UKHSA MERS-CoV Risk Assessment & Updates

 

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The month of May has already borne witness to a high-profile Andes Hantavirus outbreak aboard the m/v Hondius and a burgeoning Bundibugyo Ebolavirus outbreak in Central Africa, which makes bringing up MERS-CoV this morning almost feel like piling on.  

But, with the 2026 Hajj only a week away, and nearly 2 million religious pilgrims expected to visit holy sites in Saudi Arabia, the low (but non-zero) possibility of seeing one or more MERS-CoV cases returning from the region cannot be ignored.

The UK's latest MERS-CoV Risk assessment reads, in part:

Risk assessment

The number of reported human MERS-CoV cases per year globally, has fallen to the lowest level since 2014. The identification of 2 imported cases of MERS-CoV in France demonstrates that MERS continues to pose a risk to UK public health, particularly in those who have travelled to the Middle East.

In addition to PCR confirmed cases in the Middle East, there is serological evidence of MERS-CoV infection of camel-workers in Nigeria, Kenya and Morocco. There is therefore a very low risk of importation of MERS-CoV from occupationally exposed individuals from those African countries. It is imperative that health professionals remain vigilant for clinical presentations compatible with Middle East respiratory syndrome. Detailed case definitions and guidance on when to suspect MERS is given in the MERS-CoV: diagnosis and management of cases and contacts.

Today, the UKHSA has published (or updated) more than a half dozen additional documents pertaining to MERS-CoV and/or travel to the Middle East. 

UKHSA risk assessment of MERS-CoV Updated: 18 May 2026

MERS-CoV: risk assessment

Guidance on reducing the risk of getting MERS-CoV for UK residents and travellers to the Middle East.Updated: 18 May 2026 

MERS-CoV: minimum data set form for possible cases
Minimum data set form for possible cases of Middle East respiratory syndrome coronavirus (MERS-CoV).

MERS-CoV: diagnostic testing
Information on taking, submitting and processing clinical samples from patients suspected of having Middle East respiratory syndrome coronavirus (MERS-CoV). Updated: 18 May 2026

MERS-CoV: diagnosis and management of cases and contacts
This guidance is for healthcare professionals and health protection teams (HPTs) on identifying and managing cases of Middle East respiratory syndrome (MERS).Updated: 18 May 2026

MERS-CoV: background information
This guidance gives advice on the transmission, diagnosis, treatment and prevention of Middle East respiratory syndrome coronavirus (MERS-CoV) to the public.Updated: 18 May 2026

MERS-CoV: clinical management and guidance
Guidance on investigating Middle East respiratory syndrome coronavirus (MERS-CoV), public health management of suspected UK cases and advice to travellers.Updated: 18 May 2026

MERS-CoV: biological principles for the control of MERS-CoV
This guidance outlines the current knowledge and assumptions about the biology and transmission of Middle East respiratory syndrome coronavirus (MERS-CoV).Updated: 18 May 2026

MERS-CoV: travel from the Middle East advice sheet
Infographic with advice on Middle East respiratory syndrome coronavirus (MERS-CoV) for people travelling to the UK from the Middle East.Updated: 18 May 2026

MERS-CoV: travel from the Middle East advice sheet (HTML version) Updated: 18 May 2026

While the number of reported cases has declined over the past 6 years, we've seen several recent high-profile reports of spillovers, including France MOH: 2 Travelers Returning From Arabian Peninsula Diagnosed with MERS-CoV and WHO: Saudi Arabia Reports 9 New MERS-CoV Cases.

