PNAS (Referral): Genomic and structural evidence of SARS-CoV-2 and MERS-CoV in migratory birds

 
Tundra Swans Flyovers, Craig Strobeck, Public Domain,
https://www.fws.gov/media/tundra-swans-flyovers

#19,237

We've a surprising report to look at this morning in PNAS (most of which is behind a paywall) which describes the first detection of Betacoronaviruses (COVID & MERS-COV) in migratory birds in China. 

Coronaviruses are divided into 4 distinct genera: 

• Alphacoronaviruses
• Betacoronaviruses (i.e. SARS-CoV, MERS-CoV, etc.)
• Gammacoronaviruses
• and Deltacoronaviruses 

Alphacoronaviruses & Betacoronaviruses primarily infect mammals, while birds are mostly affected by Gammacoronaviruses, such as infectious bronchitis virus (AIBV) and occasionally by Deltacoronaviruses.

We've seen a few crossovers - particularly with Deltacoronaviruses - which have been detected mostly in birds and but occasionally in mammals (see Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus . . . . ). 

Numerous studies have tried (and failed) to infect birds with Betacoronaviruses, including: 

Lack of susceptibility of poultry to SARS-CoV-2 and MERS-CoV

Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS–coronavirus 2

All of which has led researchers to long assume that birds aren't susceptible to either SARS-CoV-2 or MERS-CoV.  But today's report calls that into question.

In brief, George F. Gao et al. report finding:

• Three nearly full‑length SARS‑CoV‑2 genomes (2 Beta-like & 1 Gamma-like VOCs) in the feces of Tundra Swans collected in Jiangxi Province in 2021.

• They also report a ~70% complete MERS‑CoV genome was recovered from a Bar‑headed goose in Tibet in 2022. 

• While the original Wuhan Strain of SARS-COV-2 was unable to infect Swans (via tsACE2 receptors), some later variants appear to have acquired the ability to do so

Since I don't have access to the full report, I'll simply refer my readers to the link and abstract below.  I'll have a brief postscript after the break. 

Genomic and structural evidence of SARS-CoV-2 and MERS-CoV in migratory birds

Jian Cao, Sheng Liu, Chao Su, +4 , and George F. Gao gaof@im.ac.cn
Contributed by George F. Gao; received January 10, 2024; accepted May 15, 2026; reviewed by Jie Cui, Yi Guan, and Lin-Fa Wang
June 29, 2026 123 (27) e2400023123
https://doi.org/10.1073/pnas.2400023123

Copyright © 2026 the Author(s). Published by PNAS. This article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).

Abstract

Migratory birds are the natural reservoir of influenza A virus (IAV), but their role as a carrier of SARS-CoV-2 remains unclear. Here, we report the identification of three almost full-length viral genome sequences of SARS-CoV-2 variants of concern (VOCs) in Tundra swans.

These sequences are named hCoV-19/Tundra swan/Jiangxi/IMCAS_M1/2021 (IMCAS_M1), hCoV-19/Tundra swan/Jiangxi /IMCAS_M2/2021 (IMCAS_M2), and hCoV-19/Tundra swan/Jiangxi/IMCAS_M3/2021 (IMCAS_M3). IMCAS_M1 and IMCAS_M3 have the same mutations as the Beta VOC (K417N, E484K, and N501Y) in the receptor-binding domain (RBD) of the viral spike (S) protein, whereas IMCAS_M2 shares the same mutations as the Gamma VOC (K417T, E484K, and N501Y) in the RBD with all three showing their distinct mutations in the genomes.

Virus receptor angiotensin-converting enzyme 2 (ACE2) proteins from both Tundra swan (tsACE2) and Black swan (bsACE2) can bind to the RBDs of all three viruses and the Alpha VOC, but not to RBD of the prototype (PT) virus. The polar contacts and hydrophobic interactions revealed by cryo-electron microscopy (cryo-EM) structures of the RBD–ACE2 complex, play key roles in virus–receptor engagement.

