H5N1

WHO: Influenza A(H1N1) variant virus - Brazil

Thanks to Mike Coston for tweeting about this WHO DON: Influenza A(H1N1) variant virus - Brazil. Excerpt:

On 7 June 2023, Brazil notified the World Health Organization (WHO) of a fatal laboratory-confirmed human case of infection with a swine-origin influenza A(H1N1) variant (v) virus in the inner state of Paraná.  

Sporadic human cases of influenza A(H1N1)v have been reported previously, including from Brazil. According to the International Health Regulations (IHR) 2005, a human infection caused by a novel influenza A virus subtype is an event that has the potential for high public health impact and must be notified to the WHO.  

Based on the information currently available, WHO considers this a sporadic case, and there is no evidence of person-to-person transmission of this event. The likelihood of community-level spread among humans and/or international disease spread through humans is low.  

Description of the case  

On 7 June 2023, the Brazil IHR National Focal Point (NFP) notified WHO of a fatal human infection caused by a swine-origin influenza A(H1N1)v virus detected by the National Influenza Centre (NIC), Oswaldo Cruz Foundation, Rio de Janeiro.  

The patient was a 42-year-old woman with underlying medical conditions who lived near a swine farm. She developed fever, headache, sore throat, and abdominal pain on 1 May 2023 and was hospitalized on 3 May with a severe acute respiratory infection. On 4 May, the patient was admitted to the Intensive Care Unit (ICU) and she passed away on 5 May.  

Ongoing investigations reported that the patient did not have any direct contact with pigs, however, two of her close contacts worked at the swine farm. The two contacts did not develop respiratory disease and tested negative for influenza. To date, no human-to-human transmission associated with this case has been identified.   

During hospitalization, a nasopharyngeal swab sample was collected from the patient for influenza and SARS-CoV-2 testing, as part of regular respiratory virus surveillance activities. Real-time Polymerase Chain Reaction (RT-PCR) was conducted at the State of Paraná Central Public Health Laboratory, where the sample was subtyped as an influenza A/H1 virus. The sample also tested positive for a swine influenza A virus marker by RT-PCR.   

The specimen was forwarded to the National Influenza Centre Oswaldo Cruz Foundation, in Rio de Janeiro, where further complementary analyses and genomic sequencing were performed. Samples received at the NIC on 25 May were confirmed to be an influenza A(H1N1)v virus by sequence analysis on 30 May. The recovered genome has a high identity (99%) with the haemagglutinin (HA) of other Influenza A(H1N1)v viruses previously detected in the municipality of Toledo state of Paraná in 2022. In addition, it has 96% identity with the HA of viruses collected from pigs in Brazil in 2015.  

On 8 June, after the Brazilian Ministry of Health (MoH) notified WHO under the IHR, the NIC started the process to send the patient's samples to the WHO Collaborating Centre at the United States Centers for Disease Control and Prevention (US CDC) for further characterization. 

What happens when flu meets Covid-19?

Via The Guardian: What happens when flu meets Covid-19? Excerpt:

Optimists had hoped Covid-19 might not withstand the blistering heat of a British summer. However those hopes have faded: the virus staged a recent resurgence in Iran amid actual blistering temperatures, and has had no trouble persisting in sultry Singapore. 

But what happens to Covid-19, and us, when the rain and chill – and flu and sniffles – of autumn set in? Especially, how will the annual winter flu epidemic play out amid a Covid-19 pandemic?  

One thing is a given. “We can expect waves of Covid in the fall,” says virologist Ab Osterhaus of the Research Centre for Emerging Infections and Zoonoses in Hanover. By then, he hopes, we might be better at treating severe cases, and more countries might be able to test, trace and quarantine all cases and their contacts, and contain the virus, better than they can now. 

The biggest worry in the UK is that hospitals can struggle to cope with the winter flu season. This year they will have to cope with Covid-19 as well, which shows no sign of going away by then, and could even surge if it turns out that cold temperatures, or the circulation of other autumn and winter viruses, boost its spread.  

The first problem will be figuring out which virus a patient has. Flu, Covid-19 and other seasonal respiratory diseases are virtually indistinguishable on the basis of symptoms, warns Barbara Rath of the University of Nottingham: even the loss of taste and smell many people get with Covid-19 is not unique. We need more and better diagnostic tests, she says, because the difference matters: medical staff need full protective gear to manage a Covid patient, but they can be vaccinated for flu. 

The real unknown is what Covid-19 does around other viruses. Every autumn there is a predictable series of outbreaks of respiratory viruses. It starts with rhinovirus, the main cause of the common cold, which breaks out every September as young children go to school and swap mucus. As no parent needs to be told, children are to sniffles what mosquitoes are to malaria. 

