There is never a dull week in New York public health news, that’s for sure.

Covid is climbing again, West Nile virus is well underway, and Cyclospora is finally declining.

But it’s not just infectious diseases we’re watching this week.

New data is showing us how congestion pricing may be affecting the air quality in New York City, and Albany county is putting up guardrails on Kratom products. Let’s jump in.

Covid going up and up

All regions of New York show elevated Covid-19 hospitalizations.

Hospitalizations are still substantially lower than they were this time last year, but are increasing.

The Northeast is typically behind the pack during the summer wave, so when we look to other leader states in the South, like Texas, it’s clear this wave is going to get bigger. How much bigger? We don’t know.

• Highest hospitalizations: New York City, Long Island, the Mid-Hudson area, and Central New York.

• Highest ED visits: newborns to 4-year-olds.

• Highest infection rates:
• Hispanic and Black New Yorkers compared with White New Yorkers recently—about 28% higher among Hispanic New Yorkers and 9% higher among Black New Yorkers.
• This reflects longstanding structural inequities, including greater exposure to risk (from factors such as relying on public transportation or working in more public-facing jobs), more crowded housing, and limitations in health care access, rather than differences in underlying health alone.

What this means for you: 

To avoid getting Covid-19 (or other respiratory viruses for that matter), wear a mask in crowded indoor areas. I’ll be reaching for mine on the train, in grocery stores, and at the airport.

It’s also a time to start thinking about vaccines (for Covid, flu, and respiratory syncytial virus, or RSV), especially with kids back in school.

YLE National shared a Fall Vaccine Guide this week. It’s a great reference for planning your personal schedule.

All vaccines are still available and legally protected in our state (New York) two bills were signed by the governor in May. This is regardless of which executive order the federal government issues. The Northeast Public Health Collaborative, New York State, and New York City have all continued to endorse the American Academy of Pediatrics vaccine schedule.

Private insurance plans will cover all these routine vaccines, and children can receive required New York school vaccines as usual. If a child’s insurance doesn’t cover vaccines or if they are uninsured, the federally funded Vaccines for Children program provides recommended vaccines at no cost for eligible kids under 19. New York also has a Vaccines for Adults program that provides free vaccines to eligible adults.

Good news: Cyclospora cases are coming down

Cyclospora, the parasite that causes explosive diarrhea, is heading in the right direction. But after a higher-than-usual summer, we still don’t have a clear answer for what drove the large increase in New York.

Seasonally, this was the normal pattern for New York. CDC defines “Cyclospora season” as May 1 through August 31. One paper found 93% of cases from 2011 to 2015 occurred during this time, with more than 80% occurring in June or July alone. This is because temperature determines how quickly and effectively the parasites mature. When it gets cooler, they stop maturing.

But the rate of increase was far from normal.

• NYC reported more than 600 cases since May 1.
• New York State has reported more than 900.
• More recent CDC totals for NYC were about 357 cases in 2023, 338 in 2024, and 414 in 2025—so this year’s totals are much larger.

Some of the increase could reflect more testing.

As Cyclospora gets more attention, doctors may be more likely to consider it and order tests for it, or patients may be more likely to ask for it. But given how much higher New York’s numbers have been than in previous years, an increase in testing alone is unlikely to explain what we saw.

We may very well finish the summer without ever knowing exactly what caused it.

West Nile Virus update Mosquitos Positive for WEST NILE IN ALL 5 BOROUGHS, ERIE, NASSAU, ROCKLAND, ST. LAWRENCE AND SUFFOLK COUNTIES

West Nile virus activity continues to heat up, and we can expect it to stay elevated until temperatures drop significantly, into the 50s. Unfortunately, over the next several weeks, we can expect more human cases.

Comparing the number of mosquito pools that have tested positive to date this year, New York State shows a similar trend to previous years: 141 positive pools in the same period in 2025 compared to 132 this year. It seems NYC, though, has more West Nile virus activity year. By this time last year, there were 628 positive pools. For this year, we’re already up to 1093.

