Lungfish

Air Sampling with a National Team at the 2026 FIFA World Cup™

Eli O'Connor — Tue, 18 Aug 2026 00:00:00 GMT

Researchers affiliated with Lungfish published a new preprint describing a study in which they ran continuous air sampling alongside an elite soccer team for a month during the 2026 FIFA World Cup™. From June 3 to July 4, 2026, the researchers followed the Canadian men’s national team across five cities hosting the tournament, running InBio Apollo bioaerosol samplers in up to four team-designated rooms per hotel on a twice daily cadence. Of the 174 filters analyzed on-site with the Cepheid Xpert® Xpress assay, 13 carried detectable respiratory virus genetic material: nine SARS-CoV-2, three influenza A, and one influenza B, with no RSV. Detections clustered late in the tournament, influenza A turned up around the time a febrile player was sent home, and SARS-CoV-2 signals coincided with visibly ill hotel staff. The researchers determined that air sampling with point-of-care testing is feasible even in the constantly moving environment of a touring team, and the signals it produces arrive early enough to be useful. Read the preprint on medRxiv.

All of the data and analysis code behind the study are available on GitHub, including the GeneXpert® results, the sequencing data from a subset of samples, and the public wastewater data used for comparison. There is also an interactive version of the manuscript with figures you can explore directly.

Back to School, Back to Enterovirus Season

Tara Ornstein — Tue, 18 Aug 2026 00:00:00 GMT

In the United States, enterovirus infections increase in September and October as children return to school and spend significant time together in crowded places. According to the U.S. Centers for Disease Control and Prevention (CDC), 10-15 million infections from different types of enteroviruses occur in the United States each year. Enteroviruses are spread through the fecal-oral route and some enteroviruses can spread when an infected person sneezes or coughs droplets into the air or onto surfaces. This is why environmental surveillance of both air and wastewater can offer useful, complementary views of enterovirus circulation.

Enterovirus refers to a group of non-enveloped RNA viruses that can cause a wide variety of illnesses. Poliovirus is itself a type of enterovirus, so in scientific literature, the term “non-polio enterovirus” is used to refer to all other enteroviruses circulating today. The Cleveland Clinic explains that enteroviruses are usually named starting with “EV,” followed by letters and numbers that note the type (like EV-D68, EV-A6 or EV-A71).

Through our air sampling in schools, clinics, and other congregate settings, the Lungfish research consortium tests for non-polio enterovirus along with other pathogens. As Dr. Shelby O’Connor noted during a webinar last May, we use air samplers, namely the InBio Apollo and the Thermo Scientific AerosolSense sampler, to capture pathogen genetic material from the air and then test that material at the O’Connor Laboratory at UW-Madison.

Schools are especially important for environmental surveillance for enterovirus and other pathogens because children are in close contact for hours at a time in a shared indoor space. During a webinar held in July 2026, our team members described how we place these air samplers in cafeterias, gyms, and libraries where they run continuously, drawing in air and collecting it in a cartridge. The team then collects the cartridges on a weekly basis and processes them at UW-Madison. Because the samplers run passively in the background, they do not disrupt the school day and do not require action from teachers or students.

This air sampling work has led to important findings. As Dr. O’Connor explained, our team has been able to confirm that the presence of pathogens in the air corresponds to the presence of sick individuals in these spaces. We have also detected circulating viruses before people seek medical care for symptoms.

In addition to our efforts to detect different types of enterovirus through the air, our team has also created the Rhinovirus Serotypes in Wastewater dashboard. Human rhinovirus is part of the Enterovirus genus in the Picornaviridae family. There are more than 100 different rhinovirus types which are further subdivided into three distinct species (Rhinovirus A, B, and C). Unlike other classical enteroviruses that tend to concentrate in the digestive system, rhinovirus usually affects the nose, throat and upper airways. As a result, rhinovirus is typically spread by coughing, sneezing and touching contaminated surfaces. According to the CDC, rhinovirus circulates all year but infection rates increase in the early fall and spring. The Rhinovirus Serotypes in Wastewater dashboard shows exactly when and where each type is circulating. One of the team’s most interesting findings is that rhinovirus types occur in nationwide waves. In other words, the most prevalent serotype in California will likely be the same as in Boston. Lungfish’s environmental surveillance of air and wastewater can provide public health professionals, educators, community members, clinicians, and parents with helpful information as children return to school.

Wastewater Surveillance: An Early Warning System for Measles

Tara Ornstein — Mon, 27 Jul 2026 00:00:00 GMT

The United States is experiencing its highest annual measles case count since the disease was declared eliminated here in 2000. As of July 21, 2026, the U.S. Measles Tracker maintained by Johns Hopkins’ International Vaccine Access Center had confirmed 2,295 cases nationwide which means that we have already surpassed the 2,289 cases reported in all of 2025, and the most cases the country has seen in a single year since 1991.

According to the World Health Organization (WHO), measles typically starts with a fever (which can spike above 105°F), cough, runny nose, and red, watery eyes. The WHO reports that symptoms usually begin 7–14 days after exposure, with the telltale rash following 3–5 days later, typically starting at the head and spreading down to the trunk and limbs.

