Influenza Virus Mashup

Via the Kyiv Post: A swine flu New Year for Ukraine’s largest cities. Excerpt:

Health Ministry officials on Dec. 30 reported the epidemiological threshold for flu-related illness has been surpassed in most Ukrainian oblasts. 

Some 3.7 million Ukrainians have suffered from flu and acute viral respiratory illness since November. Some 700 patients have died, and hundreds more are currently in intensive care.

Via the Hong Kong government website: Dead magpie suspected to have H5 virus. Excerpt:

Preliminary tests on a dead Oriental magpie robin found in Hok Tau, Pat Sin Leng, indicate a suspected case of H5 avian flu, the Agriculture, Fisheries & Conservation Department announced today.
  

The carcass was found December 29 near the Hok Tau Management Centre in Pat Sin Leng Country Park. There are no commercial chicken farms within three kilometres of the site.
  

The species is a common resident bird in Hong Kong.

Via Focus Information Agency: Romania reports 5 new A/H1N1 deaths.

Romanian heath ministry announced Thursday five more A/H1N1 flu deaths were registered in Romania over the past 24 hours, Romanian Mediafax agency informed. 

Thus the total number of the sick in the country reached 5 680, including 58 deaths.

Via Thaindian News: 3 die, 204 sick with swine flu in armed forces. Excerpt:

The armed forces had 204 cases of swine flu in 2009, leading to death in three cases. 

In the latest case, an officer, also suffering from multiple organ failure, Wednesday succumbed to swine flu in Delhi. The other two swine flu deaths were reported in Pune and Bangalore. 

“We had 204 confirmed cases of swine flu among the three services. Three deaths have occurred,” Director General Armed Forces Medical Services Lt. Gen. N.K. Parmar told reporters here, at the annual press conference of the service ahead of their 246th anniversary. 

“An advisory with detailed preventive measures has been issued in this regard. Also stock of Tamiflu have been made readily available. We have also screened 5,000 cases among civilian population at Pune and Bangalore,” Parmar added. 

The armed forces are equipping 10 hospitals across the country to contain pandemics in future.

(Thu, 31 Dec 2009 14:06:00 +0000)

# 4205

The HPA (Health Protection Agency) of the UK releases surveillance data not unlike that we get from the CDC’s FluView and Canada’s FluWatch reports.

Like the US, Canada, and much of western Europe, the numbers in the UK (consultations, illnesses, hospitalizations) are all decreasing.

Weekly pandemic flu media update

31 December 2009

KEY POINTS

• Most indicators show that flu activity is continuing to decrease across the UK. Some caution must be exercised, however, as the indicators may be influenced by the holiday period.
• The consultation rate for flu-like illness in England from the Royal College of General Practitioners (RCGP) scheme has decreased to 12.7 per 100,000 in week 52 compared to 24.7 in week 51. This is below the English baseline threshold of 30/100,000.
• The estimated cases self referring to the National Pandemic Flu Service have shown decreases in all areas of assessments, authorisations and collections. This is across all regions and all age groups. 

 

VIRAL CHARACTERISTICS

To date (as of 30 December 2009) 4,563 viruses have been analysed by the HPA Centre for Infections for the genetic marker commonly associated with resistance to oseltamivir in seasonal H1N1 flu (H274Y). 31 viruses have been found to carry this marker in the UK with three of these, through additional testing, showing evidence of resistance when viral growth is tested in the presence of oseltamivir. These viruses are still sensitive to zanamivir. In addition, 293 specimens have been fully tested for susceptibility to antivirals.

 

Information on medical history was available for 17 cases, all of whom had an underlying medical condition: 14 were immunosuppressed and three had chronic respiratory or neurological illnesses.

 

Testing of samples, taken before and after treatment with oseltamivir, show that the antiviral resistance in 14 of the cases was treatment-induced, four are probably acquired through person to person transmission, and in four cases the origin of the resistant virus is still under investigation.

 

The agency is continually assessing its advice to government on health protection policies such as antiviral use. Currently there is no requirement to change existing guidance.

 

There have been no significant changes in the virus.

