National COVID-19 trends, September 29

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Graphic from The Sick Times sharing the latest COVID-19 trends for September 29, 2026. The graphic presents trends for three metrics: WastewaterSCAN category for SARS-CoV-2, which is "high" (represented with red) and slightly decreasing (represented with a diagonal down arrow); CDC wastewater viral activity level for SARS-Cov-2, which is "low*" (darker yellow) and stable (side to side arrow); and CDC COVID-19 test positivity, which is moderate (darker yellow) and slightly decreasing. Text below these metrics reads: "*CDC wastewater viral activity levels are calculated based on measurements in the last two years only. They do not account for the lower spread that could be possible with more widespread precautions."
Heather Hogan / The Sick Times

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Here are the latest national COVID-19 trends, according to the U.S. Centers for Disease Control and Prevention (CDC) and major wastewater surveillance providers:

  • SARS-CoV-2 concentration in wastewater decreased 10% between September 9 and September 16, and the national wastewater trend is “high”  (high concentration and no trend), per WastewaterSCAN.
  • SARS-CoV-2 concentration in wastewater decreased 4% between September 5 and September 12, and the national wastewater viral activity level is “low,” per the CDC.
  • COVID-19 test positivity decreased 15%, from 5.6% of COVID-19 tests returning positive results during the week ending September 12 to 4.7% positive during the week ending September 19.

The current COVID-19 picture remains varied by region: as the summer wave continues into early fall, cases are trending up in the Northeast and parts of the West and down in the South. And an upcoming gap between CDC contracts will further restrict available data.

National metrics report plateaus and slight declines in average COVID-19 levels, masking regional differences. The CDC’s infectious disease forecasting center, which uses emergency department data, estimates that COVID-19 cases are “growing or likely growing” in 14 states, “declining or likely declining” in five states, and “not changing” in 18 states as of September 23.

The West coast remains a major hotspot for COVID-19 spread as it’s been throughout the summer. The CDC describes average SARS-CoV-2 levels in wastewater as “high” for California, Oregon, and Washington and “very high” for Hawaii; what the CDC calls “high,” I would characterize as actually very high given the agency’s high baseline for this metric. Levels might be declining in some parts of this region but are still going up in others, based on wastewater, testing, and emergency department visits.

COVID-19 levels in the South seem to be on the decline, but remain higher as this region has also been a hotspot this summer. In Texas and surrounding states (health region 6), test positivity was about 6.8% for the week ending September 19, down from a high of 10.5% for the week ending August 22 but still much higher than levels throughout the winter and spring months.

Chart from WastewaterSCAN showing national and regional trends for SARS-CoV-2 . Text above the line chart reads, "WastewaterSCAN Regional Overview, Data for last 12 months 09/29/2025 - 09/29/2026 (365 days)." The X axis of the chart represents time and the Y axis represents quantity of SARS-CoV-2 nucleic acids, PMMoV normalized (x1 million). Colored lines represent averages from the different regions: black for national trends, green for the Northeast, yellow for the South, orange for the Midwest, blue for the West. In winter 2025-26, the Midwest and Northeast saw major waves while increases were more muted in the South and levels stayed fairly consistent in the West. In summer 2026, the South has seen the largest wave, followed by the West. The latest data (as of late September) show levels declining in the South, remaining higher in the West, and increasing in the Northeast and to a lesser extent in the Midwest.
Regional COVID-19 trends from WastewaterSCAN, as of September 29

The Northeast might be the next hotspot, with wastewater as well as healthcare system data reporting potential increases. For example, some sewage testing sites in New York City and nearby counties are reporting high SARS-CoV-2 levels as of late September. New York City is often one of the first places in the region to see increasing cases with new variants or seasonal changes.

Cases seem to be mostly lower in the Midwest still, with lower SARS-CoV-2 levels in wastewater and test positivity rates here than other regions throughout the summer and early fall. The Midwest tends to see bigger waves in the winter in recent years, so increases could start as the weather gets colder there.

This week, the CDC’s wastewater dashboard includes a note that data will be interrupted for about 200 testing sites. The note describes this as a “brief gap” in data while the agency awards a new contract to a biotech company that will supplement testing programs at state and local public health departments. My story from last June includes more context on the prior version of that contract, with the company Verily, as well as the complex — and threatened — funding system that supports U.S. wastewater surveillance.

While the CDC says there will be a “brief gap” in data from these sites under the Verily contract, it doesn’t provide any specifics on when a new contract will be awarded or how the agency will support places impacted by this break in testing. I expect the gap in data could be longer if the CDC awards its new contract to a different company from Verily; the last time the CDC switched contractors (from Biobot Analytics to Verily), there was a break in data for hundreds of sites over several weeks.

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