Measles spreads through the air when an infected person coughs, sneezes, or even just breathes and talks, and the virus can remain infectious in the air or on surfaces for up to two hours after that person has left the room. The WHO explains that one infected person can go on to infect as many as 18 others.

Because measles spreads so efficiently, and because unvaccinated pockets of people can be scattered, public health departments need every early signal they can get to plan prevention and response activities which may include organizing community vaccination campaigns, educational and referral materials, and surge staffing at healthcare facilities. This is where wastewater surveillance comes in. Timely wastewater surveillance can provide this early warning signal that is desperately needed. Every day counts, and the Lungfish team’s turnaround time for wastewater surveillance is now less than 7 days from collection to data delivery.

People infected with measles shed the virus in respiratory secretions and, it turns out, in wastewater and they start shedding the virus in urine before the illness is obvious. The CDC notes that infected people are contagious from four days before the characteristic rash appears to four days after it fades, and shedding is often already underway during the earlier days of fever, well before most people would think to see a doctor. That gap between infection and diagnosis is exactly where environmental surveillance can add value: sequencing a community’s wastewater doesn’t depend on someone deciding to get tested, or having access to testing at all.

Detection Before Clinical Reporting

In 2025, the Lungfish team detected measles in nine different locations, some of which didn’t know that they had cases. This early warning gave public health officials precious lead time to respond and to encourage vaccination among hesitant residents, as described in our 2025 annual report.

In April 2026, researchers affiliated with Lungfish and the CASPER wastewater network (Coalition for Agnostic Sequencing of Pathogens from Environmental Reservoirs) published a case study in NEJM Evidence that demonstrated just how sensitive this kind of surveillance can be.

Another related study, co-authored by Martin Shafer, a researcher affiliated with the CASPER network mentioned above, along with colleagues at the Wisconsin Department of Health Services and CDC, was published in Morbidity and Mortality Weekly Report earlier this month and described two travel-associated measles cases in Wisconsin. Wastewater surveillance detected one case, caused by the D8 genotype, before it was reported to health officials, while a separate case, caused by the B3 genotype, was missed by the standard wastewater assay due to a mutation in the circulating virus. Untargeted metagenomic sequencing helped confirm this gap and prompted developers to update the assay.

Identifying Measles in Urban Environments

In a wastewater sample collected on September 14, 2025, from a treatment plant serving more than a million people in Cook County, Illinois, the team’s untargeted metagenomic sequencing turned up 43 reads matching measles genotype B3 out of more than 900 million total sequencing reads from that sample. That’s roughly 0.000005% of the data. Local health officials were notified.

It turned out those 43 reads corresponded to a single known case: an unvaccinated child from suburban Cook County who had contracted measles during international travel and whose home and treating hospital both fell within the catchment area of that wastewater sample. Because the local health department was already aware of and managing this case, the wastewater detection didn’t change the public health response in this instance. But the finding matters for what it demonstrates: that untargeted metagenomic sequencing can pick out the genetic signal of a single measles infection in the wastewater of an entire metropolitan area, without anyone having told the system in advance what to look for.

Potential for the Future

Measles is making a comeback in places that had gone decades without seeing it, at the same time that vaccine coverage has been sliding and federal support for traditional disease surveillance has been shrinking. Wastewater surveillance can give communities something traditional case reporting often can’t: an early, unbiased read on whether measles is already circulating, before people start showing up sick.

Environmental Surveillance: Timely Disease Intelligence for a Strained System

Tara Ornstein — Sat, 18 Jul 2026 00:00:00 GMT

Highlights from Lungfish’s presentation to the National Board of Public Health Examiners’ Webinar Wednesday series

As traditional public health surveillance systems come under increasing strain, environmental surveillance is emerging as a vital source of timely disease intelligence. Because it draws on signals from entire communities rather than the subset of people who seek care and get tested, environmental surveillance can offer a more representative picture of pathogen circulation, often well before clinical systems register a change.

On July 8, 2026, Heidi Horn, Tara Ornstein, and Sasha Tretyakova presented Lungfish’s work as part of the National Board of Public Health Examiners’ Webinar Wednesday series. The team explained how wastewater and air monitoring, paired with metagenomic sequencing, can identify circulating pathogens days or weeks before cases surface through clinical channels.

Tara Ornstein walked through the publicly available wastewater surveillance dashboards, describing what each one offers and how public health practitioners can use them to strengthen their programs. Heidi Horn provided an overview of air sampling and described Lungfish’s work detecting Mycobacterium tuberculosis in the air in Nepal. Sasha Tretyakova presented Lungfish’s work in Wisconsin schools, illustrating how data from air sampling can complement other surveillance efforts.

The well-attended session closed with a robust discussion of the practical realities of implementing environmental surveillance and its potential role in outbreak response. Participants were especially interested in the use of wastewater surveillance for measles. The Lungfish team noted that researchers affiliated with Lungfish have published important new work on detecting measles in wastewater, underscoring how the approach can help identify measles activity and complement traditional public health reporting.

