Oregon Wastewater Surveillance

  

What is RNA? The viruses we routinely test for in wastewater samples are RNA viruses. We search for these viruses based on specific regions, or sequences, in their RNA. RNA (ribonucleic acid) is structurally similar to DNA (deoxynucleic acid) except that it is usually single stranded rather than double stranded, contains an uracil base rather than a thymine base, and contains an extra oxygen molecule to make a ribose sugar. Viral RNA is replicated and used to produce viral proteins using the host cell’s machinery.

Genomic Surveillance. From the CDC (https://www.cdc.gov/coronavirus/2019-ncov/variants/genomic-surveillance.html) “All viruses change (or mutate) as they replicate and spread in a population. Viruses that have RNA as genetic material, such as SARS-CoV-2 (the virus that causes COVID-19) and influenza, mutate much faster than viruses with DNA. Every time SARS-CoV-2 replicates, there is an opportunity for the virus to change. Many mutations do not affect the virus’s ability to spread or cause disease because they do not alter the major proteins involved in infection and transmission.

 

When one of these changes does affect the virus’s ability to spread or cause disease, there may be a competitive advantage over the other lineages of SARS-CoV-2. Over time, certain lineages with these advantages become more prevalent and circulate in a population. When a lineage or group of lineages have characteristics that impact public health, CDC may classify them as a “variant of interest”, or “variant of concern”.”

 

OSU sequences all wastewater samples that have positive COVID-19 measurements above 4.0 log copies per liter of wastewater, and reports the variants found to OHA and NWSS-CDC where the information is included on the public dashboards.

  

The JN.1 Sars-CoV-2 variant has been detected in Oregon wastewater samples since October of 2023. Starting this month, the JN.1 variant will be listed in its own column in the email results attachment. According to the CDC:

 

“JN.1 is closely related to the variant BA.2.86 …. Even though BA.2.86 and JN.1 sound very different because of the way variants are named, there is only a single change between JN.1 and BA.2.86 in the spike protein. JN.1 was first detected in the United States in September 2023….CDC projects that JN.1 will continue to increase as a proportion of SARS-CoV-2 genomic sequences. It is currently the fastest-growing variant in the United States. The continued growth of JN.1 suggests that it is either more transmissible or better at evading our immune systems. At this time, there is no evidence that JN.1 presents an increased risk to public health relative to other currently circulating variants.”

 

See the image below for frequently detected Sars-CoV-2 lineages, including JN.1: