Monday, March 20, 2023

Vietnam MOH Statement On Preventing Avian Influenza


In 2004 and 2005, Vietnam was the world's epicenter for human infections with HPAI H5N1, recording 90 cases and 39 deaths (CFR 43.33%) in less than 2 years.  By 2006, Vietnam had brought the virus largely under control, although another 38 human infections would be reported between 2007 and 2022. 

Last year's case was their first since 2014. It isn't known whether it belonged to the same sublineage (clade as recent cases in China, the Americas, and Europe or to the clade ( recently reported in two cases in neighboring Cambodia

Either way, Vietnam is taking the threat seriously, and is working to bolster their border screenings, and increase surveillance within their borders.  Today their MOH published the following (translated) statement from their editorial board. 
Strengthening the prevention and control of avian influenza to humans


According to the World Health Organization, the world has so far recorded 873 cases of influenza A (H5N1) infection, of which 458 deaths. According to a notice from the Cambodian Ministry of Health, from February 22, 2023, Cambodia recorded 02 cases of influenza A(H5N1) infection in Prey Veng province, of which 01 case died. This is the latest case of influenza A(H5N1) in Cambodia since 2014. In the context of expanding trade exchanges between Vietnam and other countries around the world, the risk of avian influenza may enter the country. spread to humans is very large, especially in provinces bordering with epidemic countries.

In Vietnam, the weather is currently in a period of changing seasons and abnormal changes favorable for the development of avian influenza viruses, and festivals after the Lunar New Year continue to be held. Poultry transport and trade may increase. Therefore, there is always a potential risk of transmission of avian influenza to humans. Previously, at the end of 2022, Vietnam also recorded the first human case of influenza A(H5N1) infection (in Phu Tho province) since 2014 until now.

To proactively prevent avian influenza from entering Vietnam and infecting humans, on February 27, 2023, the Ministry of Health issued Official Dispatch No. 258/CD-BYT to the Chairman of the People's Committees of the provinces. , the city proposes to pay attention to directing units in the area to urgently implement a number of key contents as follows:
- Strengthening close monitoring of people on entry to detect suspected/infected cases early, especially people who slaughter, trade in poultry, live poultry products, and people with a history of coming from epidemic-affected areas. (including epidemics in poultry and humans), promptly take samples for testing and send them to the Institutes of Hygiene and Epidemiology/Pasteur for diagnostic testing; case management (if any) and handling to prevent the disease from spreading to the community.
- Strengthen surveillance of acute respiratory infections, severe viral pneumonia and influenza syndrome to promptly detect cases of influenza A(H5N1); hospitals are ready to collect, isolate and treat according to regulations of the Ministry of Health and promptly notify the Center for Disease Control to take timely measures to prevent and control the epidemic; ready drugs, supplies, chemicals and means of timely support for localities to implement measures to handle the outbreak.
- Strengthen inter-sectoral coordination between health agencies, veterinary authorities and relevant departments and agencies in monitoring and detecting avian influenza, especially at border gates and live poultry markets, promptly sharing information information on the epidemic situation in poultry and coordinate in the investigation and handling of the outbreak.
- Increase communication on measures to prevent transmission of avian influenza to humans, with special attention to high-risk areas and poultry farmers, traders and slaughterers about the risk of disease, preventive measures measures to prevent and strongly encourage people not to use food of unknown origin; implement food safety in slaughtering and processing poultry and poultry products, do not eat blood pudding and do not use sick or dead poultry of unknown cause.
- To coordinate in the prevention and control of diseases transmitted from animals to humans in accordance with the provisions of Joint Circular No. 16/2013/TTLT-BYT-BNN&PTNN dated May 27, 2013 of the Ministry of Health and the Ministry of Health. Agriculture and Rural Development; Report on infectious diseases according to the Circular No. 54/2015/TT-BYT dated December 28, 2015 of the Minister of Health on the Department of Preventive Medicine.
Editorial board of the website of the Department of Preventive Medicine

Through aggressive culling, poultry vaccination, surveillance, and public education, Vietnam went from being the worst afflicted country in the world to being viewed as the `poster child’ for successful bird flu containment. 

Hopefully, by preemptively implementing those same tactics today, they can avoid a repeat crisis.  

China CDC Weekly: First Case of Co-Infection with Omicron Subvariants BA.5.2.48 and BF.7.14


While SARS-CoV-2 appears to evolve primarily via simple replication errors, it can also reinvent itself by recombination - a process which can occur when a host is infected by 2 or more COVID strains simultaneously (see A COVID Recombination Review)

The XBB subvariant is a prime example, as it is recombinant of BA.2.10.1 and BA.2.75 sublineages.

Severely immunocompromised individuals have been linked to long-term carriage of SARS-CoV-2 and the generation of new variants (see SARS-CoV-2 Variants in Patients with Immunosuppression and Persistent COVID-19 infections in immunocompromised people may give rise to variants of concern). 

Most of these variants are doomed to becoming evolutionary failures, unable to compete with existing strains.  But given enough opportunities, there is always the possibility of seeing a biologically superior variant emerge.

China's CDC Weekly is practically a clone of the U.S. CDC's MMWR, and is published in English, making it easily accessible. This week they describe the detection of a novel variant (an apparent recombinant of BA. and BF.7.14) in an immunocompromised patient, who consistently tested positive for COVID while hospitalized over a 6 week period. 

First the dispatch, after which I'll return with a brief postscript.

Notes from the Field: The First Case of Co-Infection with Omicron Subvariants BA.5.2.48 and BF.7.14 — Chongqing Municipality, China, February 2023

Kun Su1,&;Ying Huang2,&; Xiaofeng Chen2; Fangyuan Liu2; Qi Yan2; Xinyu Jiang2; Jing Xu2; Yongdong Hao2, , ; Jin Yan2, , View author affiliations

On February 14, 2023, a co-infection of Omicron strains was detected in a sample collected and submitted for examination at the Third Affiliated Hospital of Chongqing Medical University.

On February 7, 2023, a 67-year-old female patient living in Yunyang County, Chongqing City, was identified with a history of malignant tumor that had been treated with chemotherapy, radiotherapy, targeting, and other treatments in the past 6 months. Low immunity was suspected, but no other basic diseases, history of smoking, or drinking habits were present. The patient had received two injections of the coronavirus disease 2019 (COVID-19) vaccine (Sinovac Life Sciences Co. Ltd.).

On December 23, 2022, the patient reported poor appetite. On December 29, she developed fatigue, cough, and tested positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigen. On January 4, 2023, she experienced chills and fever (temperature of 38.9 ℃) with accompanying cough symptoms. She was admitted to the Traditional Chinese Medicine Hospital of Yunyang County, but did not show significant improvement and was discharged on January 5. On January 6, she was admitted to the Department of Infectious Diseases at the Third Affiliated Hospital of Chongqing Medical University, where she continued to have symptoms of fever and cough. From January 6 to February 12, eight nucleic acid tests were positive in the hospital.

In the investigation, her family members and neighbors were found to be infected in late December, suggesting a potential exposure. During her two hospitalizations, she may have come into contact with other individuals infected with the SARS-CoV-2.

Upper respiratory tract samples were collected from the patients on January 28 and February 7, 2023 and designated as YB20230158 and YB20230202, respectively, to rule out contamination. SARS-CoV-2 whole-genome multiplex polymerase chain reaction (PCR) amplification was performed using the commercial SARS-CoV-2 whole-genome multiplex PCR kits (MicroFuture, Beijing, China). Libraries were prepared using the VAHTS® Universal Plus DNA Library Prep Kit for Illumina (Vazyme Biotech Co.,Ltd.) following the manufacturer’s instructions and sequenced on the NextSeq2000 platform, a combination of metagenomic sequencing and tiling amplicon approaches.
The seqtk-1.3 tool ( was used to excise primer sequences and prevent the introduction of mutations caused by primers. The coverage of the two sequencing tests reached 99.7% and 99.8%, respectively, with sequencing depths of 4,142 and 6,551. Phylogenetic analysis (maximum likelihood method) revealed that these two samples formed a separate branch distinct from Omicron subvariants BA.5.2.48 and BF.7.14 (Figure 1).
Mutation sites analysis showed that both samples contained the specific defining sites of Omicron subvariants BA.5.2.48 and BF.7.14, including G1085T, C2710T, C7528T, C8626T, G1085T, C11824T, G12310A, G14181C, C16616A, T17208C, G22599C, T22917G, and G25290T. Verification of the heterozygosity status and frequency of specific mutations in these positions using IGV 2.10.2 (Figure 2) indicated that the patient was simultaneously infected with Omicron subvariants BA.5.2.48 and BF.7.14.

According to the “National Report on the Epidemic of SARS-CoV-2 Infection” released by China CDC, the predominant SARS-CoV-2 strain circulating in Chongqing is BA.5.2.48 (>90%), followed by BF.7.14 (about 3.8%) (1). To date, there have been no reports of co-infection with BA.5.2.48 and BF.7.14 in China, particularly in Chongqing, where the proportion of BF.7.14 is relatively low, making its report more meaningful. 

Monitoring SARS-CoV-2 variants should be popularized as an important strategy to identify co-infections and recombination cases. As the risk of various variants co-circulating in a region continues to increase, the monitoring of SARS-CoV-2 variants, especially for key populations with immune deficiencies, is becoming increasingly essential.

Online Date: March 17 2023
doi: 10.46234/ccdcw2023.046
         (Continue . . . )

There is no indication that this particularly variant was transmitted onward, or poses any additional risk to the public, but it does demonstrate the potential for new recombinants to emerge, particularly from severely immunocompromised hosts. 

While we appear to have entered a relatively stable period for COVID (knock on wood) - given the proven mutability of the SARS-COV-2 virus - there are no guarantees how long that will last.  

Sunday, March 19, 2023

WHO Statement On Newly Released SARS-CoV-2 Data from China CDC on GISAID

Asian Wet Market - Credit Wikipedia


The origins of the SARS-CoV-2 pandemic remain murky, and the subject of much impassioned debate. Some favor the theory that the virus evolved naturally in a mammalian host - possibly spreading from the massive Wuhan seafood market - while other strongly suspect it had `help' via experiments in a nearby Chinese lab. 

Based on limited physical evidence, reasonable arguments can be made for either scenario.  Although I slightly gravitate (60/40) towards an animal origin, I don't dismiss the lab theory. 

While vigorously denying the lab leak theory, China hasn't exactly helped its case by stonewalling investigations, selectively releasing details on the initial outbreak, and by destroying and/or holding back data. 

Earlier this month - three years after the fact - raw genetic sequences collected from the Huanan Seafood market were briefly uploaded to GISAID by Chinese researchers working on a revision to a preprint (Surveillance of SARS-CoV-2 in the environment and animal samples of the Huanan Seafood Market) that was first posted more than a year ago.

These sequences were then abruptly removed, but not before several researchers from around the world were able to download them.  

While they don't prove an animal origin for SARS-CoV-2, they do show that several suspected hosts (including raccoon dogs) were present in the market at the time of the outbreak, which some believe bolsters the `natural emergence' theory.   

This new information comes as Congress has opened investigations into the origins of the pandemic so make of that what you will. 

The WHO was made aware of these new sequences a week ago, and has been in contact with the Chinese government in an attempt to get access to them (and presumably any others) the Chinese may have. 

Yesterday the WHO published the following statement.

SAGO statement on newly released SARS-CoV-2 metagenomics data from China CDC on GISAID
18 March 2023
On 12 March 2023, WHO was made aware of new SARS-CoV-2 sequences and metagenomics data associated with samples collected in the Huanan Seafood Wholesale Market, Wuhan, China, from January 2020, that became available on GISAID for a short period of time. The data had subsequently been downloaded by a number of researchers from several countries. Access was restricted shortly after, apparently to allow further data updates by China CDC. WHO then immediately reached out to China CDC and to the Chair and Vice-Chair of SAGO. Upon discussions between WHO and Chinese colleagues, it was explained that the genomic data are the basis for an expected update to the existing Liu et al. 2022 preprint (1), which is in the process of being re-submitted for publication to Nature by China CDC.
After discussions with the WHO secretariat and the SAGO Chair and Vice-Chair, a call was arranged on 12 March with the scientists involved from China CDC, and some of those who had accessed the data from GISAID, to gauge the significance of this data and the analyses of this data. WHO subsequently organized a meeting on 14 March 2023 with all SAGO members, and invited researchers from China CDC to present the updated analysis of their data. WHO and SAGO also invited the researchers who had informed WHO that they had accessed data from GISAID, to present their analysis of the temporarily released sequences.
The presentations from China CDC and invited international researchers indicated that there were newly available data from the Huanan Seafood Wholesale Market. This included metagenomic data of environmental samples from various stalls and wastewater collection sites collected as early as January 2020. Analyses of these data suggest that apart from SARS-CoV-2 sequences, some samples also contained human DNA, as well as mitochondrial DNA of several animal species, including some that are known to be susceptible to SARS-CoV-2. This included DNA from wild raccoon dogs, Malaysian porcupine, and bamboo rats among others, in SARS-CoV-2 positive environmental samples.

The findings suggest that animals were present at the market shortly before the market had been cleared on 1 January 2020, as part of the public health measures by Chinese authorities. These results provide potential leads to identifying intermediate hosts of SARS-CoV-2 and potential sources of human infections in the market.

According to the Chinese’s authors pre-print (Liu et al 2022), of 1380, samples collected from the environment and animals within the market in early 2020, 73/923 environmental samples tested positive for SARS-CoV-2-specific RT-qPCR, from various stalls and sewerage systems in and around the market, but no virus was detected in 457 animal samples tested. The animal samples included animal bodies, frozen animal carcases and animal products, as well as stray animals around the market, and covered 18 species. According to the preprint, raccoon dogs were not amongst the animals tested. However, the presence of high levels of raccoon dog mitochondrial DNA in the metagenomics data from environmental samples identified in the new analysis, suggest that raccoon dog and other animals may have been present before the market was cleaned as part of the public health intervention.

Historical photographic evidence was provided that shows raccoon dogs and other animals were sold at these specific stalls in the past. Although this does not provide conclusive evidence as to the intermediate host or origins of the virus, the data provide further evidence of the presence of susceptible animals at the market that may have been a source of human infections.

SAGO will continue to evaluate any and all scientific data shared by Chinese and other researchers from anywhere in the world. SAGO encourages any and all data related to the studying of the origins of SARS-CoV-2 be made available immediately for robust and comprehensive review.

As mentioned in SAGO's preliminary report (2), the SAGO strongly recommends that researchers in China investigate the upstream sources of the animals and animal products present in Huanan market just before its closure and removal of all animal products on 1 January 2020.

Furthermore, SAGO would like to encourage any and all available sequencing and metagenomic data to be made public on GISAID, or any other sequence database, and the pre-prints that are in review to be shared as soon as possible so the scientific community has the opportunity to analyse these further. In addition, SAGO encourages researchers using this data to collaborate and engage with Chinese researchers. WHO and SAGO are happy to facilitate these collaborations.

(1) Liu et al, 2022. Surveillance of SARS-CoV-2 in the environment and animal samples of the 2 Huanan Seafood Market, Available:

(2) Preliminary Report for the Scientific Advisory Group for the Origins of Novel Pathogens (SAGO) June 2022, Available:

This month marks the 20th anniversary of our first learning about SARS-CoV, which had been covered by the Chinese government since November of the previous year (see SARS and Remembrance).