Furthermore, HeLa cells expressing bsACE2 and tsACE2 proteins could be transduced by pseudotyped SARS-CoV-2 variants (Alpha, Beta, and Gamma) but not PT SARS-CoV-2.

In addition, we obtained one partial genome of MERS-CoV named Bar-headed goose/Tibet/IMCAS_M4/2022 (IMCAS_M4) with 20,180 bp (~70.0% coverage). Our findings highlight the importance of migratory birds as potential carrier of both SARS-CoV-2 and MERS-CoV, thereby posing potential threat to public health.

For years, the role of migratory birds in the spread of avian flu was bitterly contested, with many scientists insisting that birds were simply incapable of flying long distances while carrying the H5 virus (see 2011's Study: The Role Of Migratory Birds In Spreading Bird Flu).

Despite abundant evidence, it wasn't until the second half of the last decade that the role of migratory birds in spreading avian flu was generally accepted (see Migratory Birds & The Spread Of Highly Pathogenic Avian Flu).

While it isn't clear how important migratory birds might be in the spread of Betacoronaviruses, this study suggests we can no longer ignore their potential as carriers of SARS-CoV-2, MERS-CoV, and possibly other coronaviruses. 

A humbling reminder that anything we say with relative certainty about avian flu, novel coronaviruses - or any other infectious disease - today, is subject to future revision as these pathogens evolve and our knowledge base expands.  

Australia: WA Designates 5th Suspected H5N1 Case as `Presumed Positive'

 

#19,236

Four days ago Western Australia announced the discovery of a suspected H5N1 infected bird in Perth (collected 6/30). To date, more than 1,000 dead birds have been reported in WA alone, but collection and testing takes time, and so only a small percentage have been processed. 

And testing - particularly of bird or animal remains - can be difficult, as the ability to detect the virus can degrade over time. 

Normally, after a local lab detects the H5 virus, Australian samples are sent to the national CSIRO lab for confirmation.  In the case of the above mentioned Perth sample, after nearly a week - while they confirmed H5 - they were unable fully sequence the virus. 

However, WA's Chief Veterinary Officer Dr Katie Webb announced today,  “This case will be considered as ‘presumed positive’ based on the available test results, species involved, coastal location and the broader epidemiological picture.”

So far WA has received more than 1,000 reports of dead birds, but due to the high volume, the DPIRD has prioritized 172 for further investigation. Of those already processed in WA, 5 have tested positive and 64 have tested negative.   

As with any disease surveillance system - whether in birds, livestock, or people - confirmed cases will represent only the tip of the pyramid. 

In the case of H5N1 in birds:

• Only a percentage of birds will sicken and die (varies by species)
• Only a fraction of those birds will be seen, reported, and collected
• Of those, only a subset will be prioritized for testing
• And of that group, some may not have detectable levels of virus

While 7 cases detected across 3 Australian states may not sound like much, it is actually a pretty strong signal that multiple incursions of HPAI have likely occurred in recent weeks. 

This update from the Western Australian government website:

WA responding to ‘presumed positive’ H5 bird flu case in Perth
Media release

Additional testing of the previously reported migratory giant petrel found in the Whitfords - Mullaloo beach area has determined the case is a ‘presumed positive’ detection of the serious H5 bird flu strain.

Last updated: 6 July 2026

Additional testing of the previously reported migratory giant petrel found in the Whitfords - Mullaloo beach area has determined the case is a ‘presumed positive’ detection of the serious H5 bird flu strain.

Testing at CSIRO’s Australian Centre for Disease Preparedness has confirmed the petrel had an influenza virus of the H5 subtype.

The case has been classified as a presumed positive because viral sequencing to confirm the virus as H5 bird flu was not able to be achieved.

The inability to obtain a sequence may be due to a range of factors, including the level of decomposition of the carcass.

WA Acting Chief Veterinary Officer Dr Katie Webb said it was considered highly likely the bird was infected with H5 bird flu, but this could not be definitively proven at this stage.