The rhinovirus subsides as most children are exposed and their immune systems activate. Then another virus breaks out: respiratory syncytial virus, or RSV. Every year in October or November, this causes mild colds in people of all ages, but sometimes severe lung infections in the youngest and oldest of us. RSV is so common that virtually all two-year-olds have already had it, and it sends more babies to hospital with pneumonia than any other virus.  

Then RSV subsides, and the annual flu epidemic sets in, anywhere from early winter to spring, driven mainly by transmission among children, but taking its main toll among the elderly: some 8,000 on average die yearly of flu in the UK. This predictable parade of infections almost seems a spiteful campaign by viruses to keep people, especially families with young kids, sick for as long as possible.  

But it is just a product of a little-understood phenomenon called “viral interference”: while one of these viruses holds sway in a person, or the population, for some reason the others can’t get a toehold. In September 2009, the swine flu pandemic that went on to sweep the world should have invaded Europe from the Americas. But the annual rhinovirus epidemic actually kept it at bay. The highly contagious new flu took over only when rhinovirus subsided, bumping RSV down the queue: RSV moved in only after that first wave of flu subsided. 

The question now is where Covid-19 is going to fit amid this viral jostling. Not every virus takes turns like this, says Ian MacKay of the University of Queensland. Sometimes you can be infected by two at once. So which kind is Covid-19?

Dr. Mackay is alert but not alarmed: What to make of new H1N1 swine flu with 'pandemic potential' found in China

Via The Conversation, Dr. Ian Mackay offers useful perspective: Alert but not alarmed: what to make of new H1N1 swine flu with 'pandemic potential' found in China. Excerpt:

Researchers have found a new strain of flu virus with “pandemic potential” in China that can jump from pigs to humans, triggering a suite of worrying headlines. 

It’s excellent this virus has been found early, and raising the alarm quickly allows virologists to swing into action developing new specific tests for this particular flu virus.  

But it’s important to understand that, as yet, there is no evidence of human-to-human transmission of this particular virus. And while antibody tests found swine workers in China have had it in the past, there’s no evidence yet that it’s particularly deadly. 

What we know so far 

China has a wonderful influenza surveillance system across all its provinces. They keep track of bird, human and swine flus because, as the researchers note in their paper, “systematic surveillance of influenza viruses in pigs is essential for early warning and preparedness for the next potential pandemic.” 

In their influenza virus surveillance of pigs from 2011 to 2018, the researchers found what they called “a recently emerged genotype 4 (G4) reassortant Eurasian avian-like (EA) H1N1 virus.” In their paper, they call the virus G4 EA H1N1. It has been ticking over since 2013 and became the majority swine H1N1 virus in China in 2018.  

In plain English, they discovered a new flu that’s a mix of our human H1N1 flu and an avian-based flu.  

What’s interesting is antibody tests picked up that workers handling swine in these areas have been infected. Among those workers they tested, about 10% (35 people out of 338 tested) showed signs of having had the new G4 EA H1N1 virus in the past. People aged between 18 to 35 years old seemed more likely to have had it.  

Of note, though, was that a small percentage of general household blood samples from people who were expected to have had little pig contact were also antibody positive (meaning they had the virus in the past).  

Importantly, the researchers found no evidence yet of human-to-human transmission. They did find “efficient infectivity and aerosol transmission in ferrets” - meaning there’s evidence the new virus can spread by aerosol droplets from ferret to ferret (which we often use as surrogates for humans in flu studies). G4-infected ferrets became sick, lost weight and acquired lung damage, just like those infected with one of our seasonal human H1N1 flu strains.  

They also found the virus can infect human airway cells. Most humans don’t already have antibodies to the G4 viruses meaning most people’s immune systems don’t have the necessary tools to prevent disease if they get infected by a G4 virus. 

In summary, this virus has been around a few years, we know it can jump from pigs to humans and it ticks all the boxes to be what infectious disease scholars call a PPP — a potential pandemic pathogen. 

If a human does get this new G4 EA H1N1 virus, how severe is it? 

We don’t have much evidence to work with yet but it’s likely people who got these infections in the past didn’t find it too memorable. There’s not a huge amount of detail in the new paper but of the people the researchers sampled, none died from this virus.  

There’s no sign this new virus has taken off or spread in the regions of China where it was found. China has excellent virus surveillance systems and right now we don’t need to panic. 

The World Health Organisation has said it is keeping a close eye on these developments and “it also highlights that we cannot let down our guard on influenza”.

