were in place, oseltamivir resistant viruses with the H274Y could be selected, and because they had no defect in fitness, they spread globally.

The conclusion is that H274Y in NA attenuates the fitness of influenza virus by reducing the amount of NA on the cell surface. Spread of such viruses in the population is impossible without secondary amino acid changes that restore adequate levels of surface NA. H274Y probably causes a defect in NA folding or transport that is balanced by the secondary mutations.

These findings are another example of how drug resistance frequently comes with a cost to protein stability or folding, and prevents evolution unless compensated by secondary mutations.

There have been scattered isolations of oseltamivir-resistant, pandemic 2009 H1N1 influenza virus with the H274Y change. Will these viruses spread globally, or are they less fit, evolutionary dead ends? Introduction of the H274Y change into the NA of 2009 pandemic H1N1 virus leads to a large decrease in surface NA. Unless the 2009 swine-origin viruses already produce excess NA, viruses with the H274Y change are not likely to spread without secondary mutations that rescue NA surface expression.

Bloom JD, Gong LI, & Baltimore D (2010). Permissive secondary mutations enable the evolution of influenza oseltamivir resistance. Science (New York, N.Y.), 328 (5983), 1272-5 PMID: 20522774