A recording of the webinar is available here. To learn more about Lungfish’s environmental surveillance work, visit lung.fish.

Innovation in Air Sampling: From Tape Samplers to Indoor Air Forecasts

Tara Ornstein — Mon, 13 Jul 2026 00:00:00 GMT

The history of air sampling stretches back further than most people realize. The Smithsonian’s National Museum of American History holds photographs of samplers dating to the 19th century, including the Sedgwick-Tucker device which aimed to detect bacteria and fungi and looks more like Victorian laboratory furniture than anything you’d recognize today. By the 1950s, the AISI automatic tape sampler had arrived, bulky and loud, but a genuine leap forward in continuous air monitoring for particulate matter.

The samplers used by the Lungfish project today look very different.

One of these samplers is InBio’s Apollo and, at just six by six inches, it’s roughly the size of two iPhones placed side by side. More importantly, it’s quiet. Earlier generations of air samplers announced themselves with mechanical whirring and hum; the Apollo blends into the background, operating unnoticed in the spaces people actually use. That combination of size and silence isn’t just convenient. It’s transformative for where and how air surveillance can happen.

Breathing new life into disease surveillance

In a webinar on May 21st hosted by InBio, Dr. Shelby O’Connor laid out an ambitious vision for what air sampling could ultimately become: a public health forecasting tool, not unlike the weather forecast you check before leaving the house. Imagine an app that tells you the risk of encountering a circulating respiratory pathogen in your neighborhood today, whether low, moderate, or high. Some people might pull on a mask for a moderate-risk day, the same way they grab an umbrella when the sky looks like it might rain. Others might skip an indoor gathering entirely when the risk is elevated, just as you would cancel a picnic in a downpour.

To get there, Lungfish is testing whether air sampling can reliably detect respiratory pathogens in real-world settings across three very different environments.

Zambia: Proving the concept in a low-resource setting

In 2025, Lungfish deployed four Apollo samplers to clinics run by the Macha Research Trust in Zambia. This site was chosen because respiratory infection surveillance is limited in low- and middle-income countries, so environmental surveillance might offer a quick and cost-effective way to obtain helpful information about circulating respiratory pathogens. After sampling three times a week, the Lungfish team and their partners found that the information detected through air sampling matched clinical data obtained from nasal swabs.

Nepal: Catching tuberculosis earlier

Tuberculosis (TB) remains the world’s deadliest infectious disease, killing more than one million people each year. In Nepal, multidrug-resistant TB is among the top ten causes of death. Treatment for drug-resistant TB is arduous, and patients may spend up to 18 months in specialized TB “hostels,” isolated from family while undergoing complex drug regimens. The earlier people are diagnosed with TB, the better their chances are for survival.

Lungfish is currently sampling the air inside three TB hostels in Nepal. The immediate goal is validation: can air sampling detect Mycobacterium tuberculosis DNA in the air of spaces where people with confirmed TB cases are residing? If so, can we use next-generation sequencing to show strain level correlation between the air samples and patient samples. And finally, can we move this process beyond sampling in hostels, to hospitals, clinics, and community spaces, to see whether air surveillance can flag TB transmission before symptoms drive anyone to test.

Wisconsin schools: ORCHARDS-Air Study

Finally, Dr. O’Connor described Lungfish’s work in Wisconsin schools. In a partnership with the team leading the Oregon Child Absenteeism due to Respiratory Disease study (ORCHARDS), Dr. O’Connor explained how Lungfish worked to determine if air sampling was feasible in households. During the 2025-2026 academic year, if a child fell ill, the family would be offered an Apollo air sampler to place in their home for 14 days along with nasal swabs of the child and family members living in the household. The results indicated, once again, that the detections found through air sampling in households matched the clinical diagnosis of the index case.

What comes next

The Lungfish project has plans to continue air sampling in schools and healthcare facilities in the United States, and also expand to clinical sites in Brazil and Taiwan. The information collected by the Lungfish project so far has confirmed that the presence of respiratory pathogens corresponds to sick individuals in these indoor spaces. Our future work will assess if we can detect pathogen signals from the air and use those findings to design interventions to prevent transmission.

World Zoonoses Day: From Pasteur's Vaccine to Environmental Surveillance

Tara Ornstein — Mon, 06 Jul 2026 00:00:00 GMT

Every year on July 6, the global health community observes World Zoonoses Day to raise awareness about zoonotic diseases, which are infections that pass from animals to humans. The date marks a profound milestone in public health: the anniversary of July 6, 1885, when Louis Pasteur successfully administered the very first rabies vaccine.

While Pasteur’s breakthrough changed history, the battle against zoonoses is more urgent today than ever before.

According to the Food and Agriculture Organization of the United Nations (FAO), 60% of all human infectious diseases are zoonotic. Furthermore, the World Health Organization (WHO) reports that 75% of new human pathogens detected over the last three decades originated in animals. From COVID-19 to avian influenza, these threats are accelerating. FAO attributes this rise to a complex web of modern factors: global travel, international trade, intensified agricultural systems, climate change, and increased animal-human interaction in wildlife habitats.

