From pandemic to endemic: Divergence of COVID-19 positive-tests and hospitalization numbers from SARS-CoV-2 RNA levels in wastewater of Rochester, Minnesota

Abstract

Traditionally, public health surveillance relied on individual-level data but recently wastewater-based epidemiology (WBE) for the detection of infectious diseases including COVID-19 became a valuable tool in the public health arsenal. Here, we use WBE to follow the course of the COVID-19 pandemic in Rochester, Minnesota (population 121,395 at the 2020 census), from February 2021 to December 2022. We monitored the impact of SARS-CoV-2 infections on public health by comparing three sets of data: quantitative measurements of viral RNA in wastewater as an unbiased reporter of virus level in the community, positive results of viral RNA or antigen tests from nasal swabs reflecting community reporting, and hospitalization data. From February 2021 to August 2022 viral RNA levels in wastewater were closely correlated with the oscillating course of COVID-19 case and hospitalization numbers. However, from September 2022 cases remained low and hospitalization numbers dropped, whereas viral RNA levels in wastewater continued to oscillate. The low reported cases may reflect virulence reduction combined with abated inclination to report, and the divergence of virus levels in wastewater from reported cases may reflect COVID-19 shifting from pandemic to endemic. WBE, which also detects asymptomatic infections, can provide an early warning of impending cases, and offers crucial insights during pandemic waves and in the transition to the endemic phase.

Fig. 1

(A) Water reclamation plant catchment area for city of Rochester and location of Byron/Stewartville (B) Testing schedule for Rochester (C) Testing schedule for Byron and Stewartville. M, Monday; T, Tuesday; W, Wednesday; R, Thursday; and S, Saturday.

Fig. 2

Representative plots of wastewater analysis by droplet digital PCR. (A) No template control. (B) Wastewater sample with low concentration of SARS-CoV-2 genomes. (C) Wastewater sample with a high concentration of SARS-CoV-2 genomes. N1, SARS-CoV-2 nucleocapsid probe 1 (red); N2, SARS-CoV-2 nucleocapsid probe 2 (gold); RPP30, probe for human ribonuclease P/MRP subunit p30 (dark blue). N1+N2; double positive droplets (tan). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3

SARS-CoV-2 genome copies (red dots) and daily positive SARS-CoV-2 cases (blue lines) in (A) Rochester, (B) Byron, and (C) Stewartville. The dotted green line indicates when case reporting guidelines changed, and the dotted red line indicates the time point after which we observe a divergence between the reported positive cases and the SARS-CoV-2 genome copies. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 4

SARS-CoV-2 variant analysis at the indicated dates. The Delta variant and several Omicron sub-variants BA.1.X to BA.5.X were detected using specific ddPCR probes.

Fig. 5

Correlation between SARS-CoV-2 genome copies in wastewater and COVID-19 positive cases in Rochester: (A) over the entire period tested, (B) before the changes in COVID-19 case reporting guidelines, and (C) after the changes in COVID-19 case reporting guidelines.

Fig. 6

(A) SARS-CoV-2 genome copies (red dots) and daily COVID-19 hospitalizations (black lines) in Rochester. The green line indicates when case reporting guidelines changed, and the red line indicates the time point after which we observe a divergence between the reported COVID-19 hospitalizations and the SARS-CoV-2 genome copies. (B) Correlation between SARS-CoV-2 genome copies in wastewater and daily COVID-19 hospitalization before September 2022, and (C) after September 2022. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)