While a bat reservoir host is strongly suspected, we still don't know the exactly how that epidemic emerged. 

None of which bodes well for getting to the bottom of this controversy anytime soon. 

Chile: SERNAPESCA Reports A Record Number of Marine Strandings In 1st Quarter of 2023


Peru first reported H5N1 last November, but by February SERNANP had Reported At Least 585 Sea Lions & 50,000 birds killed by Avian Flu.  That number was sharply revised earlier this month when SERNANP Reported Nearly 3,500 Sea Lions Killed By H5N1 Avian Flu

Avian flu was first confirmed in Chile in early December, but so far we've only seen a handful of HPAI related marine strandings reported (see Chile: SERNAPESCA Reports Avian H5N1 In Dead Sea Otter (Lontra feline)

At roughly 4,000 miles, Chile's coastline is 3 times longer than Peru's, with many remote and secluded areas.  Laboratory testing takes time, and some animal carcasses may be too badly deteriorated to be properly tested. 

Yesterday Chile's National Fisheries and Aquaculture Service (SERNAPESCA) released a preliminary report on marine strandings during the first 3 months of 2023, which finds a tremendous increase over past years.  

532 sea lions, 234 Humboldt penguins and 6 chungungos (marine otters) have been found dead in those 3 months, compared to just 131 during all of 2022.

There are a few caveats. Only about 1/3rd of these carcasses have been sampled (n=187), and only small number of those (n=13) have tested positive for HPAI H5N1. Surveillance is obviously heightened due to the arrival of HPAI, which may skew the comparison to past years, and the condition of the recovered carcasses is not mentioned in this report. 

Given the nearly 6-fold increase in marine animal deaths, and their concentration in the northern regions where HPAI first arrived, authorities are attributing most of this unusual mortality event to H5N1. 

The full (translated) report follows.

SERNAPESCA delivers report of stranded marine animals dead due to Avian Influenza situation

Saturday March 18, 2023 - There are more than 700 specimens of common sea lions, Humboldt penguins and chungungos that have been stranded dead on the coasts of our country during the first quarter of 2023, mainly in the north. The figure is 482.4% higher than the total number of strandings, corresponding to these species, registered in 2022.

The National Fisheries and Aquaculture Service has reported a considerable increase in the strandings of dead marine animals on the Chilean coasts during the first quarter of 2023. In total, 532 specimens of sea lions, 234 Humboldt penguins and 6 chungungos are reported. that have stranded dead on the coasts of the northern macrozone, the main affected regions being: Arica and Parinacota with 292 dead sea lions and Atacama with 139 dead Humboldt penguins.

“During these three months of the year we recorded a historical number of dead stranded marine animals, corresponding to 763 specimens of these three species. The total number of these stranded animals dead for a full year in 2022 was 131, and in 2021 there were 120 dead specimens in total. This shows that we are clearly facing an anomalous situation, which we attribute to the phenomenon of highly pathogenic avian influenza, especially since the strandings in these months are concentrated in the northern zone," said Soledad Tapia, National Director of Sernapesca.

In the context of the Avian Influenza emergency, work has been reinforced with other entities such as the Presidential Delegations, Regional Governments, SAG, Seremías, Municipalities and others, in order to support an active surveillance plan throughout the coastline with the in order to reduce the risks of viral circulation of said disease, through the detection, testing and final disposal of affected animals.

The epidemiological situation of highly pathogenic avian influenza (HPAI) by H5 subtype of Eurasian lineage has continued to spread. There are 4 regions of the northern macrozone that have registered marine fauna protected by the Fisheries and Aquaculture Law with positivity for avian influenza, only excepting the Atacama region that does not register official positive cases sampled, for now.