To stop the next pandemic, we cannot afford to play catch-up. We have to see it coming.

The Lungfish Approach: Turning Environmental Signals into Action

This is where the innovative environmental surveillance led by Lungfish researchers becomes vital. Long before a patient steps into a clinic or hospital, pathogens leave distinct genetic traces in our air and water. By capturing these signals early, Lungfish provides communities with a critical head start to inform outbreak responses and deploy resources.

A prime example of this proactive defense is Lungfish’s wastewater surveillance, which has successfully detected several zoonoses, including the H5N1 avian influenza virus.

What sets the Lungfish team apart is our use of metagenomic sequencing. Rather than testing exclusively for known targets, this advanced technique captures all genetic material within a sample. This is a game-changer for public health because traditional diagnostic panels often miss a novel virus simply because no one knows to look for it yet. Metagenomic sequencing ensures that emerging, unidentified threats have nowhere to hide.

Empowering Global Health Through Data Transparency

Robust data is only as powerful as its accessibility. The Lungfish team is committed to rapid, transparent data sharing. We actively collaborate with public health partners across the United States and around the world, making our findings actionable in real time.

To facilitate data sharing, we have developed several public-facing dashboards. Among them is our Species Frequency Dashboard, which analyzes a genetic marker called 12S rRNA in wastewater to map out which animal species are present in a given geographic area. Should a new virus emerge, this information will help scientists and public health officials to rapidly narrow down and identify potential animal hosts. As an example, the Nipah virus is one of the most well-known zoonotic diseases. It first emerged in late 1998 after fruit bats migrated from Indonesia to pig farms in Malaysia, driven from their traditional habitats by severe droughts and forest fires. The virus spilled over from its natural reservoir, fruit bats, to pigs, and then from pigs to humans. People fell ill after contracting the virus, but local health professionals initially thought their illness was caused by Japanese encephalitis, a mosquito-borne disease. It took time to discover the real cause of the outbreak. A tool like the Species Frequency Dashboard could help public health professionals facing a new virus identify the source much faster. By providing an immediate, verified baseline of which species are interacting in a specific area, it eliminates weeks of ecological guesswork and points investigators exactly where to look.

By bridging the gap between biology and public health, the Lungfish team isn’t just monitoring the current landscape. Instead, we are building the early-warning architecture needed to protect global communities from the threats of tomorrow.

Seeing the invisible: Promoting Health and Safety in the Workplace with Environmental Pathogen Surveillance

Tara Ornstein — Thu, 21 May 2026 00:00:00 GMT

We recently observed International Day for Safety and Health at Work to mark the importance of protecting people from hazards in the places where they live, learn, and work. While many safety risks are visible, some of the most important threats to health, including viruses and other pathogens, are invisible. New environmental surveillance approaches are helping communities detect these hidden dangers earlier than ever before.

Environmental surveillance is based on a simple idea: pathogens leave traces in the environments we share. Viruses can appear in air and water days or even weeks before people begin showing symptoms or seeking medical care. By collecting and analyzing samples from these environments, researchers can identify circulating pathogens and provide early warnings about potential outbreaks.

Wastewater surveillance has become one of the most powerful tools for this type of early detection. Because people often shed viruses before they feel sick, wastewater samples can reveal emerging infections across an entire community without requiring individual testing. The Lungfish team conducts similar wastewater surveillance using metagenomic sequencing, which is an approach that analyzes all genetic material present in a sample and enables our team to detect thousands of viruses and microbes simultaneously. By using this type of surveillance, the Lungfish team has been able to detect a wide range of pathogens including avian influenza H5N1 during initial dairy cattle outbreaks, West Nile virus, and measles, along with thousands of viral taxa.

Environmental surveillance also extends beyond water. The Lungfish project has conducted air sampling to monitor pathogens in shared indoor spaces to capture genetic material from viruses circulating in the air, including respiratory pathogens like influenza, Respiratory Syncytial Virus (RSV), and SARS-CoV-2. Up to now, air sampling workplace responses to respiratory illness have been reactive. Typically, employers have to wait for workers to develop symptoms and then wait again for laboratory confirmation. By the time results are available, transmission may already be widespread, staffing shortages may be unfolding, and many others may have been exposed. The Lungfish project is working to change that timeline.

Monitoring air in these environments can help identify potential outbreaks before they lead to widespread illness. In healthcare facilities and clinics, detecting viruses in the air can help professionals anticipate increased infection risk and adjust infection control measures or staffing plans accordingly. For example, this information could inform transmission-based precautions or staffing procedures.

These technologies are also being applied internationally. Air sampling programs have detected influenza A and ongoing SARS-CoV-2 circulation in hospital settings in Zambia, demonstrating that environmental monitoring can reveal pathogen activity even in well-ventilated spaces and in areas where traditional testing resources may be limited.