Mosquitoes testing positive are in all five boroughs and in Erie, Nassau, Rockland, St. Lawrence, and Suffolk counties.

Expect public health departments to keep treating for mosquitoes. Keep an eye on your local health department updates to find out if spraying is happening in your neighborhood.

Congestion pricing is having very little effect on air quality—says one report

Since January 2025, any time a driver enters Manhattan below 60th street, they are charged $9. The program was pitched as a way to reduce traffic in Manhattan, improve air quality on the island, and bring in some extra income for the MTA, the city’s transit system.

This is now 18 months in, and the NYC health department released the most comprehensive report to date this week, sharing insights on what it’s done for our air quality.

The short answer: Not much.

Congestion pricing did not change pollution levels within the congestion relief zone.

While that result is pretty lackluster, the good news is that they also found no increase in air pollution near major highway corridors outside the zone. This is good news for the communities we feared might have seen traffic diverted as drivers sought to avoid toll roads.

You’ll notice that two of the pollutants measured, BC (black carbon) and NO (nitric oxide), were already projected to go down, even without congestion pricing. This is because these pollutants have been gradually declining in the City over the past 18 years, so some decrease was expected even without congestion pricing.

While the results of the report seem simple, I’m actually a little more confused. Why?

Columbia and Cornell Universities issued recent reports with conflicting findings.

A Columbia University study released earlier this year found air pollution rose in the South Bronx after tolling began. I covered it here. And a 2025 Cornell study found significantly cleaner air in Lower Manhattan. (I also covered this one.)

These are three different conclusions. I’m chalking it up to early-stage science that is still not settled. It will be crucial to keep studying these patterns using consistent methods so that the findings are comparable over time.

It’s important to get this right.

In the Bronx, where there are concerns about traffic diversion following congestion-relief tolling, asthma rates are among the highest in the county. That’s why the MTA has committed $70 million to pollution mitigation for the borough, including $20 million for clean refrigerator trailers at Hunts Point Produce Market, and $20 million towards childhood asthma programs.

What this means for you: Don’t just rely on this policy to help clean the air you breathe.

• Check real-time air quality at airnow.gov.
• Consider limiting outdoor exercise on high-pollution days.
• If you or your child has asthma and lives near the Cross-Bronx, Major Deegan, or another high-traffic route, it’s still a good idea to make sure your asthma action plan is up to date.

Something to watch: Albany County bans Kratom products

Albany County is banning the sale of all kratom products beginning September 1, following a public health order from the county health department. Officials cited safety concerns and one death in the county this year linked to a kratom product.

Kratom is a plant native to Southeast Asia whose compounds interact with opioid receptors. Some people use it for pain or to manage opioid withdrawal, but it’s not FDA-approved for any medical use. Kratom products have been associated with dependence and withdrawal, seizures, liver problems, and some deaths, although other substances are often involved. The FDA has also found contamination with heavy metals and bacteria in some products.

Kratom regulation is complicated.

Federal officials have recently focused particularly on 7-OH, a potent opioid-like compound that can be concentrated in some kratom products, while distinguishing those products from natural kratom leaf. Albany County’s order goes further and bans both.

For now, this is a local Albany County policy, but it’s worth watching to see whether other New York counties or the state follow suit. (For example, Massachusetts just banned the sale of Kratom completely.)

Bottom line

Now is a good time to be Covid-aware, think about fall vaccines (especially with schools starting), and wear that mosquito repellent. And beyond infectious diseases, there are a couple of public health developments to keep an eye on: more data and analysis on how congestion pricing affects air quality, and whether other New York communities follow suit in regulating Kratom products.

With that, you’re all caught up!

Love,

Your NY Epi

Dr. Marisa Donnelly, PhD, is an epidemiologist, science communicator, and public health expert. This newsletter exists to translate complex public health data into actionable insights, empowering New Yorkers to make informed and evidence-based health decisions.