(Thu, 31 Dec 2009 13:15:00 +0000)

# 4204

Readers with long memories may remember that last July I reported in this blog that researchers from Columbia University’s Mailman School of Public Health were to travel to Argentina to investigate the perceived high CFR (Case Fatality Ratio) among H1N1 cases there.

Jason Gale and Eliana Raszewski, writing for Bloomberg news, described the project in a story entitled: Argentina Flu Death Mystery Sparks Probe for Virus Mutation.

Scientists from Columbia University and Argentina’s National Institute of Infectious Diseases now plan to decode the complete genomic sequences of at least 150 virus samples over the next 10 days to gauge the frequency of the changes and whether they are linked to more severe illness. Major changes in the pandemic virus could erode the effectiveness of vaccines being prepared to fight the scourge.

You’ll find further details on these deaths, and the planned investigation, in the following blogs.

Argentina Working To Release Viral Sequences

Follow Up On Yesterday’s Report On Argentina Sequences

Since that report in July, we’ve heard very little other than the fact that no unusual viral mutations had been discovered in Argentina that could account for the higher CFR.   

That is, until November of last month, when two of the authors of the following PLoS One  study appeared on Vincent Racaniello’s excellent podcast, TWiV  (This week In Virology) to discuss their upcoming paper.

TWiV 59: Dog bites virus

by Vincent Racaniello on 22 November 2009

Hosts: Vincent Racaniello, Alan Dove, Rich Condit, Gustavo Palacios, and Mady Hornig

A TWiV panel of five considers the finding of Streptococcus pneumoniae in fatal H1N1 cases in Argentina, hysteria in the Ukraine over pandemic influenza, and human vaccinia infection after contact with a raccoon rabies vaccine bait.

TWiV is both entertaining and informative, and I highly recommend it to anyone with curiosity about the field of virology.   While sometimes it can’t avoid being a bit technical, the panel does a great job making the information accessible and understandable to the general public.

In this episode, Gustavo Palacios, and Mady Hornig reveal that it was the presence of S. pneumoniae in those infected with H1N1 that often led to the heightened severity of their illness.

Excerpts from the PLoS One  study are posted below. 

In it, the authors suggest that testing for the presence of S. pneumoniae may accurately predict who will develop severe disease.  They write:

In our study of Argentinean victims of H1N1pdm, the presence of S. pneumoniae in NPS predicts severe disease outcome. The risk associated with S. pneumoniae is particularly prominent in 6-to-55 year-old individuals.

 

Indeed, severity of disease in this low risk group can be predicted with 90.97% accuracy via a multivariable logistic regression model that considers the presence of S. pneumoniae together with viruses other than influenza and a risk-associated medical condition.

But before we go there, a reminder:

I have suggested on numerous occasions that people should consult with their health care provider about the advisability of taking the Pneumococcal polysaccharide vaccine (PPSV) – even if you aren’t sure you fall into a recommended category.

Along the way, a few of my blogs on the subject include:

CDC Promoting Better Uptake Of PPSV in Adults

An Appropriate Level Of Concern (Revisited)

Referral: Effect Measure On Pneumococcal Vaccines

CDC Issues Pneumococcal Vaccine Recommendations

The PPSV is designed to help protect against many (but not all) strains of S. pneumoniae.  

Something to bear in mind as you read this report.

 

Streptococcus pneumoniae Coinfection Is Correlated with the Severity of H1N1 Pandemic Influenza

Initial reports in May 2009 of the novel influenza strain H1N1pdm estimated a case fatality rate (CFR) of 0.6%, similar to that of seasonal influenza. In July 2009, however, Argentina reported 3056 cases with 137 deaths, representing a CFR of 4.5%. Potential explanations for increased CFR included virus reassortment or genetic drift, or infection of a more vulnerable population.

 

Virus genomic sequencing of 26 Argentinian samples representing both severe and mild disease indicated no evidence of reassortment, mutations associated with resistance to antiviral drugs, or genetic drift that might contribute to virulence. Furthermore, no evidence was found for increased frequency of risk factors for H1N1pdm disease.

 

We examined nasopharyngeal swab samples (NPS) from 199 cases of H1N1pdm infection from Argentina with MassTag PCR, testing for 33 additional microbial agents. The study population consisted of 199 H1N1pdm-infected subjects sampled between 23 June and 4 July 2009. Thirty-nine had severe disease defined as death (n = 20) or hospitalization (n = 19); 160 had mild disease.