“This case will be considered as ‘presumed positive’ based on the available test results, species involved, coastal location and the broader epidemiological picture,” Dr Webb said.

“This does not change our response in WA. We are treating this the same as a positive case based on the available epidemiological and laboratory evidence.”

This presumed positive case adds to the six confirmed positive detections of H5 bird flu nationally, including four in WA on the southern and south west coasts, one in South Australia and one in New South Wales.

Importantly, there is no evidence the virus has spread beyond these individual migratory seabirds, but we ask the community to be alert and follow advice about reporting sick or dead wildlife.

People should AVOID and not handle the animals, RECORD and take photos or a video and REPORT to the Emergency Animal Disease (EAD) Hotline on 1800 675 888.

There have been more than 1000 reports from WA to the EAD hotline since Friday 19 June. Of these reports, 172 have been prioritised by DPIRD for further investigation or testing based on the risk of H5 bird flu.

To date, a total of 64 negative test results have been recorded across the State.

More information is available on the Australian Government's Bird flu (avian influenza) website.

Watching Bird Flu in Nepal (H5N1)

 

#19,235

Nestled between India and China, Nepal is no stranger to HPAI H5N1 - including at least 1 human case in 2019 - along with sporadic outbreaks in poultry over the years.  

In recent months, however, FluTrackers has been following an increasing number of reports of outbreaks in both wild birds and poultry. 

Since early March, WOAH reports 66 outbreaks across the country, involving the loss of more than 500,000 domestic birds, and reports of die offs of wild birds (mostly wild house crows).  

While official government reports are infrequent and hard to access, local and international media have reported increasing concern over the spread of H5N1 in Nepal, with Nepal News reporting yesterday (Jul 4th) Health Ministry issues nationwide alert over spreading bird flu outbreak.

Ministry Joint Spokesperson Samir Mani Adhikari is quoted as urging `. . . the public to completely avoid direct contact with sick, dead, or infected poultry, to consume meat and eggs only after they are thoroughly cooked, and to report dead birds to nearby veterinary authorities.'

The subclade currently circulating in Nepal remains a bit of a mystery. I've not seen any recent mention, but we know that both clade 2.3.4.4b (the primary global subclade) and a more regional 2.3.2.1a have been reported in Nepal. 

A 3rd possibility exists, as eight months ago, in Viruses: Zoonotic Implications of the Co-Circulation of Clade 2.3.4.4b and 2.3.2.1a H5N1 Avian Influenza Viruses in Nepal in 2023, we looked at a report of a reassortment event which combined genetic elements from both subclades. 

This event was not unlike what we saw 3 years ago with the emergence of a new, more transmissible H5 Clade 2.3.2.1e virus in Cambodia & Vietnam that subsequently sparked an abrupt uptick in human infections between 2024-2026.

Zoonotic Implications of the Co-Circulation of Clade 2.3.4.4b and 2.3.2.1a H5N1 Avian Influenza Viruses in Nepal in 2023

Pragya Koirala 1, Manju Maharjan 2, Sharmila Chapagain 3, Barun K. Sharma 1,
Tirumala B. K. Settypalli 4, Charles E. Lamien 4 and William G. Dundon 4,*

Viruses 2025, 17(11), 1481; https://doi.org/10.3390/v17111481    

Abstract

Samples collected from two avian influenza outbreaks in Bagmati Province in central Nepal between January and March 2023 were positive for H5N1. Full genomes were generated for both viruses, which revealed that one of the viruses was very similar to clade 2.3.4.4b H5N1 identified in Bangladesh in 2021/2022.

The second virus was a reassortant H5N1 virus consisting of four genes (HA, NA, NP, and M) originating from a clade 2.3.2.1a H5N1 and the remaining four genes (NS, PB1, PB2, and PA) originating from a 2.3.4.4b H5N1. Notably, this second virus had a high identity with 2.3.2.1a clade viruses identified in humans and cats in India in 2024–2025.