To date, a total of 13 specimens of marine animals confirmed as HPAI-positive have been counted, corresponding to 1 chungungo in the Arica region; 8 sea lions, 2 in the Arica Region, 3 in Tarapacá, 2 in Antofagasta and 1 in Coquimbo; and 4 Humboldt Penguins, 1 in Tarapacá, 2 in Antofagasta and 1 in Coquimbo. This from a total of 183 specimens that were sampled.

It should be noted that SERNAPESCA is prioritizing assistance to the strandings of animals with symptoms associated with avian influenza. As for the disposal of, please report to 800 320 and Aquaculture Service to protect the biosafety protocols.

The service reiterated the emphatic call to people who are on the coastline not to touch or manipulate, keep their distance, and report in the event that a dead bird or marine animal is detected on the coastline or that shows signs such as: decay, coughing, breathing difficulties or muscle spasms. This includes not moving them, not returning them to the sea or burying them on beaches at your own expense. Therefore, in case of observing cases of marine animals stranded on beaches, please report to 800 320 032.


Aside from tragic loss of these animals, there is the obvious concern that the virus may becoming better adapted to mammalian hosts. While mammal-to-mammal transmission of the virus has not been confirmed in these cases, it remains a distinct possibility.

For recent research articles on HPAI H5 in marine mammals, you may wish to revisit:

Saturday, March 18, 2023

US & UK Report More Mammalian H5N1 Infections



While H5N1's endgame is far from assured, it continues to make news as it spills over into mammals around the globe. Over the past 7 days alone, we've seen:

UK Reports 2 Dolphins With HPAI H5N1 & EID Report On Infected Harbor Porpoise in Sweden

CDC EID Journal: HPAI A(H5N1) Virus Outbreak in New England Seals, United States

PLoS Pathogens: Evolution of Highly Pathogenic H5N1 Influenza A Virus in the Central Nervous System of Ferrets

British Columbia Press Release: Government Reports 8 Skunks Infected With HPAI H5N1

Preprint: Pathology Of HPAI H5N1 clade in Wild Terrestrial Mammals in the United States in 2022

Emerging Microbes & Inf.: Neurotropic HPAI H5N1 Viruses with Mammalian Adaptive Mutations in Free-living Mesocarnivores in Canada

Earlier this week, in ECDC/EFSA Avian Influenza Overview December 2022 – March 2023, researchers described recent changes to the virus that may make it more of a threat to mammalian hosts.

Mutations identified in A(H5N1) viruses from mammals 

About half of the characterized viruses contain at least one of the adaptive markers associated with an increased virulence and replication in mammals in the PB2 protein (E627K, D701N or T271A) (Suttie et al., 2019). These mutations have never (T271A) or rarely (E627K, D701N) been identified in the HPAI A(H5) viruses of clade collected in birds in Europe since October 2020 (<0.5% of viral sequences from birds). 

This observation suggests that these mutations with potential public health implications have likely emerged upon transmission to mammals. Moreover, the viruses collected in October 2022 from a HPAI A(H5N1) outbreak in intensively farmed minks in northwest Spain (Aguero et al., 2023) shows mutations in the NA protein which cause disruption of the second sialic acid binding site (2SBS). This feature is typical of human-adapted influenza A viruses, which may favour the emergence of mutations in the receptor binding site of the HA protein (de Vries and de Haan, 2023). These same mutations were detected also in seven A(H5N1) viruses from birds. 

All of which means, that while often repetitive, reports of additional spillovers into mammals are of great importance.   

Yesterday the USDA updated their list of confirmed mammalian infections from H5N1, adding 4 new cases since their last update on March 9th. This brings the number of laboratory confirmed H5N1 positive mammals in the United States to 148although that likely represents only a tiny faction of the actual number of mammals infected.

Added were 3 skunks and a raccoon (see list below). 

Even though we looked at this week's totals from the UK on Thursday, yesterday Lisa Schnirring at CIDRAP forwarded a report from the UK government to me on an unusual outbreak in captive South American Bush Dogs (see CIDRAP report). 