Researchers are also exploring whether air monitoring can improve detection of Mycobacterium tuberculosis in treatment facilities in Nepal, where the disease remains a major challenge to health workers and the broader community.

Together, these efforts represent a new model for protecting health and safety. As we observe the International Day for Safety and Health at Work, we recognize that environmental surveillance provides workplaces with timely, unbiased insight into circulating pathogens. These innovations underscore a critical shift: environmental surveillance equips workplaces to respond more quickly and build safer environments for everyone.

Detecting Measles in Wastewater: New Findings in NEJM Evidence

Lungfish — Fri, 01 May 2026 00:00:00 GMT

Researchers affiliated with Lungfish have published important new work on detecting measles in wastewater, highlighting how wastewater surveillance can help identify measles activity and complement traditional public health reporting. Read the paper in NEJM Evidence.

For a shorter overview, see Marc Johnson’s thread on X.

Is BA.3.2 Disproportionately Infecting Children? A Look at the Age Distribution Data

Marc Johnson — Mon, 06 Apr 2026 00:00:00 GMT

Ryan Hisner and others recently observed something unusual in the GISAID sequence data: the emerging SARS-CoV-2 lineage BA.3.2 appeared to have a disproportionate number of sequences from children compared to other circulating lineages. We decided to take a closer look.

Analyzing the Data

To investigate, we queried GISAID for all countries that included patient age metadata in their sequence submissions and identified the five countries with the most BA.3.2 sequences: Luxembourg, the Netherlands, Ireland, France, and the USA. For each country, we compared the age distribution of BA.3.2 sequences to non-BA.3.2 sequences from the same country and time period (December 2025 to present).

The results were striking. In Luxembourg, children under 10 made up 23.4% of BA.3.2 sequences (n=141) versus just 4.8% of non-BA.3.2 (n=377), an over 4-fold increase.

In the Netherlands, 16.3% of BA.3.2 sequences (n=135) came from children under 10, compared to just 3.8% of non-BA.3.2 (n=308), also a 4-fold increase.

France showed a clear skew in the pediatric age group: 27.0% of BA.3.2 sequences (n=111) were from patients under 18, versus just 8.5% of non-BA.3.2 (n=514). The difference was most pronounced in children 2-17, which was 21.6% of BA.3.2 sequences and only 2.5% of non-BA.3.2 sequences, an 8-fold increase in this category.

In Ireland, 38.8% of BA.3.2 sequences (n=103) were from children aged 0-18, compared to just 7.5% of non-BA.3.2 (n=67), a 5-fold increase.

In the USA, 49.1% of BA.3.2 sequences (n=59) were from children under 10, compared to 17.5% of non-BA.3.2 sequences (n=3,867). The most pronounced group was 3-9, which was 22% of BA.3.2 sequences but only 3.6% of non-BA.3.2 sequences, a 6-fold increase.

Why Might This Be Happening?

Hypothesis 1: Immunological Naivety

One straightforward explanation is that younger individuals have had fewer prior SARS-CoV-2 infections and therefore less immune experience. If BA.3.2 is antigenically distinct enough from previously circulating lineages, children — who may have only been exposed to one or two prior lineages — could be more susceptible to infection by something new, leading to higher rates of clinical presentation and sequencing.

To test this, we looked back at the last major lineage shift: the displacement of XBB lineages by BA.2.86/JN.1 in late 2023 to early 2024. If immunological naivety were the primary driver, we would expect to see a similar skew toward younger age groups in BA.2.86 sequences compared to XBB.

We did not. The age distributions of XBB (n=4,772) and BA.2.86 (n=8,476) were virtually identical, with no enrichment of children in the newer lineage.

This suggests that immunological naivety alone does not explain the BA.3.2 age skew.

Hypothesis 2: The ORF7/8 Deletion

Ryan Hisner has proposed that the ORF7/8 deletion carried by BA.3.2 may be responsible for the age-skewed pattern. To explore this, we looked for a historical comparator: GW.5.1.1, another lineage that carried a similar ORF7/8 deletion. We compared its age distribution to HV.1.1, a lineage that circulated at the same time but lacked this deletion.

The results were suggestive. Among US sequences, GW.5.1.1 (n=35) showed a notably younger age distribution than HV.1.1 (n=468), with a higher proportion of sequences from children and young adults.

Conclusions

The data clearly show that BA.3.2 sequences are enriched for younger individuals compared to other lineages circulating at the same time and place. The consistency of this pattern across five countries with different sequencing practices and healthcare systems makes it unlikely to be an artifact of sampling bias.

The immunological naivety hypothesis — that children are simply more susceptible to any new lineage — is not supported by the XBB/BA.2.86 comparison, where no age skew was observed during a comparable lineage transition.

The ORF7/8 deletion hypothesis, proposed by Ryan Hisner, is more consistent with the data. The similar age skew seen in GW.5.1.1, another lineage with a comparable deletion, suggests that this genomic feature may play a role in altering the age distribution of infections. Further investigation into how ORF7/8 deletions affect viral tropism, immune evasion, or disease presentation across age groups is warranted.