These are the first full genome sequences of H5N1 avian influenza viruses from Nepal and given the recent human infections by 2.3.2.1a H5N1 viruses in the region, these data will be of interest to both public health and veterinary authorities. 

(Continue . . .)

The caveat here is, this study analyzed only two poultry isolates - taken from two different farms roughly 10 km apart in early 2023 - which tells us very little about prevalence or spread of variants the region. 

Regardless of the subclade involved, a large and escalating bird flu outbreak lying beneath the flyway between the two most populous countries (India & China) on the planet is very much worth our attention. 

Stay tuned. 

Australia: NSW H5N1 Detection Confirmed

 

#19,234

Overnight Australia has confirmed the previously suspected H5 detection on NSW's Bennetts Beach, bringing the number of confirmed detections in Australian birds to 6.  There are, however, hundreds of as-yet uninvestigated reports of dead birds in WA alone.

This report from New South Wales is concerning because they are the largest poultry producing state in the the country, producing nearly 40% of the nation's chicken meat and 1/3rd of its eggs.

This from NWS's DPIRD (Department of Primary Industries and Regional Development).

Current situation

New South Wales is responding to a confirmed detection of H5 bird flu in a giant petrel found near Hawks Nest. This is the first confirmed detection of H5 bird flu in NSW. 

The NSW Government is working in collaboration with other jurisdictions and the Australian Government, with increased surveillance now underway.

At this stage, bird flu has not been detected in commercial poultry flocks, captive birds or any other birds in NSW. There is no evidence of any mass mortality in wildlife or spread to other animals.

Confirmed Australian cases to date:

• Western Australia: 4 confirmed
• South Australia: 1 confirmed
• New South Wales: 1 confirmed

This strain of avian influenza has had significant impacts overseas, causing widespread mortality in poultry, wild birds and some mammals.

It is important that we all continue to remain vigilant and report any sick or dead poultry, wild birds or wildlife.

If you see sick or dead birds or other animals, do not touch them.

Avoid contact. Record what you see. Report it to the Emergency Animal Disease Hotline on 1800 675 888 from anywhere in Australia.

Australia has well-established national response arrangements in place to respond to animal disease incidents, including H5 bird flu.

The NSW Government is reminding poultry producers that on-farm biosecurity practices are crucial to protect the health of their flocks.

For more information, visit Bird flu (Avian influenza) - DAFF.

 

mGem: A perfect storm in the era of global warming—the convergence between thermotolerant fungi and altered immunity

 

#19,233

While most of our infectious disease discussions center around viruses and bacteria, from time to time we delve into fungi (see CDC: Candida auris Update & Fungal Awareness Week 2019)) and parasites (see Cyclosporiasis Reports: CDC & Michigan DOH).

In 2012's Four Fungal Foes we reviewed three endemic (Coccidioidomycosisis, Histoplasmosis, Blastomycosis) - and one emerging tropical (Cryptococcus gattii) fungi causing a significant health burden in the North America. 

Ten years ago (June 24th, 2016) the CDC issued a Clinical Alert to U.S. Healthcare facilities about the Global Emergence of Invasive Infections Caused by the Multidrug-Resistant Yeast Candida auris.

C. auris is an emerging fungal pathogen that was first isolated in Japan in 2009. It was initially found in the discharge from a patient's external ear (hence the name `auris'). Retrospective analysis has traced this fungal infection back over 20 years.

Over the past 10 years the reported incidence of this (mostly) healthcare-facility-acquired fungal infection has increased more than 100-fold in the United States. 

In 2019's mBio: On the Emergence of Candida auris: Climate Change, Azoles, Swamps, and Birds, researchers argued that it may be the first example of a new fungal disease emerging - at least in part - due to climate change.

Updating and expanding this growing concern, we have a perspective published in mGems, which argues that the rise of global warming has created a `perfect storm' for the emergence of new fungal threats. 