Research and analysis
Confirmed findings of influenza of avian origin in captive mammals

Published 17 March 2023
Applies to England, Scotland and Wales

Details of confirmed findings of influenza of avian origin in captive mammals in Great Britain (England, Scotland and Wales).

South American bush dogs, March 2023

Ten South American bush dogs (Speothos venaticus venaticus) have tested positive for highly pathogenic avian influenza (H5N1) in March 2023.

These animals were part of a captive breeding programme at a zoological premises in England. They were tested as part of a routine investigation into an unusual mammal die-off in November 2022. Ten animals died or were euthanised in a group of 15 bush dogs, over a 9 day period.

The bush dogs had minimal clinical signs before death, and APHA cannot definitively state whether or not H5N1 caused the clinical signs. Influenza of avian origin was not suspected at the time; the virus has since been detected in postmortem samples.

There is no clear evidence suggesting mammal to mammal transmission. It is very likely all animals were exposed to the same source of infected wild birds.

It's not clear why it took nearly 5 months to identify the cause of this unusual mortality event, although the lack of overt symptoms may have been a factor.  We've seen ample evidence in the past that dogs and other canids are susceptible to HPAI H5 viruses, including:

Study: Dogs And H5N1

J. Vet. Sci.: Experimental Canine Infection With Avian H5N8

Norwegian Veterinary Institute Reports Avian H5N1 Spillover Into Red Foxes

MAFRA: H5N8 Antibodies Detected In South Korean Dogs (Again)

Given the susceptibility of both dogs and cats to avian influenza (see HPAI H5: Catch As Cats Can), and the elevated levels of the virus in wild birds, it makes sense to heed the advice of the CDC and other health entities when it comes to protecting your companion animals from infection. 

As a general precaution, people should avoid direct contact with wild birds and observe wild birds only from a distance, whenever possible. People should also avoid contact between their pets (e.g., pet birds, dogs and cats) with wild birds. Don’t touch sick or dead birds, their feces or litter, or any surface or water source (e.g., ponds, waterers, buckets, pans, troughs) that might be contaminated with their saliva, feces, or any other bodily fluids without wearing personal protective equipment (PPE).

More information about specific precautions to take for preventing the spread of bird flu viruses between animals and people is available at Prevention and Antiviral Treatment of Bird Flu Viruses in People. Additional information about the appropriate PPE to wear is available at Backyard Flock Owners: Take Steps to Protect Yourself from Avian Influenza.

ECDC: Reports Of Severe Influenza B Among Young People In Sweden

Credit Swedish Public Health Agency


We've a bit of a medical mystery this morning, as Sweden is reporting an unusual spike in severe influenza B infections among young people which appears to be clustered in the Örebro County region.  More than half of all influenza ICU admission in Sweden the past few weeks (see chart above) have been for Influenza B. 

First a (translated) statement from Sweden's Public Health Agency.

The Public Health Agency, together with the Infection Control Unit in the Örebro County region, is investigating a few cases of influenza B with serious complications that have been reported in the region. The cases, which have been among people under the age of 18 without an underlying disease or condition, have been very seriously ill with complications such as myocarditis or encephalitis. It is already known that the reported complications can occur in connection with influenza infection, but this is unusual.

The investigation aims to assess whether there are more influenza B cases with serious complications than expected and whether there is any common contributing cause in addition to the influenza infection. Therefore, the Public Health Authority has asked other infection control units to investigate whether there are similar cases in other regions. The Public Health Authority is also investigating whether there are similar accumulations of cases in other European countries, but nothing of the sort has been reported so far.

Virological analyzes show that all Swedish characterized influenza B strains in the 2022–2023 season, including samples from severe cases, belong to the same genetic group of lineage type B/Victoria that dominates in the rest of Europe and that is included in the season's influenza vaccines.

Since March 14, Region Örebro län has been offering, in consultation with the Public Health Authority, school-aged children free vaccination against influenza for a limited period.

