Trends in SARS-CoV-2 clinically confirmed cases and viral load in wastewater: A critical alignment for Padua city (NE Italy)

Abstract

Since the beginning of the COVID-19 pandemic, wastewater-based epidemiology (WBE) has been depicted as a promising environmental surveillance tool and early warning system. Predictive models for the estimate of COVID-19 cases from wastewater viral loads also earned lot of interest and are currently under development. Hereby a pilot study that compares WBE surveillance data with confirmed cases, total hospitalizations, doses of vaccine administered and predominance of coronavirus variants. Composite 24hrs wastewater samples were collected weekly between September 2021 and July 2022 from Padua wastewater treatment plant. Samples were processed following a previously published method. One-step RT-qPCR was performed for quantification, adapting an Orf1b-nsp14 gene assay. Variant replacement was derived from the monthly bulletins of the Italian National Health Institute. Aggregate data on vaccine doses administered and on COVID-19 prevalence and hospitalizations were retrieved from official reports. Eighty-two samples were processed. Viral loads highlighted 3 major peaks in January, April and July 2022. Quantitation of SARS-CoV-2 in wastewater and clinical surveillance resulted temporally juxtaposable. However, variation of the two curves is not proportional. SARS-CoV-2 showed its highest peak in April, whereas maximum COVID-19 prevalence was achieved in January. Total hospitalizations followed the prevalence trend. Omicron BA.1 started to replace the Delta variant in December 2021. Subsequently, the shift towards Omicron BA.2 occurred between February and April 2022. Finally, BA.4/5 attested around June, somehow preceding the summer peak. Emergence of Omicron BA.1 over Delta could be a possible driver of the increase in both clinical cases and wastewater viral load in January 2022. In late March 2022, Omicron BA.2 replaced BA.1: this reflected in a steep increase of wastewater viral load, but not of COVID-19 confirmed cases. When a dramatic drop in the testing capacity of clinical surveillance occurred, WBE was possibly capable of detecting a substantial increase in viral circulation.

Keywords: COVID-19; Environmental surveillance; SARS-CoV-2; Sewage; WBE.

Graphical abstract

Fig. 1

SARS-CoV-2 in Padua Province (NE Italy): surveillance data; administered vaccine doses and dominant Variant of Concern. a) Viral RNA titres found in wastewater samples are reported as genome copies per litre (gc/L). Although single data-points were collected, a straight line follows the general trend for better readability. Estimated prevalence of COVID-19 (confirmed cases) is provided by the number of daily confirmed cases detected by the clinical surveillance network in the considered period. Daily number of total hospitalizations is also plotted. b) Number of vaccine doses administered. The increase around December 2021 in the daily number of doses is mainly due to boosters and the start of paediatric vaccination campaign. c) Turnover of the dominant variant of concern (VoC). Progressive substitution is represented as percentage. Table 1 also reports the genomic surveillance data point depicted by this plot.