H5N1

Flu News Europe, week 2

Via Flu News Europe, an excerpt from the week 2 update:

Week 02/2020 (6-12 January 2020) 

• Activity increased compared to week 01/2020, particularly in the southern part of the Region, with two Member States reporting high intensity and six reporting medium intensity. The remainder reported baseline or low intensity levels. 

• The percentage of samples from sentinel ILI surveillance patients that tested positive for influenza virus increased from 27% in the previous week to 40% this week. 

• The majority of reported influenza virus detections from sentinel ILI surveillance across the Region for week 02/2020 were type A (67%): this percentage has decreased from a high of 78% in week 49. The distribution of viruses detected varied between Member States and areas and within sub-regions. 

• Data from the 22 countries or regions reporting to the EuroMOMO project indicated that all-cause mortality was at expected levels for this time of the year. 

• ECDC published an Influenza virus characterization report, summarizing surveillance data in Europe through December 2019 

2019/20 season overview  

• For the Region as a whole, influenza activity commenced earlier than previous years. 

• Influenza activity in the European Region, based on sentinel sampling, first exceeded a positivity rate of 10% in week 47/2019 and has remained over 10% for 8 weeks. There has been an overall increasing trend in the weekly positivity rate for influenza virus detections among sentinel ILI surveillance patients, following a dip in week 52. 

• Type A viruses have dominated across the European Region, though several Member States and areas have reported influenza type B virus dominance or co-dominance of types A and B viruses. 

• In sentinel sources, both influenza A subtypes, A(H3N2) and A(H1N1)pdm09, are co-circulating and of the influenza B viruses, the vast majority (98%) have been B/Victoria lineage. 

• Influenzanet, which uses self-reported symptoms for ILI surveillance in the general population of European countries, is included in the bulletin as a pilot for the 2019/2020 season. 

• ECDC and WHO Regional Office published a joint Regional Situation Assessment for the 2019–2020 influenza season up to week 49/2019, which focused on disease severity and impact on healthcare systems to assist forward planning in Member States.

Pneumonia in Ukraine 2020: 3 dead, over 50 hospitalized

Thanks to FluTrackers for posting this report from 24 Channel earlier today: Pneumonia in Ukraine 2020 - how many people died from pneumonia. The Google translation:

Ternopol hospitals recorded an outbreak of viral pneumonia. In the 2nd city hospital, there are more than 50 patients with viral pneumonia. Five people in intensive care, and three have already died.  

It is reported by TSN. It is noted that patients began to massively seek help in medical institutions after the New Year. Patients in hospitals have the same symptoms - at the beginning the temperature rises, which is difficult to bring down, and a cough appears.

Pulmonologist Alla Pasternak urges, at the first manifestations of the symptoms of pneumonia, to immediately consult doctors in order to start treatment on time. Without specialized help, a sick person can "burn out" in a few days.  

Previously, such pneumonia occurred in people when 10 years ago there was an epidemic of swine flu in Ukraine. 

In a commentary to UNIAN, the director of the city hospital No. 2 Rostislav Levchuk said the first patient died in mid-December, he was taken in serious condition from a district hospital. The man was 45 years old. Two more died in early January, both of working age. 

The director of the hospital added that patients who died were admitted to the hospital on the 5-10th day of the course of the disease with advanced forms.  

"Yesterday, a 36-year-old man came to us, he did not apply for qualified help for a month, you can imagine what condition he is in. Two doctors also came to us, in particular a midwife. They were also self-medicating,” added Rostislav Levchuk.  

Note that in Ukraine, from December 31 to January 14, 5 deaths from complications of swine flu have already been recorded! None of the dead were vaccinated. We emphasize that the best prevention of influenza is annual vaccination.

Flu News Europe: Week 1 update

Via Flu News Europe:

Week 01/2020 (30 December 2019-5 January 2020) 

• One Member State reported high intensity activity for the first time this season and three reported medium intensity activity; however, the remainder reported baseline or low intensity levels. 

• The percentage of sentinel ILI surveillance patients positive for influenza virus remains elevated, but has varied in the last three weeks, probably related to under-reporting during the Christmas/New Year period. 

• The majority of reported influenza virus detections from sentinel ILI surveillance across the Region were type A (60%). This percentage has decreased each week from 78% in week 49 but varied between Member States and areas and within sub-regions. 

• Influenzanet, which uses self-reported symptoms for ILI surveillance in the general population of European countries, is included in the bulletin for the first time this week as a pilot. For the last several weeks, activity has been moderate and is currently increasing in the majority of participating countries. 