It isn't readily apparent what `a few cases' means, since no hard numbers are provided. In Sweden, much as we've seen in the United States, flu season peaked early (in December) and after a sharp fall, has leveled off.  Influenza B however, often appears in the spring after influenza A has run its course. 

While influenza B infection can be every bit as severe as influenza A (see Influenza B: A Virus Not To Be Underestimated), reports of severe neurological or cardiac complications are uncommon.  

The ECDC included the following update in yesterdays' Communicable Disease Threat Report.  I'll have a bit more after the break.
Severe Cases of Influenza B among Young People


As of 15 March 2023, Sweden has reported cases of laboratory-confirmed influenza B infection, associated with severe outcomes among children and adolescents with geographical proximity to one another. There were no underlying medical conditions.
Complications included myocarditis and meningoencephalitis.  All cases have been severe, requiring critical intensive care.

As of 14 March, influenza vaccination is being offered free of charge to children 6-17 years of age in the region in question through the regional healthcare system. Case finding is ongoing to further investigate whether the cases are within the expected range of severe outcomes and explanatory factors.

So far, sequencing has been completed for some of the cases, all B/Victoria lineage. Phylogenetic analysis of HA1 suggests they are genetically similar to other circulating influenza B viruses in Sweden this season, belonging to genetic subgroup V1A.3a.2. This is the dominant subgroup across Europe and the northern hemisphere in the 2022-23 season and the northern hemisphere 2022-23 and 2023-24 influenza vaccine strain (B/Austria/1359417/2021-like virus) [1].

No antiviral resistance in influenza B viruses has been observed in the current season in Sweden or globally [2]. Further analysis of other samples from both severe and mild cases in the region and from the rest of Sweden is ongoing.

ECDC assessment

Very few influenza virus detections in humans were observed in the EU/EEA during the 2020/21 and 2021/22 seasons. The 2022/23 influenza season started early (W45-2022), with widespread circulation and intensity levels comparable to pre-COVID-19-pandemic seasons. In Sweden, influenza type A(H3N2) and A(H1N1)pdm09 cocirculated between W45-2022 and W07-2023, with virus detections peaking in W52-2022. Influenza detections have gradually declined since W52-2022, albeit with the proportion of influenza type B virus detections among all positive samples increasing since W07-2023.

This mirrors the trend observed across the EU/EEA. Although the influenza type B virus cases reported in Sweden have been detected in the same region, only two confirmed and one suspected case are known to share an epidemiological link. So far, there is no indication that the influenza B viruses circulating in Sweden differ from those circulating elsewhere in the EU/EEA or globally.

It is unknown whether cases had been vaccinated against seasonal influenza or had had COVID-19 prior to the onset of the influenza infection. None of the cases have a co-infection with COVID-19 and influenza B. Reduced circulation of, and population exposure to influenza viruses during the preceding seasons may have had an impact on immunity to the influenza viruses currently in circulation, so it is important to remain vigilant for signals of increased severity in different population groups.


An EpiPulse event item has been launched to facilitate reporting of epidemiological information from all EU/EEA countries. ECDC will continue to monitor the event in EpiPulse and via Epidemic Intelligence activities. ECDC encourages countries to provide information on cases of laboratory-confirmed influenza B infection observed among children and adolescents, associated with severe outcomes. Countries are encouraged to determine the lineage, as well as perform genetic and antigenic characterisation for such cases.

It would also be advisable for countries to share either clinical specimens or virus isolates with the WHO Collaborating Centre (London) for further characterisation. Where available, countries are asked to provide GISAID accession numbers for sequenced isolates, to enable genomic analyses and comparisons. ECDC can offer sequencing and virus characterisation support through contracted activities.

While unusual, this isn't the first time we've seen severe influenza B reported.  
Exactly what is driving Sweden's spike in severe influenza B infections isn't clear, although plenty of theories abound.  So far, it appears to be localized, but it is certainly worth keeping an eye on it.

Stay tuned.