Pathogens We Monitor

We work closely with public health officials to understand what disease information is most useful, then research if it’s possible to detect the disease in wastewater reliably.


WastewaterSCAN’s researchers use a thorough and intentional process to determine which disease targets to monitor. Our process is transparent, open-access, and vetted through peer review. 

We use droplet digital polymerase chain reaction (PCR) testing to measure concentrations of viral DNA or RNA in wastewater. 

Jump to a pathogen

Influenza (Flu)

Influenza is an upper respiratory virus affecting the nose, throat, and lungs, Symptoms begin 1-4 days after acquiring infection and can include fever, cough, sore throat, headache, muscle and joint pain, fatigue, and a runny nose. 

Influenza is spread when uninfected people breathe in droplets produced by infected people. Influenza is more common in the fall and winter – the traditional “flu season” –  but can spread anytime during the year.

Those at highest risk include people 65 and older, especially if in a nursing home or long-term care; children younger than 2; pregnant women; those with chronic medical conditions such as asthma, heart disease, kidney disease and diabetes; and those with compromised immune systems such as from HIV or chemotherapy. Effective annual vaccines are available, and antiviral drugs specific to influenza can also be prescribed by a doctor to treat the flu. Learn more about the flu.

National data (past 180 days): Quantity of nucleic-acids, PMMoV Adjusted (x1M)

Respiratory Syncytial Virus (RSV)

Respiratory syncytial virus (RSV) is a common upper and lower respiratory virus with typically mild, cold-like symptoms – runny nose or congestion, cough, low-grade fever, sneezing, and headache. Severe cases can cause difficulty breathing and/or wheezing, sometimes requiring hospitalization. RSV is transmitted both by inhaling droplets from infected people, or by direct contact, such as kissing a child with RSV or indirectly by touching a surface and then touching one’s face. RSV can remain on surfaces and potentially infect people for many hours. Individuals are most contagious in the first week of infection. RSV is most commonly spread during the winter and early spring months. Most people recover quickly, but RSV can be serious. Infants and older adults are more prone to severe RSV that may require hospitalization for difficulty breathing or dehydration. Vaccines are available for older adults over age 60, and for pregnant women. There is also a monoclonal antibody treatment for infants younger than 8 months to prevent severe RSV infection. Current treatment consists mainly of supportive care. Learn more about RSV.

National data (past 180 days): Quantity of nucleic-acids, PMMoV Adjusted (x1M)


SARS-CoV-2 is the virus that causes COVID-19, a respiratory disease affecting lungs, throat, and sinuses that also affects other parts of your body. Primary symptoms include fever, cough, and fatigue. While many cases are mild, the virus can also cause severe disease resulting in hospitalization and death. Some people experience persistent symptoms after COVID-19 infection. COVID-19 spreads easily by airborne droplets produced when an infected person coughs, sneezes, breathes, talks, or even sings. People can spread the virus before they have symptoms or know they are sick. Symptoms appear, on average, 3-4 days after infection. Infections occur year-round and may not happen according to predictable seasonal patterns. COVID-19 can cause severe medical complications and death, particularly for older people, those with preexisting conditions such as heart disease and diabetes, and those with compromised immune systems. Vaccines are available for COVID-19 and are effective in preventing the spread of the disease and lessening severity. Learn more about COVID-19.

National data (past 180 days): Quantity of nucleic-acids, PMMoV Adjusted (x1M)

Human Metapneumovirus (HMPV)

Human metapneumovirus (HMPV) is an upper and lower respiratory tract virus that is related to RSV. Typical symptoms of infection include cough, fever, shortness of breath, and nasal congestion, and it can sometimes cause more severe lung infections similar to RSV. HMPV is typically spread when an infected person coughs and sneezes producing virus droplets that infect others. It can also be spread by direct contact such as shaking hands with an infected person or touching a surface that has the virus on it and then touching one’s face. Symptoms usually start 3 to 6 days after acquiring infection. HMPV cases typically rise in late winter and into spring, but could spread at any time of year. Young children, older adults, and those with weakened immune systems are at greatest risk. More severe cases can turn into lung infections that cause difficulty breathing. There is no specific antiviral to treat or vaccine to prevent HMPV. Learn more about HMPV.

National data (past 180 days): Quantity of nucleic-acids, PMMoV Adjusted (x1M)

Norovirus GII

Norovirus is a highly contagious virus  and the leading cause of foodborne illness in the U.S. Symptoms typically include diarrhea, vomiting, nausea, and stomach pain, and may be referred to as a “stomach flu” although unrelated to the actual “flu” – influenza. WWSCAN monitors GII, the form that is more common in the United States. People do not develop immunity, meaning norovirus can be contracted by anyone. Symptoms set in 12-48 hours after exposure. Norovirus is spread by ingestion of the virus. A few norovirus particles are enough to cause illness and are spread by direct contact with infected persons, eating contaminated food or drink, and touching contaminated surfaces and then one’s mouth. Norovirus can remain infectious on surfaces for weeks, and does not respond to some disinfectants. Norovirus cases are usually highest November to April in the United States, but occur year-round. Most people get better within 1-3 days, but dehydration is common (especially in young children). There is no vaccine or treatment other than supportive care. Learn more about norovirus.