 

At least one additional agent of potential pathogenic importance was identified in 152 samples (76%), including Streptococcus pneumoniae (n = 62); Haemophilus influenzae (n = 104); human respiratory syncytial virus A (n = 11) and B (n = 1); human rhinovirus A (n = 1) and B (n = 4); human coronaviruses 229E (n = 1) and OC43 (n = 2); Klebsiella pneumoniae (n = 2); Acinetobacter baumannii (n = 2); Serratia marcescens (n = 1); and Staphylococcus aureus (n = 35) and methicillin-resistant S. aureus (MRSA, n = 6).

 

The presence of S. pneumoniae was strongly correlated with severe disease. S. pneumoniae was present in 56.4% of severe cases versus 25% of mild cases; more than one-third of H1N1pdm NPS with S. pneumoniae were from subjects with severe disease (22 of 62 S. pneumoniae-positive NPS, p = 0.0004). In subjects 6 to 55 years of age, the adjusted odds ratio (OR) of severe disease in the presence of S. pneumoniae was 125.5 (95% confidence interval [CI], 16.95, 928.72; p<0.0001).

 

The association of S. pneumoniae with morbidity and mortality is established in the current and previous influenza pandemics. However, this study is the first to demonstrate the prognostic significance of non-invasive antemortem diagnosis of S. pneumoniae infection and may provide insights into clinical management.

Gustavo Palacios1#*, Mady Hornig1#, Daniel Cisterna2, Nazir Savji1, Ana Valeria Bussetti1, Vishal Kapoor1, Jeffrey Hui1, Rafal Tokarz1, Thomas Briese1, Elsa Baumeister2, W. Ian Lipkin1*

(Continue. . . )

Via BBC News: Children more likely to catch swine flu, study suggests. Excerpt:

Children are twice as likely as adults to catch swine flu, according to a joint UK-US study. 

Imperial College London researchers and a team from the US looked at how the virus spread among families. 

In a study of more than 800 people, one in eight people developed the infection after someone in their house got it. 

But the team also dismissed suggestions that children may be “super spreaders” as they were found to be no more contagious than older people. 

Rates of swine flu have tended to be higher among younger age groups, the official figures have shown. 

What is more, there is thought to be a large pool of children who have been infected but not displayed symptoms. 

This research, published in the New England Journal of Medicine, confirmed that children were more likely to become infected. 

The team looked at the families and household contacts of 216 people infected with swine flu. 

Of that group of 600, the under-18s were most likely to get it - twice as likely as adults under 50 - while those over the age of 50 were the least likely.

Via CIDRAP,Robert Roos writes: Indonesia reports 20 H5N1 cases — 19 fatal — since January. Excerpt:

Indonesia’s Ministry of Health, updating information on H5N1 avian influenza for the first time since January, quietly reported this week that the country has had 20 human cases so far this year, with 19 of them fatal—a 95% case-fatality rate (CFR). 

A terse notice from the Ministry of Health on Dec 28 listed the figures and said the latest reported case was identified in South Jakarta on Sep 23. Indonesia’s cumulative H5N1 toll since 2005 is now 161 cases with 134 deaths, for a CFR of 83%. 

The World Health Organization (WHO) updated its chart of H5N1 cases and deaths today to include the new numbers from Indonesia, but it posted no report on the cases. The global H5N1 total is 467 cases with 282 deaths, a CFR of 60%. Indonesia is the hardest-hit country overall, though Egypt has had more cases this year—39, with just 4 deaths.

Only the longtime Flublogians will really appreciate what the WHO chart means. After all these months of stubborn, dishonest zeros in Indonesia’s 2009 column, we now see something resembling the truth.

WHO has probably been fully aware of the cases and deaths in Indonesia, but has had to keep silent rather than break all ties with that country’s stubborn, dishonest government.

(Thu, 31 Dec 2009 03:39:00 +0000)

# 4203

A study today from the NEJM which suggests the novel H1N1 virus isn’t as easily transmissible as other novel pandemic viruses of the past. 