Data & Acknowledgments

Data were downloaded from GISAID’s EpiCoV database. We gratefully acknowledge all data contributors, i.e., the Authors and their Originating laboratories responsible for obtaining the specimens, and their Submitting laboratories for generating the genetic sequence and metadata and sharing via the GISAID Initiative, on which this research is based.

All genome sequences and associated metadata supporting the findings of this study can be accessed through the persistent digital object identifier https://doi.org/10.55876/gis8.260406wc. GISAID also communicates the aggregation of GISAID accession numbers (EPI_ISL_IDs) through the corresponding EPI_SET_260406wc identifier to facilitate both the acknowledgment of all data contributors and the direct retrieval of the underlying data from GISAID used in this study.

World TB Day: Advancing Tuberculosis Detection and Care in Nepal Through Partnership and Innovation

Tara Ornstein — Tue, 24 Mar 2026 00:00:00 GMT

Tuberculosis (TB) remains one of the world’s deadliest infectious diseases. Despite being preventable and curable, TB is the leading cause of death from a single infectious agent worldwide and consistently ranks among the top ten causes of death globally. TB also disproportionately affects people living with HIV and is a major contributor to deaths associated with antimicrobial resistance. Each year, millions of people fall ill with TB, yet many are never diagnosed or receive care in time.

TB is caused by the bacterium Mycobacterium tuberculosis (M. tuberculosis) and is transmitted through the air when a person with active TB disease coughs, speaks, or breathes. Early diagnosis and timely treatment are essential to save lives and prevent ongoing transmission.

Tuberculosis in Nepal

World Health Organization (WHO) reports consistently rank Nepal among countries with the highest TB burden. Geographic barriers, limited access to specialized care, and delays in diagnosis all contribute to the spread of the disease.

In addition, Nepal faces a significant number of cases of multidrug-resistant TB (MDR-TB). MDR-TB develops when TB bacteria mutate or change in ways that make them resistant to the most effective standard treatments. As a result, receiving care becomes a longer and more complex process.

For people diagnosed with MDR-TB, care often requires extended stays at specialized treatment centers far from home. This can create serious economic and social challenges for patients, their families, and communities, adding to the difficulty of what can already be an overwhelming diagnosis.

Partnering to improve patient-centered TB care

The Birat Nepal Medical Trust (BNMT) is a Nepalese non-governmental organization dedicated to improving the health and well-being of people across Nepal. For decades, BNMT Nepal has worked closely with communities and national partners to strengthen TB prevention, diagnosis, and care.

One major challenge in MDR-TB care in Nepal is the limited availability of inpatient treatment facilities. To address this gap, BNMT Nepal worked with partners on improving holistic, patient-centered care at MDR-TB treatment hostels. These hostels provide essential support for people undergoing treatment, which often lasts several months and requires individuals to travel days away from their home districts. During this time, patients are separated from family, work, and community, making supportive care environments especially critical.

Air sampling as an additional tool in TB detection and prevention

While strengthening clinical care is essential, ending the TB epidemic will also require new tools to detect and interrupt transmission earlier. Although TB is airborne, most diagnostic approaches rely on identifying disease after people develop symptoms and seek care. Globally, a substantial proportion of people with TB are never diagnosed, allowing transmission to continue unnoticed.

To help address this challenge, BNMT and Lungfish have partnered to explore air sampling as an additional tool for TB detection and prevention. Air sampling aims to detect M. tuberculosis directly from the environment by capturing airborne bacteria. If successful, this approach could help identify locations where TB transmission may be occurring and enable medical and public health professionals to prioritize those areas for targeted outreach, testing, and infection prevention measures. Air sampling is intended to complement existing diagnostic tools.

Latest activities in Nepal

In early 2026, BNMT and Lungfish began conducting air sampling activities in MDR-TB treatment hostels, where the TB presence is already known, to evaluate whether samplers such as InBio’s Apollo Air Sampler and the InnovaPrep Cub sampler can collect M. tuberculosis in real-world conditions. Detection of the bacteria is facilitated by Cepheid GeneXpert instruments that BNMT obtained through their IMPACT TB program. These hostels provide an important pilot environment to assess the feasibility and performance of air sampling over time.

Sampling activities are being carried out over several months to determine whether airborne M. tuberculosis can be consistently captured and detected. Findings will be shared with partners and community stakeholders in Nepal to inform future research, implementation strategies, and potential integration into TB control efforts.

Looking ahead: future plans

On this World TB Day, we recognize that ending TB will require sustained collaboration, innovation, and a commitment to equity in global health. By combining patient-centered care with new tools to better understand where transmission occurs, BNMT and Lungfish aim to contribute to a future where TB is detected earlier, treated more effectively, and ultimately eliminated as a public health threat. Together, we remain committed to advancing solutions that put people, communities, and science at the center of TB care.

ORCHARDS-AIR Study Launched!

Tara Ornstein — Fri, 27 Feb 2026 00:00:00 GMT

What if we could detect respiratory viruses circulating in your home before anyone gets sick? That’s what we hope to learn in a new study combining air sampling technology with community-based surveillance.