Not surprisingly, over the past year we've also seen a resurgence in MERS-CoV-related studies, including:

The Lancet: The Threat of Another Coronavirus Pandemic

Health Sci Rpts (Narrative Review): Pathogenicity and Potential Role of MERS-CoV in the Emergence of “Disease X”

IJID Editorial: Al-Tawfiq on Global Epidemiology and Public Health Challenges of Middle East Respiratory Syndrome Coronavirus (MERS-CoV)

JEGH: Epidemiological Characteristics of MERS-CoV Human Cases, 2012- 2025

JEGH: Al-Tawfiq & Memish On Recurrent MERS-CoV Transmission in Saudi Arabia

As recently as last March - a WHO-authored commentary, published in Nature - warned that the MERS-CoV continues to circulate in dromedary camels in the Middle East, that it appears to maintain its virulence, and it remains a plausible pandemic threat.

I consider trying to predict the next big global health crisis a mug's game, since so many things could come at us out of left field with little or no warning.  

But recent studies suggest that the frequency, and impact, of pandemics are only expected to increase in the years ahead.

BMJ Global: Historical Trends Demonstrate a Pattern of Increasingly Frequent & Severe Zoonotic Spillover Events

PNAS Research: Intensity and Frequency of Extreme Novel Epidemics

So, while I can't tell you what type of emerging disease will spark the next pandemic - or when - it is all but guaranteed to happen again.  

The only question is; when that day comes, will we be ready?

Canada: PHAC Statement on `Presumed Positive' Hantavirus Case in Vancouver

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One of the m/v Hondius passengers, recently repatriated to Canada, has developed symptoms and has presumptively tested positive for the Hantavirus. Their spouse is also reportedly mildly symptomatic, and both have been hospitalized (along with a 3rd contact). 

The phrase `presumptive positive' simply means a local laboratory has obtained a positive result, confirmation of these results by the PHAC's National Microbiology Laboratory in Winnipeg will take a couple of days.

While concerning, known cases continue to be reported only among passengers and crew of the m/v Hondius.  Whether additional - `off-ship' infections - will emerge remains to be seen. 

Canada's PHAC released the following statement late Saturday afternoon.

Media update on Andes hantavirus situation

From: Public Health Agency of Canada
Statement

May 16, 2026 | Ottawa, ON

On May 16, 2026, the British Columbia Provincial Health Officer reported that one of the four high risk individuals who was self-isolating and being monitored for symptoms has tested presumptive positive for Andes hantavirus. The person was transported to hospital for assessment and care on May 14 along with their spouse who also has mild symptoms. The couple were passengers on the MV Hondius. Both will remain in isolation in hospital. Out of an abundance of caution, a third individual who was in secure lodging for isolation has been transferred to hospital for assessment and testing.

All infection prevention and control protocols are being followed, including the use of personal protective equipment by healthcare workers and personnel involved in the repatriation. Those involved in the repatriation are not considered at risk given the public health protective measures that were in place, in addition to the length of time between repatriation and the onset of symptoms.

Samples have arrived at the Public Health Agency of Canada’s National Microbiology Laboratory (NML) in Winnipeg for confirmatory testing. Results are expected in the next two days.

The Public Health Agency of Canada, the province of British Columbia, and local public health are working together to ensure all public health measures continue to be followed to protect the health of Canadians.

The overall risk to the general population in Canada from the Andes hantavirus outbreak linked to the MV Hondius cruise ship remains low at this time. But, given the severity of this virus, we are taking a precautionary approach to ensure Canadians are protected.

The Public Health Agency of Canada will continue to actively monitor the situation, provide guidance and support to provincial/territorial public health partners and share updates as needed.

WHO Director Declares DRC Outbreak of Bundibugyo Ebolavirus a PHEIC (Public Health Emergency of International Concern)

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Overnight, roughly 72 hours after the first reports, the Director of the World Health Organization declared the Bundibugyo virus outbreak in the DRC to constitute a PHEIC. 

This should give us some idea of their level of concern, as previous PHEIC declarations have generally taken weeks or even months.

On Friday we discussed some of the concerning aspects of this latest outbreak, including the fact it has flown under the radar for weeks or months, that the number of cases and deaths is quite high, and that the only vaccine for the ebolavirus is unlikely to be effective against this strain.