2019/20 season overview  

• For the Region as a whole, influenza activity commenced earlier than previous years, increasing each week until week 51; since then it has remained elevated but variable. 

• Influenza activity in the European Region, based on sentinel sampling, first exceeded a positivity rate of 10% in week 47/2019 and has remained over 10% for 7 weeks. 

• Type A viruses have dominated across the European Region, although the proportion has been decreasing since week 49 and a number of countries have reported influenza type B virus dominance or co-dominance of types A and B viruses. 

• In sentinel sources, both influenza A subtypes, A(H3N2) and A(H1N1)pdm09, are co-circulating and of the influenza B viruses, the vast majority (97%) have been B/Victoria lineage. 

• ECDC and WHO Regional Office published a joint Regional Situation Assessment of the 2019–2020 influenza season up to week 49/2019, which focuses on disease severity and impact on healthcare systems to assist forward planning in Member States.

Flu News Europe, week 51

Via Flu News Europe:

Week 51/2019 (16-23 December 2019) 

• The majority of reported influenza virus detections across the Region were type A, although 5 countries reported type B virus dominance and 2 reported co-dominance of type A and B viruses. 

• Data from the 21 countries or regions that reported to the EuroMOMO project up to week 50/2019 indicated that all-cause mortality was at expected levels for this time of the year. 

• ECDC and WHO Regional Office published a joint Regional Situation Assessment of the 2019–2020 influenza season up to week 49/2019, which focuses on disease severity and impact on healthcare systems to assist forward planning in Member States. 

2019/20 season overview  

• Influenza activity has increased in the European Region, although most countries still reported influenza activity rates below/at baseline levels or low levels. 

• Influenza activity in the European Region, based on sentinel sampling, first exceeded a positivity rate of 10% in week 47/2019. 

• Type A viruses have dominated across the European Region, although a number of countries reported influenza type B virus dominance or co-dominance of types A and B viruses. 

• In sentinel sources, both influenza A subtypes, A(H3N2) and A(H1N1)pdm09, are co-circulating and of the influenza B viruses, the vast majority (97%) are B/Victoria lineage.

ECDC: Influenza virus characterisation, November 2019

ECDC has published Influenza virus characterisation, November 2019.

This is the second influenza characterisation report for the 2019–20 influenza season. As of week 48/2019, 6 887 influenza detections across the WHO European Region had been reported; of which 84% were type A viruses, with A(H3N2) prevailing over A(H1N1)pdm09, and 16% type B viruses, with 123 of 137 (90%) ascribed to a lineage B/Victoria.

New discovery could spell end to seasonal flu

Via Deutsche Welle: New discovery could spell end to seasonal flu. Excerpt:

A potential breakthrough discovery of new antibodies could lead to a universal vaccine. If successful, it could protect against all types of deadly influenza viruses and even prevent pandemics, a study shows. 

 Immunologist Ali Ellebedy was working on a study analyzing the immune response to flu infection in humans. During his research, he spotted a new type of powerful antibody in a blood sample from a patient infected with human influenza virus.   

Ellebedy then sent samples of the antibody to Florian Krammer — a microbiologist who proved the effectiveness of the antibodies by testing them against extensive samples of virus proteins dating back to the 1970s. These proteins, called neuraminidase, enable the virus to spread through the human body. 

The study, which was jointly conducted by Scripps Research, Washington University's School of Medicine in St. Louis and the Icahn School of Medicine in New York, was published in the October 25 issue of Science.  

Future vaccine could survive antiviral resistance  

Krammer told DW that the beauty of this new antibody, called 10G1, is that it binds to the parts of the virus that never change. This means that even if new strains of influenza viruses are detected, a potential vaccine containing new antibodies would still be effective. 

Moreover, the antibody has a powerful potential to attack both A and B subtypes of influenza viruses, making it an even better candidate for a universal vaccine that would combat human, swine, and bird strains, as well as other rarer strains of lethal flu viruses.

Flu News Europe, week 40

An excerpt from Flu News Europe:

Week 40/2019 (30 September– 6 October 2019) 

• This is the first weekly report for the 2019–2020 influenza season. 

• Influenza activity was low throughout the European Region. Influenza viruses were detected sporadically in specimens from persons with respiratory illness presenting to medical care. 

• Both influenza A and B type viruses were detected. 