The Lungfish team is excited to partner with Jonathan Temte, MD, PhD, and Shari Barlow at the UW–Madison Department of Family Medicine to launch the ORCHARDS-AIR study (ORegon CHild Absenteeism due to Respiratory Disease Study–Air Surveillance). This study aims to identify families whose children report acute respiratory symptoms associated with respiratory viruses, including influenza and SARS-CoV-2, and to better understand how these viruses spread within homes using air sampling technology. Participants include students in the Oregon School District and their families.

Why Air Surveillance Matters

In a recent podcast, Temte and Barlow discussed how air surveillance could transform the way we detect and respond to respiratory infections.

First, air sampling may allow researchers to detect viruses before household members develop symptoms. Early detection could provide critical time to implement interventions and reduce further spread.

Second, measuring the genetic material of viruses collected from indoor air can help clarify how respiratory viruses are transmitted. By understanding when airborne transmission occurs and the best methods of detection, researchers can develop strategies to interrupt transmission early in an outbreak.

Building on a Strong Foundation

ORCHARDS-AIR builds on the success of the original ORCHARDS project, which ran from 2015 through 2024 and demonstrated the power of sustained, community-based surveillance. The original study generated important insights into how influenza spreads within households. ORCHARDS also identified an early documented case of household transmission during the initial stages of the COVID-19 pandemic and later provided evidence of reinfection from one SARS-CoV-2 variant to another. These findings underscore the value of tracking respiratory viruses in real-world settings over time.

Get Involved

ORCHARDS-AIR is currently underway through June 2026. Families interested in participating or anyone wanting to learn more are encouraged to visit the ORCHARDS website: https://www.fammed.wisc.edu/orchards/

This study represents an exciting step forward in our ability to understand and ultimately control the spread of respiratory infections in our communities.

World Wetlands Day: Why Wetlands Matter for Environmental Surveillance

Tara Ornstein — Fri, 30 Jan 2026 08:00:00 GMT

Every year on February 2nd, people around the world mark World Wetlands Day to recognize ecosystems that are among the most productive and most threatened on Earth. The date commemorates the signing of the Convention on Wetlands of International Importance in 1971, an international treaty created to protect wetlands and the benefits they provide to people and wildlife alike.

Wetlands are landscapes shaped by water, with water present at or just below the ground surface for much of the year. Though often overlooked, they play an essential role in maintaining environmental health. In many ways, wetlands function like natural water filters and sponges.

Stormwater runoff picks up lawn chemicals, fertilizer, pet waste, oil, and other pollutants and carries them directly into creeks, streams, and groundwater. Wetlands intercept this polluted runoff before it reaches waterways. Wetland plants and soils store pollutants and nutrients like nitrogen and phosphorus, then release them slowly as plants die and decompose. Plants also trap silt, preventing it from clouding streams and degrading habitat. As a result, water exits wetlands cleaner than when it arrived.

Wetlands also help reduce flooding by temporarily storing water and releasing it slowly over time. An acre of wetland can hold about a million gallons of water. In addition, wetlands provide habitat for a remarkable diversity of plants and animals.

Despite their importance, wetlands are disappearing at an alarming rate. According to the United Nations, wetlands are being lost three times faster than forests, making them the most threatened ecosystem on the planet. Since 1971, an estimated 35% of the world’s wetlands have been lost. Human activities such as drainage and infilling for agriculture and development, pollution, invasive species, overexploitation of resources, and climate change are the primary drivers of this decline. The United Nations has also highlighted a widespread misperception of wetlands as wastelands rather than life-sustaining systems that support livelihoods and essential ecosystem services. Scientists and public health experts warn that continued wetland loss would have serious consequences for both ecological and human health.

Protecting wetlands begins with understanding them. The U.S. National Park Service emphasizes that spending time in wetlands and learning about their functions is one of the most effective ways to foster protection and stewardship.

That connection between understanding and protection is central to the Lungfish project, which has prioritized wetlands as key sites for environmental sampling. Since early 2025, we have conducted weekly environmental sampling at two ecologically important wetland sites in Missouri.

The first site, Eagle Bluffs Conservation Area, is a restored floodplain wetland sustained primarily by treated effluent from the Columbia Wastewater Treatment Facility, with additional seasonal river inputs. Located along the Mississippi Flyway, it provides critical habitat for nearly 300 species of migrating and wintering birds.

The second site, the 3M Flat Branch–Hinkson Creek Wetland, also known as the MKT Wetlands, is a natural, stormwater-fed ecosystem that supports hundreds of freshwater-dependent species. Built to help protect Hinkson Creek from urban runoff, the wetlands filter an estimated 10 million gallons of stormwater before it reaches the creek, turning a pollution problem into a nature-based solution. What was once a degraded site near an old sewer plant has been reclaimed and restored into a thriving streamside corridor. These wetlands restore important ecological functions to the landscape and enhance water quality for people living in Columbia, Missouri.

