Lungfish

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!