While stating that this outbreak  `. . . does not meet the criteria of pandemic emergency, as defined in the IHR.' this declaration does find that neighboring countries to the DRC are at `High Risk ' of seeing imported cases. 

I've posted excerpts from the PHEIC declaration below, follow the link to read the full document. Given the logistics of containment in this part of the world, this is likely to remain a big story for months to come. 

Epidemic of Ebola Disease caused by Bundibugyo virus in the Democratic Republic of the Congo and Uganda determined a public health emergency of international concern
17 May 2026
Statement
Geneva
Reading time: 8 min (2150 words)

Pursuant to paragraph 2 of Article 12 - Determination of a public health emergency of international concern, including a pandemic emergency of the International Health Regulations (2005) (IHR), the Director-General of the World Health Organization (WHO), after having consulted the States Parties where the event is known to be currently occurring, is hereby determining that the Ebola disease caused by Bundibugyo virus in the Democratic Republic of the Congo and Uganda constitutes a public health emergency of international concern (PHEIC), but does not meet the criteria of pandemic emergency, as defined in the IHR.

The Director-General of WHO expresses his gratitude to the leadership of the Democratic Republic of the Congo and Uganda for their commitment to take necessary and vigorous actions to bring the event under control, as well as for their frankness in assessing the risk posed by this event to other States Parties, hence allowing the global community to take necessary preparedness actions.

In his determination the Director-General of WHO has considered, inter alia, information provided by the States Parties – the Democratic Republic of the Congo and Uganda – scientific principles as well as the available scientific evidence and other relevant information; and assessed the risk to human health, the risk of international spread of disease and of the risk of interference with international traffic.

The Director-General of WHO considers that the event meets the criteria of the definition of PHEIC, contained in Article 1 - Definitions of the IHR, for the following reasons: 

1. The event is extraordinary for the following reasons:As of 16 May 2026, eight laboratory-confirmed cases, 246 suspected cases and 80 suspected deaths have been reported in Ituri Province of the Democratic Republic of the Congo across at least three health zones, including Bunia, Rwampara and Mongbwalu.

In addition, two laboratory confirmed cases (including one death) with no apparent link to each other have been reported in Kampala, Uganda, within 24 hours of each other, on 15 and 16 May 2026, among two individuals travelling from the Democratic Republic of the Congo. On 16 May, a laboratory confirmed case has also been reported in Kinshasa, the Democratic Republic of the Congo, among someone returning from Ituri.

Unusual clusters of community deaths with symptoms compatible with Bundibugyo virus disease (BVD) have been reported across several health zones in Ituri, and suspected cases have been reported across Ituri and North Kivu. In addition, at least four deaths among healthcare workers in a clinical context suggestive of viral haemorrhagic fever have been reported from the affected area raising concerns regarding healthcare-associated transmission, gaps in infection prevention and control measures, and the potential for amplification within health facilities.There are significant uncertainties to the true number of infected persons and geographic spread associated with this event at the present time.

In addition, there is limited understanding of the epidemiological links with known or suspected cases.However, the high positivity rate of the initial samples collected (with eight positives among 13 samples collected in various areas), the confirmation of cases in both Kampala and Kinshasa, the increasing trends in syndromic reporting of suspected cases and clusters of deaths across the province of Ituri all point towards a potentially much larger outbreak than what is currently being detected and reported, with significant local and regional risk of spread. Moreover, the ongoing insecurity, humanitarian crisis, high population mobility, the urban or semi-urban nature of the current hotspot and the large network of informal healthcare facilities further compound the risk of spread, as was witnessed during the large Ebola virus disease epidemic in North Kivu and Ituri provinces in 2018-19. However, unlike for Ebola-zaire strains, there are currently no approved Bundibugyo virus-specific therapeutics or vaccines. As such, this event is considered extraordinary.