National data (past 180 days): Quantity of nucleic-acids, PMMoV Adjusted (x1M)


Rotavirus is a highly contagious diarrheal disease that can cause severe stomach and intestinal inflammation, primarily in children. It causes diarrhea, vomiting, fever, abdominal pain, electrolyte imbalance, and sometimes fever. Infections in adults are usually not symptomatic. Rotaviruses are spread by accidental ingestion of the virus from the stool of infected persons, through close direct contact with an infected person, or when touching a contaminated surface and then the mouth. Rotavirus can remain infectious in the environment for weeks to months. Symptoms often begin less than 48 hours after acquiring infection and resolve in 3-7 days. Without vaccination, most children will have been infected with rotavirus by age 5. First infection after age 3 months is generally the most severe. Risk is greater for immunocompromised children. Effective vaccines were first offered in the United States in 2006. Two vaccines are now approved for use and part of routine vaccination for infants in the United States. Learn more about rotavirus.

National data (past 180 days): Quantity of nucleic-acids, PMMoV Adjusted (x1M)

Enterovirus D68

Enterovirus D68 usually causes mild respiratory illness. Runny nose, sneezing, coughing, and body aches are common. Most infections are asymptomatic or mild. Severe cases can result in wheezing and difficulty breathing. Enterovirus D68 is believed to play a role in acute flaccid myelitis (AFM), a rare-but-serious neurological condition, mostly in young children, causing muscle and reflex weakness. Symptoms include new arm or leg weakness, difficulty swallowing or slurred speech, drooping eyelids, or facial droop after a respiratory illness. The virus is transmitted in respiratory secretions, or by touching a contaminated surface and then one’s mouth or nose. Infections tend to peak in summer and fall. Infants, children, and teenagers are most susceptible, especially those with asthma. There is no vaccine, and treatment is supportive. Learn more about Enterovirus D68.

National data (past 180 days): Quantity of nucleic-acids, PMMoV Adjusted (x1M)


Mpox is a rare viral disease, previously known as monkeypox, causing skin lesions and sometimes flu-like symptoms. Mpox can produce a blistering rash on hands, feet, chest, face, mouth, or near the genitals. Other symptoms may include fever, chills, swollen lymph nodes, fatigue, and muscle aches; headache; respiratory symptoms such as sore throat; congestion; and cough. Rashes begin as flat, red bumps that blister, fill with pus, then crust over and fall off; a process that lasts two to four weeks. In some cases, people who are infected do not experience symptoms. Mpox is spread through direct, personal, often skin-to-skin contact with rash and scabs, saliva, upper respiratory secretions (snot, mucus); and sexual transmission. Symptoms usually begin 3-17 days after exposure. Infected persons without symptoms can spread mpox. Mpox is not a seasonal disease, but occurs in outbreak clusters. There are antiviral medications available that can be used to treat mpox. A two-dose vaccine is also available to prevent infection. Learn more about mpox.

National data (past 180 days): Quantity of nucleic-acids, PMMoV Adjusted (x1M)

Candida auris

Candida auris (C. auris) is an often-drug-resistant yeast (fungus) that can cause severe bloodstream infections. C. auris often exists on skin and other body parts of healthy people, without symptoms or infection, who are then a “colonized” person. A “colonized” person, even when asymptomatic, can transmit C. Auris onto surfaces or objects by touch, which can then spread to others. Infections can occur year-round. C. auris  is easily transmitted among high-risk patients in healthcare settings. Use of invasive breathing tubes, feeding tubes, and catheters increases risk of infection. Treatment is possible, but there are now drug-resistant strains of the fungus. Learn more about candida auris.

National data (past 180 days): Quantity of nucleic-acids, PMMoV Adjusted (x1M)

Hepatitis A

Hepatitis A (HAV) is a highly contagious, viral infection of the liver. Symptoms may include tiredness, nausea and diarrhea, abdominal pain, loss of appetite, low-grade fever, and jaundice lasting up to 2 months. HAV can cause liver failure and even death, but these cases are rare and usually affect older people and those with pre-existing serious health issues, like liver disease or HIV. HAV is found in the stool and blood of infected people and spread through close personal contact with an infected person or eating contaminated food or drink. Infection can occur throughout the year, and the virus can survive for months in the natural environment. A vaccine is available to prevent infection. Treatment is supportive. Learn more about HAV.

National data (past 180 days): Quantity of nucleic-acids, PMMoV Adjusted (x1M)

Explore current data

View Dashboard