By sampling these two wetlands in parallel, we can directly compare human-influenced and wildlife-driven viral communities. Eagle Bluffs reflects downstream viral diversity shaped by municipal wastewater, while the MKT Wetlands captures a baseline viral signature from a largely natural ecosystem. Together, these sites offer a powerful framework for studying viral persistence, ecological transport, and the boundary between engineered and natural microbial systems. These insights are increasingly important as wetlands continue to change worldwide.

Options for Bioaerosol Samplers

Ari Machtinger — Wed, 03 Sep 2025 00:00:00 GMT

Do you want to detect pathogens in the air? You should know what sampling instruments are available.

We use bioaerosol samplers to detect pathogen genetic material in the air in real-world settings like schools and healthcare facilities. We learned about as many air sampling instruments as we could to supplement our knowledge of bioaerosol research. In this blog post we share those options to lower the barrier for others who would like to get started on air sampling for pathogens.

This list covers commercially available options. The list does not include air samplers that are designed for capturing PM2.5/PM10, total suspended solids, or other related aerosols. It also excludes samplers that have been discontinued from the market such as, notably, the ThermoFisher AerosolSense which we use for most of our air sampling programs. The list also excludes air samplers which were developed and described in peer-reviewed publications but are not sold commercially.

We maintain and update the list when we learn about new information. If you are aware of other samplers that should be included in the list, please email machtinger@wisc.edu.

See the list here!

Initial Testing of the InBio Apollo Air Sampler vs. Thermo Fisher AerosolSense in Public Settings Using Standard Biotools Biomark X9 platform

Amy Ellis — Wed, 09 Apr 2025 00:00:00 GMT

As part of our ongoing efforts to evaluate alternative air sampling technologies for monitoring respiratory viral pathogens, we recently conducted a comparative study between the InBio Apollo air sampler and the Thermo Fisher AerosolSense air sampler at three locations.

Our goal was to assess the performance of the InBio Apollo air sampler in detecting respiratory pathogens and to determine its relative sensitivity in real-world environments compared to the Thermo Fisher AerosolSense air sampler.

Field Test Overview

The study occurred at three different sites: two were elementary schools, and the third was a skilled care facility. We deployed the Apollo air samplers in areas with traffic patterns similar to the AerosolSense air samplers already at the same locations. Of note, the samplers were not always placed in the same rooms at each site. Samples were collected from both Apollo and AerosolSense samplers every 3-4 days from the elementary schools and every 24 hours from the skilled care facility. Over several weeks, we collected air samples, isolated RNA from each sample, and performed PCR using a custom probe-based assay from Standard Biotools run on the Biomark X9 system. The Standard Biotools custom Respiratory Pathogen Panel (RPP) assay utilizes microfluidic chambers to simultaneously run 2304 individual PCR assays to detect multiple respiratory pathogens (Figure 1A).

While other platforms, such as digital PCR (dPCR), may be more sensitive for the comparative analyses performed here, they currently do not allow for high sample throughput while maximizing the number of targets detected. The RPP assay assesses the presence of RNAse P, a commonly used marker for human genetic material, and the presence of genetic material from several seasonal respiratory pathogens (Figure 1A).

Key Findings

Apollo detected less RNAse P – One of the primary observations from our study was that the Apollo air samplers had higher Ct values (detected less RNAse P) than the AerosolSense air samplers (Figure 1B). RNAse P serves as an indicator of human biological material in the air, and its lower detection in Apollo samples suggests differences in either air collection or genetic material elution efficiency between the two different sampling platforms.
Detection of respiratory pathogen genetic material – Despite the lower RNAse P levels, the Apollo air sampler could still effectively capture genetic material from several seasonal respiratory pathogens at all three testing sites (Figure 1C). While the pathogens detected by the Apollo did not always match what was detected by the AerosolSense air sampler for the same site/date, the pathogens detected by the Apollo and AerosolSense were similar to viruses observed on other air samplers in the greater community. This demonstrates that while there may be variations in biological material collection, the Apollo unit can detect relevant genetic material from seasonal respiratory viruses.

Figure 1

Implications for Airborne Pathogen Monitoring

Our findings suggest that while there are differences in air collection or genetic material elution efficiency from Apollo samples compared to AerosolSense samples, the Apollo is a viable option for detecting respiratory pathogens in indoor environments. It also has several advantages compared to the AerosolSense air sampler: the Apollo is smaller, quieter, easier to operate, and less expensive than the AerosolSense air sampler. Overall, this could have important implications for schools, healthcare facilities, and other settings where air monitoring could be used to track the presence of airborne pathogens.

Next Steps

Moving forward, we aim to conduct additional testing to:

Further evaluate and improve elution of genetic material from Apollo filters.
Continue to assess the performance of the Apollo at the three sites throughout the remainder of the respiratory virus season.
Train new laboratory staff members on how to elute genetic material from Apollo filters.

Testing new air samplers that are less expensive, quieter, and easier to operate is appealing to staff members at these sites. Furthermore, the Apollo’s ease of use may make air monitoring more feasible and attractive for new sampling sites. We continue to improve air monitoring technologies and expand our air sampling program!