2. The event constitutes a public health risk to other States Parties through the international spread of disease. International spread has already been documented, with two confirmed cases reported in Kampala, Uganda on 15 and 16 May following travel from the Democratic Republic of the Congo. Both confirmed cases were admitted to intensive care units in Kampala. Neighboring countries sharing land borders with the Democratic Republic of the Congo are considered at high risk for further spread due to population mobility, trade and travel linkages, and ongoing epidemiological uncertainty.

3. The event requires international coordination and cooperation to understand the extent of the outbreak, to coordinate surveillance, prevention and response efforts, to scale up and strengthen operations and ensure ability to implement control measures.

The Director-General of WHO, under the provisions of the IHR, will be convening an Emergency Committee, as soon as possible to advise, inter alia, on the proposed temporary recommendation for States Parties to respond to the event.

(Continue . . . ) 

 

OFID: Central Nervous System Involvement by Novel Clade 2.3.2.1e H5N1 Avian Influenza Virus in a Paediatric Patient

 

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While seasonal flu can occasionally cause neurological symptoms (see 2018's Neuroinfluenza: A Review Of Recently Published Studies) it is relatively rare, and usually only results in mild, and transient symptoms.

Similarly, avian influenza typically presents as a pulmonary infection, but over the past 2 decades we've seen growing evidence of neurological involvement as well.

A few early reports include: 

• A 2009 PNAS study (Highly pathogenic H5N1 influenza virus can enter the central nervous system and induce neuroinflammation and neurodegeneration) found that the H5N1 virus was highly neurotropic in lab mice, and in the words of the authors `could initiate CNS disorders of protein aggregation including Parkinson's and Alzheimer's diseases’.

• Six years later - following the 2014 death of the first imported H5N1 case in Canada - we saw a study (see CJ ID & MM: Case Study Of A Neurotropic H5N1 Infection - Canada), where the authors wrote: `These reports suggest the H5N1 virus is becoming more neurologically virulent and adapting to mammals'.

• In a 2015 Scientific Reports study on the genetics of the H5N1 clade 2.3.2.1c virus - Highly Pathogenic Avian Influenza A(H5N1) Virus Struck Migratory Birds in China in 2015 – the authors described its neurotropic effects, and warned that it could pose a ` . . . significant threat to humans if these viruses develop the ability to bind human-type receptors more effectively.'

HPAI H5Nx's threat largely receded between 2016-2020, but since 2021 has been on the ascendent again, primarily due to highly successful clades like 2.3.4.4b and 2.3.2.1c/e. Along with this renewed vigor we've also seen a rise in reports of neurological manifestations:

CDC EID Journal: Encephalitis and Death in Wild Mammals at An Animal Rehab Center From HPAI H5N8 - UK

Ontario: CWHC Reports HPAI H5 Infection With Severe Neurological Signs In Wild Foxes (Vulpes vulpes) 

In 2022, in Clinical Features of the First Critical Case of Acute Encephalitis Caused by Avian Influenza A (H5N6) Virus, we saw the first known case of neuroinfluenza in an H5N6 patient; a 6-year-old girl who was admitted to a hospital with mild pneumonia - but severe encephalitis - in January of that year. 

The following year, in Cell: The Neuropathogenesis of HPAI H5Nx Viruses in Mammalian Species Including Humans, we looked at an excellent review of recent surge in neurological infections reported in mammals and humans.

Highlights

• Highly pathogenic avian influenza (HPAI) H5Nx viruses can cause neurological complications in many mammalian species, including humans.

• Neurological disease induced by HPAI H5Nx viruses in mammals can manifest without clinical respiratory disease.

• HPAI H5Nx viruses are more neuropathogenic than other influenza A viruses in mammals.

• Severe neurological disease in mammals is related to the neuroinvasive and neurotropic potential of HPAI H5Nx viruses.

• Cranial nerves, especially the olfactory nerve, are important routes of neuroinvasion for HPAI H5Nx viruses.

• HPAI H5Nx viruses have a broad neurotropic potential and can efficiently infect and replicate in various CNS cell types.

• Vaccination and/or antiviral therapy might in part prevent neuroinvasion and neurological disease following HPAI H5Nx virus infection, although comprehensive studies in this area are lacking.