Due to its length, I've only posted the abstract and a few excerpts. Follow the link to read it in its entirety.

mGem: A perfect storm in the era of global warming—the convergence between thermotolerant fungi and altered immunity

Frederic Lamoth , Dimitrios P. Kontoyiannis 

https://doi.org/10.1128/mbio.00750-26

Published 1 July 2026

ABSTRACT

The evidence supporting the impact of global warming on the epidemiology of infectious diseases, including fungal infections, is increasing. Fungi have a remarkable ability to adapt to heat and pollution, and to disseminate via air, water ecosystems, or wildfire smoke. Their genetic plasticity can lead to thermotolerance, the ability to find new ecological niches, and fitness gains.

Natural reservoirs of the fungal biomass, which are heavily affected by global warming, may serve as the environments from where new fungal diseases originate, as illustrated by the recent emergence of Candidozyma auris and Rhodosporidiobolus fluvialis.

Moreover, global warming also affects human skin/mucosal integrity and local or systemic immune responses, which could increase host susceptibility to fungal infections.

This review examines the impact of global warming on the complex fungi-host interactions, which can lead to new challenges in mycology, and discusses possible mitigation strategies.

PERSPECTIVE

The accelerated effect of global warming on Earth is one of the most important challenges in our century. Consequences of climate change are multiple, including progressive alterations of ecosystems and increases in the frequency of natural disasters, which may lead to the emergence of new pathogens and the expansion of the epidemiological footprint of existing pathogens. For humans, adaptive mechanisms to global warming that may affect our vulnerability to infections are both societal (migration, famine or poor sanitary conditions resulting from natural disasters, changes in industry/agriculture practices, and alterations in lifestyle), environmental (loss of biodiversity in land and aquatic systems, expansion of the geographic range of vectors and changes in their ecology, changes in migratory patterns of birds), and biological (modifications of microbiota and changes in innate and adaptive immune responses).

While emerging waterborne or arthropod-associated viral (e.g., dengue) or bacterial diseases (e.g., enteric bacterial pathogens) have drawn most attention, there is increasing awareness of the role of fungi (1–4). A systematic search found 24 examples of fungal diseases with some link to climate change hazards, which represents about 10% of all impacted infectious diseases (5). This may only represent the tip of the iceberg considering the rich diversity and environmental adaptability of fungal species and the spectrum of diseases they cause. In the animal kingdom, we had a recent example of the potential of fungi in taking advantage of global warming and profoundly disturbing living ecosystems with the emergence of the fungus Batrachochytrium dendrobatidis leading to mass extinction of amphibian species (6). In this review, we will discuss the potential of fungi to thrive in a warming planet, and the preventive strategies we could employ to meet this new public health threat.

       (Continue . . . )

 

Australia: NWS & Perth (WA) Report Suspected Positive HPAI H5 Detections

#19,232


Overnight Australia has reported two new suspected (preliminarily positive) H5 detections some 3,300 km apart, with one in Perth (WA) and the other on NSW's Bennetts Beach.

The report from New South Wales is particularly concerning, because NSW is the largest poultry producing state in the the country, producing nearly 40% of the nation's chicken meat and 1/3rd of its eggs.  

This from NWS's DPIRD (Department of Primary Industries and Regional Development).

Current situation

New South Wales is currently responding to a suspected positive case of H5 bird flu.

The Giant Petrel, found at Hawks Nest was sampled as a result of a Hotline report and was sent for testing at Elizabeth Macarther Agricultural Institute where it tested positive for H5 bird flu.

Samples have been sent to CSIRO’s Australian Centre for Disease Preparedness (ACDP) for confirmatory testing.

This is the first suspect positive case in NSW.

At this stage, bird flu has not been detected in commercial poultry flocks, captive birds or any other birds in NSW. There is no evidence of any mass mortality in wildlife or spread to other animals.

