Influenza Virus Mashup

Via CIDRAP: NEWS SCAN: H1N1 and antiviral resistance, H5N1 in Egypt and South Korea, sprout recall. Excerpt:

Suspected H5N1 avian flu has been reported on two poultry farms in South Korea. Hundreds of birds have died and thousands have been slaughtered, including at a chicken farm in Iksan, North Jeolla province, that is very near the country’s largest chicken factory, and at a duck farm in Cheonan, South Chungcheong province. 

Quarantines are expected if H5N1 is confirmed; testing should be complete very shortly. South Korea declared itself free of H5N1 in late 2008 but has seen three confirmed cases in wild birds just this month. 

The country is simultaneously struggling with a major outbreak of foot-and-mouth disease in livestock.

Via The Guardian: Flu deaths continue to rise. Excerpt:

The government has been forced to take new steps to tackle seasonal flu after new figures showed there were 12 more deaths in the past week, and 738 people seriously ill in hospital. 

The total number of deaths from this winter’s outbreak now stands at 39, up from 27 last week, the Health Protection Agency confirmed. 

Of those, 36 died from H1N1 swine flu, which is the most virulent of the two main flu strains circulating this winter. The other three died from Influenza B. All but one of the 39 was under 65, and four were under five years old. 

The government will now reintroduce a media campaign to help tackle the outbreak. Labour, which earlier this week claimed the campaign had been axed, accused the government of a U-turn. 

Some 61% of this year’s victims were in one of the “at risk” groups who qualify for a free NHS seasonal flu jab, which include pregnant women, those with breathing conditions such as asthma and those whose immune systems are weak. 

But just two of the 23 individuals had received the jab, which for the first time this year includes protection against swine flu, which claimed hundreds of lives when it began circulating in the UK in early 2009. 

The figure serves to underline doctors’ concerns that millions of people run the risk of infection, with potentially serious effects, because they have not been vaccinated. 

The number of people with known or suspected flu being treated in critical care units in hospitals has jumped from 460 to 738 - a rise of 278 in a week.

(Thu, 30 Dec 2010 17:23:00 +0000)

# 5193

Maryn McKenna has posted a very nice overview of this winter’s influenza season – on both sides of the Atlantic ocean.  As you are probably aware, while things remain quiet here in `the colonies’, the UK is in the midst of a major flu outbreak.

Among the many points she makes, Maryn links to Helen Branswell’s recent SciAm podcase on Flu Factories, and the Taubenberger/Morens/Folkers/Fauci paper on Pandemic Influenza’s 500th Anniversary.

Flu: Still a problem, just not here

• By Maryn McKenna  December 30, 2010  | 
•  

WHO has published Avian influenza - situation in Egypt - update 39.

The Ministry of Health of Egypt has announced two new cases of human infection with H5N1 avian influenza. 

A 28 year-old woman from Damanhour district of El Beheira governorate developed symptoms on 12 December. She was admitted to hospital on the 14th and subsequently discharged on the 22nd in good and stable condition. She has a history of exposure in a market where live animals are sold. 

An 11 year-old girl from Esna district of Luxor governorate developed symptoms on 18 December and was admitted in the hospital the following day. She experienced severe respiratory symptoms requiring mechanical ventilation and died on 23 December. No information is available regarding poultry exposure. Investigations into the source of infection are underway.

Laboratory tests have confirmed H5N1 virus and both patients were treated with antiviral medications. Of the 115 cases confirmed to date in Egypt, 38 have been fatal.

Via JoongAng Daily: After foot-and-mouth, avian flu feared spreading. Excerpt:

Avian influenza, the bird flu that can also sicken and kill humans, could be spreading in Korea after poultry farms in both South Chungcheong and North Jeolla reported suspected cases, according to the government yesterday. 

If these poultry farms are confirmed to have the H5N1 flu virus, Korea will be plagued with infectious animal diseases on a nationwide scale, except for South Gyeongsang, South Jeolla and Jeju. Since Nov. 29, foot-and-mouth disease has spread to five cities and provinces and led to the culling of around 550,000 livestock. 

The Ministry for Food, Agriculture, Forestry and Fisheries said yesterday that one duck farm in Cheonan, South Chuncheong, and a chicken farm in Iksan, North Jeolla, reported suspected cases of the avian flu virus the day before. 