Even the relatively mild `bovine' H5N1 strain (B3.13) has been shown to have neurotropic qualities (see Preprint: Recent Bovine HPAI H5N1 Isolate is Highly Virulent for Mice, Rapidly Causing Acute Pulmonary and Neurologic Disease), at least in mice.

Thirteen months ago (April 2025) we saw a preliminary report on a neuroinvasive infection in an 8-y.o. girl (see Vietnam: Ho Chi Minh DOH Reports A Rare H5N1 Encephalitis Case In a Child), which reported:

As noted by infectious experts, this is a rare case in which the A/H5N1 avian influenza virus damages the central nervous system and does not attack the respiratory tract.

While much of the following report will be primarily of interest to clinicians, we have a detailed follow up on the Vietnamese case. Follow the link to read it in its entirety.

Central Nervous System Involvement by Novel Clade 2.3.2.1e H5N1 Avian Influenza Virus in a Paediatric Patient

Phung Nguyen The Nguyen , Nguyen Thanh Hung , Ngo Ngoc Quang Minh , Nguyen Thi Thu Hong , Nguyen Thi Thanh Huong , Cao Minh Hiep , Le Nguyen Thanh Nhan , Tran Van Dinh , Du Tuan Quy , Tran Thanh Thuc
Open Forum Infectious Diseases, ofag283, https://doi.org/10.1093/ofid/ofag283

Published: 07 May 2026

Novel clade 2.3.2.1e A(H5N1) virus was detected in cerebrospinal fluid but not in respiratory,rectal-swab and blood samples of an eight-year-old boy presenting with meningoencephalitis without respiratory symptoms. Cerebrospinal fluid A(H5N1)-hemagglutinin-specific antibody levels were higher than that of sera. Clinicians should be aware of emerging clade 2.3.2.1eA(H5N1) associated meningoencephalitis.

       (SNIP)

A(H5N1)-associated CNS infection in humans has rarely been reported but typically present as a complication, following respiratory symptoms [3-5]. Notably, our patient presented with meningoencephalitis in the absence of respiratory symptoms. Additionally, unlike the previously reported patients, who had viral RNA detected in both CSF and non-CSF samples [3-5], our patient only had viral RNA detected in serial CSF samples in the absence of viral RNA detected in urine, blood, rectal swab and respiratory samples.

Low respiratory-tract viral loads, transient viral replication in the respiratory tract, and/or delayed sample collection (illness day 6 onward) might explain the negative PCR findings in non-CSF samples, including the endotracheal aspirate sample. 

Notably, HPAI A(H5N1) viruses can infect human respiratory tissues by binding to receptors bearing sialic acids linked to galactose by α2,3-linkages, which are found in the lungs and lower respiratory tract, supported by the chest radiograph findings suggestive of lower left lung pneumonia.

        (SNIP)

In summary, we report on a HPAI A(H5N1) infection in a child presenting with  meningoencephalitis in the absence of respiratory symptoms. Viral RNA was detected in cerebrospinal fluid but not in respiratory, rectal-swab and blood samples.

Testing for IAV and  A(H5N1) virus should be considered in patients presenting with CNS infection with a history of exposure (e.g. dead poultry). Clinicians should be aware of meningoencephalitis associated with A(H5N1) infection in the absence of respiratory symptoms.

       (Continue . . . )

Not only can these neurological complications prove quite serious, atypical presentations can significantly delay proper diagnosis, isolation, and treatment. 

A reminder that HPAI H5 isn't your father's influenza. 

And we continue to treat it as such at our considerable peril.

Africa CDC Convenes Emergency Meeting After Reports of a Large Outbreak of Non-Zaire Ebola In the DRC

 

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While details remain scant, overnight Africa CDC released an urgent statement overnight on what appears to be an unusually large outbreak of a non-Zaire Ebola virus in Ituri province, Democratic Republic of the Congo; centered primarily in the Mongwalu and Rwampara health zones. 