How H1N1 lessons can help Canada handle the COVID-19 crisis

Via Policy Options, a thoughtful article by Regan P. Watts: How H1N1 lessons can help Canada handle the COVID-19 crisis. Excerpt:

Canada’s Health Minister Patty Hajdu and a team of public servants from Health Canada and the Public Health Agency of Canada offered their best guidance this week on how to respond to the spread of the coronavirus – or COVID-19. The news conference reminded me of the last time our country faced a similar outbreak back in 2009 with H1N1. Canadians are once again facing a public health outbreak with the backdrop of the politics of a minority government in Ottawa. 

The last time we had a major public health outbreak in Canada was with H1N1. I was a director in the health minister’s office from November 2008 to July 2009, and during that time, Canada was faced with a significant health crisis in what later became known as the H1N1 influenza pandemic. 

 The crisis began to unfold several months after the federal election had returned the Conservatives to minority status. The political backdrop on Parliament Hill was not ideal – a disastrous fall Economic and Fiscal Update had brought the government to the brink of collapse. There was deep distrust between the political parties. To put it bluntly – it was a tough, weird time on Parliament Hill. 

My boss, Leona Aglukkaq, was not new to being a health minister – she had held the post previously in Nunavut. Still, she did not have experience dealing with a flu pandemic. None of us working in her ministerial office did. 

As a governing, political, and communications exercise, managing this major public health influenza outbreak was a high wire act. 

As with any outbreak, the biggest challenge in managing H1N1 was our responsibility to educate the public while not raising alarm. Typically, the public servants write a first draft (and even a second) of communications materials before they are given to the minister’s office. Given the nature of the issue and how fast the media cycle moved, we didn’t have this luxury, and a pair of us political staffers worked concurrently with the public service. 

Our communications and political challenges for H1N1 could be summarized as: 

• Needing to inform and educate the public while not scaring people; 

• Navigating the minority Parliament and figuring out how to engage with our political counterparts; 

• Advising and supporting a minister who was not experienced in high stakes politics and whose communications skills were still being developed. 

To respond to these challenges, we made a strategic communications decision early on – which the Liberal government in Ottawa appears to be doing now – to lean heavily on the public service and public health professionals and let them lead. The last thing the public wants in a time like H1N1 or COVID-19 is the appearance of a politician managing public health.  

We were lucky to have one of the most experienced deputy ministers in Ottawa on our side, Morris Rosenberg. Morris was deputy minister of justice when 9/11 occurred, so he had seen this type of movie before. We were also supported by the late Dr. Frank Plummer and Dr. David Butler-Jones as chief public health officer (CPHO). Coincidentally, Dr. Theresa Tam – Canada’s current CPHO – was also involved as director general for the Public Health Agency of Canada’s Centre for Emergency Preparedness and Response. 

These career public servants were used to being the unsung heroes, but our decision to put them front and centre was easy: they were highly credible government spokespeople. 

The other strategic decision was political. We decided to engage our opposition critics and bring them inside the tent. Why? Because, you’ll remember, this was a minority Parliament and we had a rookie minister who would have been shredded by her opponents and the media if we weren’t careful. I remember the look on people’s faces when I suggested the idea. After a short conversation with the PMO, we made the calls to our critics to open a dialogue and brief them on the ongoing issues.  

Why would we brief our critics? A few reasons. For one, briefing opposition MPs and seeking their input meant they became vested in our overall success. Secondly, the Liberal party actually had two health critics; one who was a licensed physician (Carolyn Bennett) and one who had an actual doctorate in pandemics (Kirsty Duncan). 

Finally, the New Democratic Party’s critic was a firebrand and legend of Parliament, Judy Wasylycia-Leis. Wasylycia-Leis could generate a headline with remarkable ease – and the support of her party in the Commons was what we need to get anything passed in Parliament connected to H1N1.

The new COVID-19 coronavirus and preparing for the next viral pandemic

An excellent perspective from Michael Specter in The New Yorker: The New Coronavirus and Preparing for the Next Viral Pandemic. Excerpt:

These viruses all pose special threats because they are new, which means that humans have no antibodies to defend against them. The 2009 H1N1 epidemic infected at least 1.4 billion people, most of them before vaccines or treatments for the virus were available. And that was in a year when, by most accounts, the W.H.O. moved as expeditiously as it ever has. That strain of influenza killed as many as two hundred thousand people in the world—but it could have been many times worse. 