In a study of 216 households where an index case of H1N1 infection was identified, only about 13% of household contacts (about 1 in 8) came down with the infection.

Looked at another way, in roughly 72% of the households where a case was identified, no one else came down with the virus.   In 21% of the households, only one additional member acquired the infection.  And in only 6% of households did more than one other family member fall ill.

Children and teens under the age of 18 were twice as likely to catch the virus than those aged 19 to 50.  Those over the age of 50 were even less likely to fall ill.

For reasons that are less than clear, the rate of viral transmission in households with just two members was much higher than in households with four or more members.  

Excerpts from the abstract are below, but follow the link to read the entire study.

Household Transmission of 2009 Pandemic Influenza A (H1N1) Virus in the United States

Simon Cauchemez, Ph.D., Christl A. Donnelly, Sc.D., Carrie Reed, D.Sc., Azra C. Ghani, Ph.D., Christophe Fraser, Ph.D., Charlotte K. Kent, Ph.D., Lyn Finelli, Dr.P.H., and Neil M. Ferguson, D.Phil.

ABSTRACT

 
Background As of June 11, 2009, a total of 17,855 probable or confirmed cases of 2009 pandemic influenza A (H1N1) had been reported in the United States. Risk factors for transmission remain largely uncharacterized. We characterize the risk factors and describe the transmission of the virus within households.

 
Methods Probable and confirmed cases of infection with the 2009 H1N1 virus in the United States were reported to the Centers for Disease Control and Prevention with the use of a standardized case form. We investigated transmission of infection in 216 households — including 216 index patients and their 600 household contacts — in which the index patient was the first case patient and complete information on symptoms and age was available for all household members.

 

Results An acute respiratory illness developed in 78 of 600 household contacts (13%). In 156 households (72% of the 216 households), an acute respiratory illness developed in none of the household contacts; in 46 households (21%), illness developed in one contact; and in 14 households (6%), illness developed in more than one contact.

The proportion of household contacts in whom acute respiratory illness developed decreased with the size of the household, from 28% in two-member households to 9% in six-member households. Household contacts 18 years of age or younger were twice as susceptible as those 19 to 50 years of age (relative susceptibility, 1.96; Bayesian 95% credible interval, 1.05 to 3.78; P=0.005), and household contacts older than 50 years of age were less susceptible than those who were 19 to 50 years of age (relative susceptibility, 0.17; 95% credible interval, 0.02 to 0.92; P=0.03).

Infectivity did not vary with age. The mean time between the onset of symptoms in a case patient and the onset of symptoms in the household contacts infected by that patient was 2.6 days (95% credible interval, 2.2 to 3.5).

 

Conclusions The transmissibility of the 2009 H1N1 influenza virus in households is lower than that seen in past pandemics. Most transmissions occur soon before or after the onset of symptoms in a case patient.

 

A few caveats to this study are in order.

First, this study took place very early in the outbreak, essentially during the first 3 weeks of May.  

While it may not have appreciably changed, this is a snapshot of the transmissibility of the virus at that time.

Second, the data was collected by interviewing (telephone or face-to-face) family members within 7 days of an index case having been identified in their household. 

Illnesses that fell outside of that 7 day follow up period were not directly identified.

Third, reports of ILI (influenza-like illness) among family members or contacts within 7 days were assumed to have been due to exposure to the index case.

Testing for H1N1 wasn’t always done, and the actual chain of infection may have been other than from the index case.

None of which is mentioned to negate the findings of this study, but simply stated to illustrate that these sorts of studies have limitations, and those must be considered when you view the data.

This study does seem to suggest that compared to teenagers and children, those over the age of 18 may have some limited immunity to the virus. And that immunity appears to increase with age, becoming more prevalent in those over the age of 50.

The authors put it this way :

. . .  our findings are consistent with serologic analyses of the 2009 H1N1 virus suggesting that there are some preexisting pandemic H1N1 immune responses in the elderly; these are present to a lesser extent in younger adults but are rarely present in children.

Just as I was about to post this entry, I noticed that Maryn McKenna, writing for CIDRAP, has posted her summary of the report.   You’ll find it at the link below.

Study: H1N1 not highly contagious in households