With the caveat that only 13 of 20 samples have tested positive - they report 246 suspected cases and 65 deaths - which (if correct) suggests this outbreak may have been ongoing for some time.

The preliminary finding of a `non-Zaire' Ebola strain is noteworthy. While a more complete genomic analysis expected within the next 24 hours, the two biggest contenders are the Sudan Ebolavirus (SEBOV) and Bundibugyo Ebolavirus (BEBOV).

Previously, 15 of the 16 confirmed Ebola outbreaks in the DRC since 1976 have been Ebola Zaire, with one outlier, an outbreak of the Bundibugyo Ebolavirus in 2012. 

A non-Zaire ebolavirus could complicate matters, since the current Ebola vaccine is designed specifically for ZEBOV, and it is not expected to provide significant cross protection against other strains. 

First, the statement from Africa CDC, after which I'll return with a bit more.

Africa CDC Calls Urgent Regional Coordination Meeting Following Ebola Virus Disease Outbreak in Ituri Province, DRC

Addis Ababa, Ethiopia / Kinshasa, DRC, 15 May 2026 — The Africa Centres for Disease Control and Prevention (Africa CDC) is closely monitoring the confirmed Ebola Virus Disease outbreak in Ituri province, Democratic Republic of the Congo, and is working with national authorities and partners to support a rapid, coordinated response.

Following consultations with the DRC’s Ministry of Health and National Public Health Institute, preliminary laboratory results from the Institut National de Recherche Biomédicale (INRB) have detected Ebola virus in 13 of 20 samples tested. The results suggest a non-Zaire ebolavirus, with sequencing ongoing to further characterise the strain. Results are expected within the next 24 hours with support from Africa CDC.

As of the latest update, about 246 suspected cases and 65 deaths have been reported, mainly in Mongwalu and Rwampara health zones. Four deaths have been reported among laboratory-confirmed cases. Suspected cases have also been reported in Bunia, pending confirmation.

Africa CDC is concerned about the risk of further spread due to the urban context of Bunia and Rwampara, intense population movement, mining-related mobility in Mongwalu, insecurity in affected areas, gaps in contact listing, infection prevention and control challenges, and the proximity of affected areas to Uganda and South Sudan.

In response, Africa CDC is convening an urgent high-level coordination meeting today, 15 May 2026, with health authorities from the DRC, Uganda and South Sudan, together with key partners including the World Health Organization, UNICEF, FAO, the United States CDC, the European CDC, China CDC, the Public Health Agency of Canada, Gilead Sciences, Merck & Co., Johnson & Johnson Innovative Medicine, Regeneron Pharmaceuticals, Roche, Abbott Laboratories, Cepheid, BioNTech, Moderna, Evotec Biologics, CEPI, Gavi, Médecins Sans Frontières, IFRC, the World Bank, the African Development Bank, Afreximbank, the Gates Foundation, the Wellcome Trust, and other partners.

The meeting will focus on immediate response priorities, cross-border coordination, surveillance, laboratory support, infection prevention and control, risk communication, safe and dignified burials, and resource mobilisation.

“Africa CDC stands in solidarity with the Government and people of the Democratic Republic of the Congo as they respond to this outbreak,” said H.E. Dr Jean Kaseya, Director General of Africa CDC. “Given the high population movement between affected areas and neighbouring countries, rapid regional coordination is essential. We are working with DRC, Uganda, South Sudan and partners to strengthen surveillance, preparedness and response, and to help contain the outbreak as quickly as possible.”

Africa CDC is preparing support across key response pillars, including coordination through emergency operations mechanisms, digital surveillance and data management, cross-border preparedness, laboratory coordination, infection prevention and control, risk communication and community engagement. In addition, Africa CDC will work with partners to assess the availability and appropriateness of medical countermeasures once sequencing results confirm the exact ebolavirus species.