Confirmed Australian cases to date: Western Australia: 4 confirmed South Australia: 1 confirmed

This strain of avian influenza has had significant impacts overseas, causing widespread mortality in poultry, wild birds and some mammals.

It is important that we all continue to remain vigilant and report any sick or dead poultry, wild birds or wildlife.

If you see multiple sick or dead birds or other animals, do not touch them.

Avoid contact. Record what you see. Report it to the Emergency Animal Disease Hotline on 1800 675 888 from anywhere in Australia.

Australia has well-established national response arrangements in place to respond to animal disease incidents, including H5 bird flu.

The NSW Government is reminding poultry producers that on-farm biosecurity practices are crucial to protect the health of their flocks.

For more information, visit Bird flu (Avian influenza) - DAFF.

NSW's is not only the largest poultry producer in Australia, it is the 2nd in the country for cattle, and 1st in raising sheep.  

If confirmed, this will no doubt raise concerns in New Zealand as well, as it brings the virus much closer to its shores (see New Zealand: DOC to vaccinate ‘at risk’ birds against bird flu).

Meanwhile, Western Australia is testing a bird carcass found on a local beach.

Suspect positive detection of H5 bird flu on northern Perth beach

Media release

 
Western Australia has recorded a suspect positive detection of H5 bird flu in a migratory seabird on a northern Perth beach (between Whitfords and Mullaloo beaches).

Last updated: 3 July 2026

Western Australia has recorded a suspect positive detection of H5 bird flu in a migratory seabird on a northern Perth beach (between Whitfords and Mullaloo beaches).

Samples from a deceased giant petrel were submitted to the Department of Primary Industries and Regional Development (DPIRD) laboratory returning a suspect positive result for H5 influenza in preliminary testing.

The deceased bird was reported on Tuesday (30 June) to the Emergency Animal Disease Hotline.

Samples have been sent to CSIRO’s Australian Centre for Disease Preparedness to confirm the results and determine if it is the H5 bird flu strain of concern.

There have been five confirmed detections of H5 bird flu in Australia, including four in WA and one in South Australia.

All of the detections have involved migratory seabirds that are known to occasionally visit southern Australia.

There is still no evidence of spread or large-scale deaths in local wildlife or any detections in poultry.

The community is encouraged to keep pets away from wildlife, including preventing cats from roaming and keeping dogs on leads in wildlife areas.

The Department of Primary Industries and Regional Development (DPIRD) is leading the response in WA, with a focus on enhanced surveillance and early detection in this investigative phase.

The response is being coordinated across multiple levels of government, involving joint efforts from DPIRD, the Department of Biodiversity, Conservation and Attractions, local governments and other State agencies.

DPIRD will be utilising its team of fisheries officers to conduct increased beach patrols along the metropolitan coast and assist with the surveillance effort.

DPIRD is encouraging the community to continue to report unwell or deceased birds through to the Emergency Animal Disease Hotline on 1800 675 888.

There has been a total of 795 reports from WA to the Emergency Animal Disease (EAD) hotline since Friday 19 June.

Of these reports, 118 have been prioritised by DPIRD based on the risk of H5 bird flu for further investigation or testing.

To date, a total of 58 negative test results have been recorded.

More information is available at birdflu.gov.au

Although the number of reported bird deaths in WA (n=759) far exceeds the testing capacity of local labs - with less than 10% processed to date - the main goal is to detect trends and expansion of the threat. 

Little can be done to prevent the spread of HPAI in the wild, but enhanced surveillance and increased biosecurity by the poultry and livestock industry (cattle/sheep/goats, etc.) can help limit both the spread an economic damage.

While this is the first incursion of HPAI H5N1 into Australia, poultry producers there are no strangers to dealing with avian flu. As recently as 2024-2025 NSW, Victoria, and ACT dealt with a prolonged outbreak of several homegrown H7 viruses. 

Hopefully some of the lessons learned from that encounter will prove helpful in dealing with this newest threat. 

Stay tuned.