Health officials are ramping up quarantine measures in case the two farms are confirmed to be infected. Hundreds of chickens at the Iksan farm have already died. Test results are expected this morning.

I’m delighted to see that Ida at Bird Flu Information Corner is back: Temanggung, Central Java ::: Bird flu in chickens. Excerpt:

Total 350 chickens died of bird flu H5N1 in Dusun Draju, Desa Mergowati, Kecamatan Kedu, Central Java. Of all, 300 are broilers from a partnership commercial farm and 50 are backyard chickens belong to locals. This incident has been confirmed by Head of Livestock and Fishery Service (Disnakkan), Slamet Saryono. 

“We received reports of bird flu suspicion, and then confirmed it by rapid test to the dead chickens,” said Slamet.

(Thu, 30 Dec 2010 12:56:00 +0000)

# 5191

Unlike its seasonal cousin (which has all but vanished), the 2009 novel H1N1 virus remains largely susceptible to the antiviral medication oseltamivir (Tamiflu).

During a 14-month period (April 2009-June 2010) 6,740 H1N1 samples were submitted to US surveillance systems for testing, and of those, only 37 (.5%) proved resistant to oseltamivir.

That’s the encouraging news from a study, published yesterday, in the CDC’s  EID Journal.

The link, and an excerpt describing the patient profile follow.  Go ahead and read it. 

I’ll be back with a bit more when you return.

Characteristics of Patients with Oseltamivir-Resistant Pandemic (H1N1) 2009, United States

Graitcer SB, Gubareva L, Kamimoto L, Doshi S, Vandermeer M, Louie J, et al. Characteristics of patients with oseltamivir-resistant pandemic (H1N1) 2009, United States. Emerg Infect Dis. 2011 Feb; [Epub ahead of print]

 

(EXCERPT)

 

Most patients infected with oseltamivir-resistant pandemic (H1N1) 2009 viruses were hospitalized (81%), had a severe immunocompromising condition (76%), and had been exposed to oseltamivir before collection of the specimen tested for antiviral resistance (89%) (Table); 9 (30%) had received oseltamivir as chemoprophylaxis, and 21 (70%) had received oseltamivir as treatment.

 

Four patients with oseltamivir-resistant pandemic (H1N1) 2009 virus infection had no documented exposure to oseltamivir before collection of the specimen for testing, including exposure to family members receiving oseltamivir.

 

No epidemiologic links were found between the 4 patients.

For now, the good news is that the 2009 H1N1 virus remains overwhelmingly sensitive to Tamiflu.

But of course, the same could have been said about the old seasonal H1N1 virus back in 2006-2007, when 99% of isolates tested showed good sensitivity to oseltamivir.

Resistance is usually caused by a mutation, known as H275Y, where a single amino acid substitution (histidine (H) to tyrosine (Y)) occurs at the neuraminidase position 275

 

(Note: some scientists use ‘N2 numbering’ (H274Y) and some use ‘N1 numbering’ (H275Y)).

 

Back in 2007, the belief was that the mutation that made the virus resistant to Tamiflu (H275Y), also reduced its biological fitness – suggesting that mutated versions of the viruses were unlikely to spread widely.

 

But those hopes were dimmed when, by the end of the 2007-2008 flu season, nearly 13% of H1N1 isolates tested the United States were resistant to the drug.

By December of 2008 nearly all seasonal H1N1 isolates tested around the world carried the H275Y mutation that conferred Tamiflu resistance.

Thus far, it appears that most of these resistant 2009 H1N1 strains have developed in immuno-compromised patients as so-called `spontaneous mutations’ – not as the result of contracting a circulating and already-resistant virus.

 

Human-to-human transmission of an oseltamivir-resistant novel H1N1 virus has only rarely been demonstrated.  A couple of reports on those include:

 

NEJM: Community Cluster Of Tamiflu Resistant H1N1

WER Review: Oseltamivir Resistance In Pandemic H1N1

Today, the news is good; resistance in novel H1N1 is rare.  But pharmacological victories over constantly evolving viruses (and bacteria) tend to be fleeting, and so the need for new classes of antivirals is great.  

The authors sum of their report this way:

Although the number of patients with oseltamivir-resistant pandemic (H1N1) 2009 virus infections was small in the United States during this period, this is the largest case-series published and confirms findings from reports with smaller samples (8–10).