• For week 40/2019, data from the 21 countries or regions reporting to the EuroMOMO project indicated all-cause mortality to be at expected levels for this time of the year. 

2018/19 season overview  

• As is usual for this time of year, influenza activity is low in the European Region. 

• During the influenza Vaccine Composition Meeting for the southern hemisphere 2020 season, held in September 2019, WHO recommended the A(H1N1)pdm09 component to be an A/Brisbane/02/2018 (H1N1)pdm09-like virus, the A(H3N2) component an A/South Australia/34/2019 (H3N2)-like virus and the B/Victoria-lineage component to be a B/Washington/02/2019-like virus. The B/Yamagata-lineage component, included only in quadrivalent vaccines is a B/Phuket/3073/2013-like virus. The full report can be found here.

ECDC: Influenza virus characterisation, September 2019

ECDC has published Influenza virus characterisation, September 2019. The executive summary:

Since the July 2019 characterisation report1, a further three shipments of influenza-positive specimens from EU/EEA countries were received at the London WHO CC, the Francis Crick Worldwide Influenza Centre (WIC). A total of 1 511 virus specimens, with collection dates after 31 August 2018, have been received.  

The 85 A(H1N1)pdm09 test viruses characterised antigenically since the last report showed equivalent good reactivity with antisera raised against both the A/Michigan/45/2015 2018–19 vaccine virus and the A/Brisbane/02/2018 2019–20 vaccine virus. The 613 test viruses with collection dates from week 40/2018 genetically characterised at the WIC, including two H1N2 reassortants, have all fallen in subclade 6B.1A, defined by S74R, S164T and I295V HA1 substitutions; 564 of these viruses also have HA1 S183P substitution, often with additional substitutions in HA1 and/or HA2.  

Since the last report, 37 A(H3N2) viruses successfully recovered had sufficient HA titre to allow antigenic characterisation by HI assay in the presence of oseltamivir; all were poorly recognised by antisera raised against the vaccine virus, egg propagated A/Singapore/INFIMH-16-0019/2016. Of the 505 viruses with collection dates from week 40/2018 genetically characterised at the WIC, 399 were clade 3C.2a (with 43 3C.2a2, 17 3C.2a3, eight 3C.2a4 and 331 3C.2a1b); 106 were clade 3C.3a.  

Ten B/Victoria-lineage viruses have been characterised in this reporting period. All recent viruses have HA1 amino acid substitutions of I117V, N129D, and V146I compared to B/Brisbane/60/2008 (clade 1A), a previous vaccine virus. Groups of viruses defined by deletions of two (Δ162-163, 1A(Δ2)) or three (Δ162-164, 1A(Δ3)) amino acids in HA1 have emerged, with the Δ162-164 group having subgroups of Asian and African origin. These virus groups are antigenically distinguishable by HI assay. Of 20 viruses from EU/EEA countries this season that have been characterised genetically, one has been clade 1A, two 1A(Δ2) and 17 1A(Δ3) (16 African and one Asian subgroup).   

Nine B/Yamagata-lineage viruses have been characterised antigenically in this reporting period, giving a total to 23 for the 2018–19 season. All have HA genes that encode HA1 amino acid substitutions of L172Q and M251V compared to, but remain antigenically similar to, the vaccine virus B/Phuket/3073/2013 (clade 3) recommended for use in quadrivalent vaccines for the next northern hemisphere influenza season. 

Branswell: The last flu pandemic was a 'quiet killer.' Why we can't predict the next one

Via STAT, Helen Branswell writes a must-read: The last flu pandemic was a 'quiet killer.' Why we can't predict the next one. This brings back a lot of memories. Excerpt:

The cryptic phone call came on a Monday. The Centers for Disease Control and Prevention was holding an important teleconference for a few reporters. I should dial in. 

When the time came, just a handful of reporters were on the line. Also there: the CDC’s top flu experts. They sounded worried. 

Two unrelated children from southern California had tested positive for flu infections caused by viruses that normally sicken pigs. This could have been a fluke, but from the unusual nature of the call and from the tension in the voices of the experts, it was clear that the CDC officials thought it might be something else: an influenza pandemic. 

 That teleconference took place on April 20, 2009. Over the next seven weeks it became apparent that any fears they had had been well-founded.  

On June 11, 2009 — 10 years ago today — the World Health Organization declared that the swine flu virus we now simply call H1N1 had indeed triggered a pandemic, the first time in four decades a new flu virus had emerged and was triggering wide-scale illness around the globe.