In 1957, for example, the Asian flu pandemic killed more than a million people. In 1968, the Hong Kong flu pandemic killed between one and four million. Maybe we will also be lucky this year. (It ought to be remembered that, even now, the seasonal flu poses a much greater threat to the health of the average American.) Unless covid-19 proves to be uniquely virulent, it will likely subside within a few months, and the danger it poses will be substantially forgotten, like that of sars, mers, avian influenza, and other zoonotic diseases. But it is too soon to know for certain. 

Scientists are moving with great speed to stop this pandemic. They sequenced the virus in less than two weeks—an essential step in creating diagnostics, drugs, and vaccines, and one that only a few years ago would have taken months. But, even with expedited trials and drug development, it could take a year to create a vaccine. If this virus were to swerve out of control before then, the death rate could soar. 

In addition to the human toll, the economic damage to China—and, eventually, to the rest of the world—would be enormous. Industrial supply chains throughout the world have already been badly disrupted. Travel to and from China has all but stopped, and xenophobic attacks against Asians are rising. Although New York City has not reported a single confirmed case of covid-19, business in Chinatown has reportedly fallen by more than fifty per cent since the epidemic began.  

Not all of this has to happen; we can do a much better job of preparing for these epidemics, just as we no longer wait to have heart attacks before we use our knowledge to limit their risk. Prevention works, and it can work with viral epidemics. For now we can be much more vigilant about improving sanitary conditions and regulating livestock in the kinds of markets where outbreaks are likely to occur. Sufficient and reliable tests for people who may have been exposed must be made readily available. There are scores of similar viruses found in host reservoirs—most notably, bats. Many of those viruses have genetic similarity to this coronavirus, and also to sars and mers. 

The time has come to use the modern tools of molecular and synthetic biology to make drugs and vaccines to protect us from them. We can make DNA vaccines in laboratories and store them as spare parts, just as we do with parts for a phone or a laptop. Why not work on making vaccines that would protect broadly against this entire class of virus, rather than waiting for each one to attack us, and then try to fight back? Today, with the annual flu, we grow most of our vaccines in eggs, just as we have for decades. It’s time to move on. 

At some point, not many years from now, we will have the capacity to instantly sequence viruses and to make and operate diagnostic tests anywhere, not just in a lab. Biology is becoming digital information, and it needn’t be stored only in Cambridge, or Palo Alto, or Paris. It is already possible to transmit and print a DNA sequence using the molecular equivalent of 3-D printers—a process that could enable scientists almost anywhere to construct vaccines. Making this technique readily available should be a national and, in fact, an international priority. 

There are other possible solutions, such as editing the genes of pigs (and bats) to repulse the viruses that can transfer to humans. This kind of ecological intervention would be scientifically difficult, and ethically questionable. But it will inevitably be discussed, so let’s do it rationally. 

Even if this pandemic passes quickly, there will be another one, possibly far more catastrophic, next year, or in ten years’ time, or twenty. All we can know for sure is that if we have any hope of containing it, the time to prepare is now.

Taiwan reports 56 H1N1 swine flu deaths amidst 2019nCoV coronavirus outbreak

Via the South China Morning Post: Taiwan reports 56 swine flu deaths amidst coronavirus outbreak.Excerpt:

Seasonal influenza has posed a greater threat in Taiwan than the coronavirus outbreak from mainland China, with at least 56 people dying of swine flu, also known as H1N1 virus-affected respiratory failure in the past three months, according to the island's Centres for Disease Control. 

CDC officials stopped short of breaking out the number of fatalities in the past week, but local news media reported that number as 13 deaths. There are only 10 confirmed cases in Taiwan of the coronavirus that originated in the mainland city of Wuhan, and no deaths so far. 

According to the Central News Agency, 13 people aged between 47 and 97 died of the seasonal flu, including an 80-year-old woman who developed a fever in late December, eventually dying of pneumonia and respiratory failure in hospital. 

The agency quoted a CDC doctor, Lin Yung-ching, as saying that the woman had received a flu vaccine before contracting the flu. Lin said that the rest of the patients who died of the flu-affected complication of pneumonia and respiratory problems had not received a vaccine. 

CDC officials said H1N1 has been the predominant virus type in Taiwan over the past three months. “During this season, there have been 771 influenza cases with severe complications since October 1, including 56 deaths,” a spokeswoman said. 

Of the severe cases, 41 per cent of the patients are older than 65; another 32 per cent are in the 50-64 age group, she said. The spokeswoman said that 98 per cent of those patients had not received any flu vaccines and close to 80 per cent have chronic diseases.

She called for residents to get the flu vaccine to better protect themselves, saying that “none of the 43 patients who died from flu complications in the past three months had been vaccinated”.

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.