Africa CDC is urging communities in affected and at-risk areas to follow guidance from national health authorities, report symptoms promptly, avoid direct contact with suspected cases, and support response teams working to protect communities. Additional information will be provided as they become available and as sequencing results are finalised.

About Ebola Virus Disease

Ebola Virus Disease is a severe and often fatal illness. It spreads through direct contact with the bodily fluids of infected persons, contaminated materials, or persons who have died from the disease. Early detection, prompt isolation and care, contact tracing, infection prevention and control, community engagement, and safe and dignified burials are critical to stopping transmission. WHO describes Ebola as spreading through direct contact with bodily fluids and contaminated surfaces or materials.

There are 6 known types of Ebolaviruses, with the most recent (Bombali) discovered in 2018. 

• Ebola virus (species Zaire ebolavirus)
• Sudan virus (species Sudan ebolavirus)
• Taï Forest virus (species Taï Forest ebolavirus, formerly Côte d’Ivoire ebolavirus)
• Bundibugyo virus (species Bundibugyo ebolavirus)
• Reston virus (species Reston ebolavirus)
• Bombali virus (species Bombali ebolavirus)

Of these, only 4 are known to infect and sicken humans (Bombali and Reston have yet to do so). These viruses are endemic in bats, can infect non-human primates and other mammalian hosts, and occasionally spill over into humans.   

While most Ebola outbreaks are contained after a few dozen - or a few hundred - cases, the 2014-2016 West African outbreak spanned 3 countries, and claimed over 11,000 lives. 

Exported cases outside of Africa are rare, but have been reported (see here, here, and here).  

All of which means we'll be keeping a close eye on this emerging regional public health emergency.  

Preprint: Outbreak of H9N2 Avian Influenza Viruses in Lesser Rhea in Peru, June-July 2025

 

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Although we spend a good deal of time looking at the Asian-lineage of LPAI H9N2, which has become particularly well adapted to poultry and which continues to spill over into humans (particularly in China), we rarely hear about it in North or South America. 

In 2019's A Global Perspective on H9N2 Avian Influenza Virus, the authors summed up its impact on the Western Hemisphere:  

2.1.6. The Americas

H9N2 viruses have been isolated from poultry in the USA periodically throughout the second half of the twentieth Century, in fact the prototypic H9N2 isolate (A/turkey/Wisconsin/1/1966) was isolated in this period. All isolated viruses have been of the American lineage and appear to be spillover events from wild birds, possibly sea birds which carry genetically closely related viruses in this region. Since 2001, there has been no evidence of the virus in poultry in North America, despite routine surveillance and extensive evidence of other non-H9N2 viruses in poultry [64,65,66,67,68].

In South America, there is serological evidence from 2005 of H9N2 infections in Colombia, however, no virus was isolated and no further evidence has been reporter since [66]. 

As we've discussed often (see Cell: Early-warning Signals and the Role of H9N2 in the Spillover of Avian Influenza Viruses) LPAI H9N2 is famous for its ability to reassort with other influenza subtypes, often enhancing HPAI viruses with improved transmissibility or replication in mammals. 

And, in addition to birds, LPAI H9N2 has a track record of infecting humans, pigs, and even bats (see Preprint: The Bat-borne Influenza A Virus H9N2 Exhibits a Set of Unexpected Pre-pandemic Features).

All of which makes the following preprint - about a particularly virulent strain of (still LPAI) H9N2 spreading through a remote Rhea Conservation Center in Southern Peru - more than a little interesting.

I've only posted some excerpts from a much longer report. Follow the link to read it in its entirety.

