H5N1

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.

Children under 10 years of age were more affected by the 2018/19 influenza A(H1N1)pdm09 epidemic in Canada

Via Eurosurveillance: Children under 10 years of age were more affected by the 2018/19 influenza A(H1N1)pdm09 epidemic in Canada: ‎possible cohort effect following the 2009 influenza pandemic. The abstract:

Introduction 

Findings from the community-based Canadian Sentinel Practitioner Surveillance Network (SPSN) suggest children were more affected by the 2018/19 influenza A(H1N1)pdm09 epidemic. 

Aim 

To compare the age distribution of A(H1N1)pdm09 cases in 2018/19 to prior seasonal influenza epidemics in Canada. 

Methods 

The age distribution of unvaccinated influenza A(H1N1)pdm09 cases and test-negative controls were compared across A(H1N1)pdm09-dominant epidemics in 2018/19, 2015/16 and 2013/14 and with the general population of SPSN provinces. Similar comparisons were undertaken for influenza A(H3N2)-dominant epidemics.  

Results 

In 2018/19, more influenza A(H1N1)pdm09 cases were under 10 years old than controls (29% vs 16%; p < 0.001). In particular, children aged 5–9 years comprised 14% of cases, greater than their contribution to controls (4%) or the general population (5%) and at least twice their contribution in 2015/16 (7%; p < 0.001) or 2013/14 (5%; p < 0.001). Conversely, children aged 10–19 years (11% of the population) were under-represented among A(H1N1)pdm09 cases versus controls in 2018/19 (7% vs 12%; p < 0.001), 2015/16 (7% vs 13%; p < 0.001) and 2013/14 (9% vs 12%; p = 0.12). 

Conclusion 

Children under 10 years old contributed more to outpatient A(H1N1)pdm09 medical visits in 2018/19 than prior seasonal epidemics in Canada. In 2018/19, all children under 10 years old were born after the 2009 A(H1N1)pdm09 pandemic and therefore lacked pandemic-induced immunity. In addition, more than half those born after 2009 now attend school (i.e. 5–9-year-olds), a socio-behavioural context that may enhance transmission and did not apply during prior A(H1N1)pdm09 epidemics.

Jamaica: Three H1N1 deaths - Opposition raps government for failing to issue advisory on deadly flu

Thanks to Sean Smith for alerting me to this story. Via The Jamaica Gleaner: Three H1N1 deaths - Opposition raps Gov’t for failing to issue advisory on deadly flu. Excerpt:

The Ministry of Health has faced scathing criticism for failing to inform the public about the presence of the influenza H1N1 in the country, following yesterday’s revelation by broadcaster Alan Magnus that his late wife Karlene ‘Kerry’ Douglas died last Friday due to complications associated with the virus.  

“I have heard of several people dying from it. [For] Kerry’s death, the paper which we got from the hospital stated that that’s what she died from,” Magnus said while speaking on RJR 94 FM.  

Yesterday, Nicole Dawkins-Wright, acting director of emergency, disaster management and special services in the Ministry of Health, confirmed that three Jamaicans have died as a result of the H1N1 influenza virus in St Ann, Kingston, and St Catherine. It was also revealed that there were six confirmed and 110 suspected cases across the island since the start of the year.  

She also told The Gleaner that the H1N1 virus present in the island is not the swine flu strain.

Meanwhile, Sean Smith also tells me, Guyana is dealing with H1N1. Via INews Guyana: BREAKING NEWS: 1 dead, 8 suspected Swine Flu cases detected in Region 1.

The Guyanese Ministry of Public Health website doesn't have anything on flu, and I can't even access Jamaica's Ministry of Health.

Flu News Europe, week 12

Flu News Europe has published its week 12 (March 18-24) update. Excerpt:

• Of 45 countries reporting on geographic spread only 11, located in northern, southern, and western areas of the European Region, reported widespread activity. Specimens collected from individuals presenting with ILI or ARI to sentinel primary health care sites yielded an influenza virus positivity rate of 38%, similar to the rate of 39% in the previous week. 

• Of 45 countries reporting on intensity, 41 reported baseline or low intensity. No countries reported high intensity levels. 

• Influenza type A virus detections dominated with more A(H3N2) than A(H1N1)pdm09 viruses among sentinel and non-sentinel source specimens. Few influenza B viruses were detected. 

• Of the specimens from patients with severe acute respiratory infection (SARI) collected in week 12/2019 that were tested for influenza viruses, 21% were positive and almost all were type A. 

• Pooled data from 22 Member States and areas reporting to the EuroMOMO project indicated that the excess mortality observed in previous weeks has returned to normal levels.

Flu News Europe, week 10

Flu News Europe has published its week 10 (March 4-10) update. Excerpt:

• Influenza activity was widespread in the European Region. Specimens collected from individuals presenting with ILI or ARI to sentinel primary health care sites yielded an influenza virus positivity rate of 42.8%. 

• Influenza type A virus detections dominated with slightly more A(H1N1)pdm09 than A(H3N2) viruses. Very few influenza B viruses were detected. 

• 28.3% of specimens from patients with severe acute respiratory infection (SARI) collected in week 10/2019 tested positive for influenza virus, and almost all were type A. 

• Pooled data from 22 Member States and areas reporting to the EuroMOMO project indicated that the excess mortality observed in previous weeks continued to decline. Excess mortality was seen in persons aged 65 years and above and, to a lesser extent, in persons 15-64 years.

Co-circulation of influenza A(H1N1)pdm09 and influenza A(H3N2) viruses, WHO European Region, October 2018 to February 2019

Eurosurveillance has published Co-circulation of influenza A(H1N1)pdm09 and influenza A(H3N2) viruses, World Health Organization (WHO) European Region, October 2018 to February 2019. The abstract:

In the World Health Organization European Region, the 2018/19 influenza season started in week 49 2018, crossing 10% virus-positivity in sentinel surveillance specimens. At week 5 2019, activity remained elevated with positivity rates at 55%. Both A(H1N1)pdm09 and A(H3N2) viruses circulated widely and detection levels in primary care and hospital settings were similar to past seasons. Hospitalisation data may suggest an increased susceptibility to A(H1N1)pdm09 virus in older age groups.

Interim 2018/19 influenza vaccine effectiveness: Six European studies, October 2018 to January 2019

Eurosurveillance has published Interim 2018/19 influenza vaccine effectiveness: six European studies, October 2018 to January 2019. The abstract:

Influenza A(H1N1)pdm09 and A(H3N2) viruses both circulated in Europe in October 2018–January 2019. Interim results from six studies indicate that 2018/19 influenza vaccine effectiveness (VE) estimates among all ages in primary care was 32–43% against influenza A; higher against A(H1N1)pdm09 and lower against A(H3N2). Among hospitalised older adults, VE estimates were 34–38% against influenza A and slightly lower against A(H1N1)pdm09. Influenza vaccination is of continued benefit during the ongoing 2018/19 influenza season.