Since it started circulating in the spring of 2009, H1N1 has infected about 100 million Americans, killing about 75,000 and sending 936,000 to the hospital, the CDC estimates. Another virus, H3N2, is responsible for more infections, but “in terms of the severity, H1 is kind of this quiet killer,” said Dr. Daniel Jernigan, head the CDC’s flu division.  

In the hands of Hollywood, pandemics tend to be of the one-size-fits-all variety. They unleash massive chaos and spread at lightning speed, as health officials in hooded biohazard suits rush to distribute vaccinations. And in real life, flu pandemics, which tend to strike only a few times each century, could be that terrifying. But, a decade onward, the experience of H1N1 is a reminder that it’s impossible to know from the get-go how a pandemic will play out. 

Science currently has no way to predict when pandemics will occur. The fact that there were 41 years between the 1968 pandemic — known as the Hong Kong flu — and the 2009 pandemic doesn’t mean the next will take another 30 years or so to materialize. There is no pattern; flu pandemics happen when they happen, and pandemic planning is ever ongoing. 

In the case of H1N1, the public health world was steeling itself for a potentially catastrophic outbreak. Just six years earlier, officials began to respond to a very dangerous bird flu virus called H5N1, first in Southeast Asia and then beyond. It was deadly to chickens and other poultry but — and this was unusual — it was also occasionally infecting people. When it did, the outcome was sobering: More than half of people known to have been infected with the virus died from the infection. 

The number of people infected with H5N1 was small, but it stoked fears that this fearsome flu might be readying itself to cause a pandemic. In its place, however, arrived H1N1. 

It was distantly related to other H1N1 viruses that had circulated among people for most of the 20th century. In fact, pigs acquired H1N1 decades before from people. But this new virus had evolved in a way that helped it unlock the mysteries of the human respiratory tract and sicken people.

Fortunately, though the infection could be severe, it was not devastating in most cases. A study published in 2013 suggested between 123,000 and 200,000 people globally may have died as a result of the 2009 H1N1 pandemic.  

This was certainly not nothing. But it was also not what people had feared would be in store, and it was a substantially lower death toll than was seen in the 1957 and 1968 pandemics, which each killed about 1 million people at a time of lower global populations. In fact, the H1N1 death toll was lower than the global death toll for typical flu seasons, as estimated by the WHO.  

But just looking at the number of deaths masks the full impact of the pandemic, because the people who died were younger than those influenza normally claims. (The elderly, whose immune systems had seen viruses similar to this one long ago, weathered the pandemic pretty well.) A group of researchers who analyzed the deaths based on years of life lost concluded the pandemic’s toll in the United States was at least as bad as an average H3N2 flu season and potentially as severe as the 1968 pandemic.

Ten years ago: The first news of H1N1

Ten years ago, this blog was just about all H5N1, and I had a lot of news on cases in Indonesia, Egypt, and Pakistan. Then, on April 21, I posted an item by Helen Branswell, then with The Canadian Press: Branswell on the California swine-flu cases. Excerpt and then a comment:

U.S. public health authorities are investigating two cases of swine flu in unrelated children in California, a development that has officials in Canada and elsewhere on alert.   

Discovery of the two cases, in children who apparently had no contact with pigs or with each other, suggests there probably has been some person-to-person spread of swine flu viruses, officials of the U.S. Centers for Disease Control said Tuesday.  

Whether the viruses continue to spread isn't currently known.   

"The investigation is not finished. It's ongoing. But of course not having that direct swine link does raise additional questions and does suggest that there may have been human-to-human transmission. And so it basically ratchets it (concern) up a bit," said Dr. Nancy Cox, head of the CDC's influenza division.  "I think this is one of those situations where everyone will want to stay tuned."  

U.S. officials notified the World Health Organization of the cases last Friday, as required under the International Health Regulations. That treaty stipulates that countries must notify the WHO when they see cases of infectious diseases that pose an international threat, such as novel subtypes of influenza with pandemic potential. 

The next day saw a "swine flu" post from the much-missed Revere, Flublogia's resident grownup in those days. Although I didn't post it, the CDC also issued a notice about it on April 22, and on the 23rd the Globe and Mail warned that Canadians returning from Mexico should be alert to the symptoms of "Mexican flu."

What followed was not so much mission creep as mission drag, as a real live serious novel influenza hauled me and the rest of Flublogia out of our comfortable niche and into a much more complicated world. That drag continues.