Outbreak of H9N2 avian influenza viruses in lesser rhea in Peru, June-July 2025

Alejandra Garcia-Glaessner, Alvin Crespo-Bellido, Breno Muñoz-Saavedra, Diana Juarez, Patricia Barrera, Gabriela Salmon-Mulanovich, Shadam E. Checahuari-Jarata, Dany Cruz, Dennis X. Huisa-Balcon, Grover Idme, Martha L. Nelson, Jesus Lescano,  Mariana Leguia

doi: https://doi.org/10.64898/2026.05.08.723762

This article is a preprint and has not been certified by peer review  

 

Preview PDF

Abstract

Avian influenza viruses (AIVs) are endemic in the Americas and responsible for outbreaks in both domestic and wild birds that occasionally spill over into humans. We report the first known outbreak of AIV H9N2 in lesser rhea (Rhea pennata), also known as Darwin’s rhea, in the region of Puno-Peru. The animals in this study lived in an isolated conservation center located in remote highlands above 4,000 m.a.s.l.

Between June and July 2025, a total of 46/92 animals were recorded sick, with symptoms including greenish diarrhea (100%), hyporexia (24%), dyspnea (76%), nasal discharge (42%), drowsiness (18%) and isolation from the flock (73%), and 94% later died. Gross pathology exams revealed septicemia characterized by severe hepatitis, pneumonia, tracheitis, enteritis, and encephalitis. Swab and necropsy samples tested positive for Influenza A by PCR and were later identified as H9N2 through whole genome sequencing.

We generated complete H9N2 genomes for two individuals. No additional pathogens were found. Phylogenetic analysis across all eight segments revealed that the viruses were low pathogenicity H9N2 AIV strains of North American origin, which indicated this outbreak was a new introduction of the virus into South America.

We also performed a comparative mutational analysis and identified multiple mutations previously associated with mammalian host adaptation, increased virulence, increased pathogenicity, and increased virus binding to α2-6 receptors, which may explain the high mortality rates observed despite the supposedly low pathogenicity of the strain. We also identified novel mutations specific to rhea viruses that will need to be experimentally validated.

This is the first report of a natural H9N2 systemic infection in an avian host, highlighting a need for increased surveillance efforts for zoonotic influenza viruses with pandemic potential.

(SNIP)

A larger concern is the potential for H9N2 AIVs to create reassortants with locally circulating strains that could make them especially well adapted to mammals [76]. H9N2 has been reported in bats during routine surveillance efforts in Egypt and South Africa [77,78], further highlighting the host range of this subtype.

The introduction of a new strain of H9N2 is therefore of particular concern, as it is a well-recognized donor of internal gene segments that have contributed to the emergence of other influenza strains through reassortment [79].

The limited availability of H9N2 sequences from South America remains a significant challenge for interpreting regional viral evolution. This is the first reported outbreak of LPAI H9N2 in lesser rheas and provides genomic evidence of a distinct introduction of this subtype of AIV into South America. 

Our findings expand our current knowledge of H9N2 host range in a high altitude environment and provide evidence that low pathogenicity strains can result in high mortality rates, perhaps linked to specific viral mutations.

Surveillance programs need to be strengthened to incorporate broad monitoring for circulating AIVs in both poultry and wild birds to enable early detection and close monitoring of regional virus circulation, cross-species transmission, viral evolution, genetic adaptation and future risk assessment.

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LPAI H9N2 was first identified in Wisconsin poultry in 1966. In the 1990s it swept across much of Eurasia, becoming `hyperendemic' in many affected countries (see 2019's Viruses: A Global Perspective on H9N2 Avian Influenza Virus).

Range Of Endemic H9N2 Viruses

Although some attempts have been made at controlling the H9N2 virus (including using largely ineffective vaccines) - since it produces relatively mild illness in poultry - it is often tolerated or ignored.

While H9N2 remains far from our biggest pandemic concern, the CDC has designated 2 different lineages (A(H9N2) G1 and A(H9N2) Y280) as having at least some pandemic potential (see CDC IRAT SCORE), and several candidate vaccines have been developed.

And many will be surprised to see that, in terms of risk of emergence, the H9N2 Y280 lineage is ranked higher than H5N1, while the G1 lineage is ranked only slightly lower.

All of which makes LPAI H9N2 - either as a standalone threat or as a co-conspirator - worthy of our attention and respect.