 

Although all patients in our comparison group of patients with oseltamivir-susceptible pandemic (H1N1) 2009 were hospitalized, most patients in the oseltamivir-resistant group were also hospitalized. Finally, we do not have a comparison group of patients with immunocompromising conditions and oseltamivir-susceptible pandemic (H1N1) 2009 virus infections; thus, risk factors for infection with oseltamivir-resistant infection among patients with immunocompromising conditions cannot be determined.

 

The finding of oseltamivir-resistant pandemic (H1N1) 2009 viruses associated with oseltamivir treatment highlights the need for new antiviral agents and new treatment strategies.

(Thu, 30 Dec 2010 11:04:00 +0000)

# 5190

While the latest numbers from the HPA haven’t been released yet, British media sources are quoting the Royal College of General Practitioners as stating that influenza cases rose by 50% last week.

Assuming those numbers hold true, then the UK remains below the epidemic threshold.

 

But not by much.

And among certain age groups, and in some geographic locations, epidemic levels of influenza are probably already being seen (defined as 200 case consults/100K pop.).

While the rest of the northern hemisphere lags behind with average (or below average) influenza activity, the UK is being hit hard - and unusually early - with influenza and other winter ailments.

With schools back in session after the Christmas Holiday (generally Dec 20th-Jan 3rd) early next week, concerns are that influenza rates may rise even further, meeting or perhaps even exceeding the rates seen in the 1999-2000 flu epidemic.

Since all flu viruses aren’t created equal, comparing epidemics based on total numbers infected doesn’t tell us much about the ultimate severity (and death toll) of an outbreak.

Unlike most seasonal flu strains, novel H1N1 tends to infect those under the age of 65, who are (on average) stronger and healthier and less likely to succumb to influenza than the elderly.

Although H1N1  can cause serious illness in a small percentage of victims – most people recover without incident.  So it remains unclear how heavy the impact from this year’s influenza outbreak will turn out to be.

That said, the `official’ number of cases and deaths attributed to the flu virus are widely assumed to be a badly undercounted, and the demands placed on the NHS over the next several weeks are likely to be heavy.

A representative round up of some of this morning’s reportage from the UK media includes:

Swine flu fears give NHS 24 its busiest four-day period ever The Scottish Herald

 

Number Of Flu Hospital Patients ‘Rises Again’ Sky News

 

Warning as NHS prepares for flu rush Shields Gazette

 

Doctors urging caution after flu cases rise South Wales Evening Post

I’ll try to update this story later today,  when the HPA is expected to release their weekly surveillance numbers.

(Thu, 30 Dec 2010 09:59:00 +0000)

# 5189

Yesterday we saw a report of suspected bird flu at a duck farm in Cheonan (see South Korea Investigating Cheonan Duck Farm).  Overnight, we’ve several media reports regarding suspected avian flu at a second farm, this time in Iksan, North Jeolla Province.

Test results on both of these farms are awaited.

Iksan is more than 100 km south of Cheonan, and is in the heart of Korea’s poultry processing region.

The past month has seen several H5N1 detections among wild birds and domesticated poultry in both Japan & Korea (Aprox. locations shown below).

This report comes from Xinhau News.

S. Korea reports suspected case of bird flu

SEOUL, Dec. 30 (Xinhua) — A suspected case of bird flu has been reported from a chicken farm in a southeastern region of the country, raising concerns over a fresh outbreak of bird flu amid South Korea’s struggle with the spread of foot-and-mouth disease, the Ministry for Food, Agriculture, Forestry and Fisheries said Thursday.

 

The ministry said a chicken farm in Iksan, North Jeolla Province, reported a suspected case of bird flu late Wednesday. Another suspected case was reported from a duck farm in Cheonan, South Chungcheong Province.

 

Health officials are testing samples from both farms, the ministry said.

(Continue . . . )

Additional media reports  (hat tips Shiloh, Arkanoid Legent, Dutchy on this FluTrackers thread) suggest that culling may have begun on at least one farm.

This is getting a little close to home—Surrey is only about 30 minutes’ drive from where I live. Via News1130: Three women at Surrey Pre-trial Centre sick with H1N1. Excerpt:

Three women inmates at the Surrey Pre-trial Centre caught the H1N1 flu just before Christmas.

The Solicitor General’s ministry says the trio were given Tamiflu as soon as they started showing symptoms and they are being kept away from other prisoners. 

One of the women has recovered while the other two are still getting better.