Flash survey on SARS-CoV-2 variants in urban wastewater in Italy 2nd Report (Investigation period: 04 – 08 October 2021) (original) (raw)
National-scale surveillance of emerging SARS-CoV-2 variants in wastewater
2022
SARS-CoV-2 surveillance is crucial to identify variants with altered epidemiological properties. Wastewater-based epidemiology (WBE) provides an unbiased and complementary approach to sequencing individual cases. Yet, national WBE surveillance programs have not been widely implemented and data analyses remain challenging.We deep-sequenced 2,093 wastewater samples representing 95 municipal catchments, covering >57% of Austria’s population, from December 2020 to September 2021. Our Variant Quantification in Sewage pipeline designed for Robustness (VaQuERo) enabled us to deduce variant abundance from complex wastewater samples and delineate the spatiotemporal dynamics of the dominant Alpha and Delta variants as well as regional clusters of other variants of concern. These results were cross validated by epidemiological records of >130,000 individual cases. Finally, we provide a framework to predict emerging variants de novo and infer variant-specific reproduction numbers from was...
SARS-CoV-2 in Wastewater: Occurrence, Detection and Implications
2022
Coronavirus Disease-19 (COVID-19) is presently wreaking havoc on public health and socioeconomic development. Besides the upper and lower respiratory tract involvement, gastrointestinal symptoms are also reported in COVID-19 patients through gut-lung axis. Finding its way through the feces of infected individuals and other sources, the genetic material of SARS-CoV-2 (ssRNA) is reported widely in wastewater and is being used as a fingerprint for its detection. With millions of cases arriving every day, there is a need to level up the testing speed efficiency. Due to the restricted sampling potential of testing laboratories, clinical testing is unable to track all the symptomatic and asymptomatic cases. Wastewater-based epidemiology (WBE) bestows an auxiliary monitoring tool that will contribute in community level screening. Sample collection, concentration, RNA extraction, quantification and data analysis are the main steps involved in implementation of WBE that can be relied upon as an alarm call for an upcoming wave, emergence of a new variant or any future pandemic. WBE can be a cheaper and more practical alternative to high end and sophisticated clinical testing for community transmission detection. Worldwide, there are more than 300 reports entailing the occurrence of SARS-CoV-2 in wastewater exhibiting unique temporal trends with five of them in India. This review aims to address the present knowledge on surveillance of SARS-CoV-2 in wastewater and its implications.
medRxiv (Cold Spring Harbor Laboratory), 2021
Wastewater-based viral surveillance is a promising approach to monitor the circulation of SARS-CoV-2 in the general population. The aim of this study was to develop an analytical method to detect SARS-CoV-2 RNA in urban wastewater, to be implemented in the framework of a surveillance network in the Lombardy region (Northern Italy). This area was the first hotspot of COVID-19 in Europe. Composite 24h samples were collected weekly in eight cities from end-March to mid-June 2020 (first peak of the epidemic). The method developed and optimized, involved virus concentration, using PEG centrifugation, and one-step real-time RT-PCR for analysis. SARS-CoV-2 RNA was identified in 65 (61%) out of 107 samples, and the viral concentrations (up to 2.1 E +05 copies/L) were highest in March-April. By mid-June, wastewater samples tested negative in all the cities. Viral loads were used for inter-city comparison and Brembate, Ranica and Lodi had the highest. The pattern of decrease of SARS-CoV-2 in wastewater was closely comparable to the decline of active COVID-19 cases in the population, reflecting the effect of lock-down. Wastewater surveillance of SARS-CoV-2 can integrate ongoing virological surveillance of COVID-19, providing information from both symptomatic and asymptomatic individuals, and monitoring the effect of health interventions.
Journal of Water and Health, 2021
The new coronavirus 2 (SARS-CoV-2) is known to be also shed through feces, which makes wastewater-based surveillance possible, independent of symptomatic cases and unbiased by any testing strategies and frequencies. We investigated the entire population of the Principality of Liechtenstein with samples from the wastewater treatment plant Bendern (serving all 39,000 inhabitants). Twenty-four-hour composite samples were taken once or twice a week over a period of 6 months from September 2020 to March 2021. Viral RNA was concentrated using the PEG centrifugation method followed by reverse transcription quantitative PCR. The aim of this research was to assess the suitability of SARS-CoV-2 fragments to relate the viral wastewater signal to the incidences and assess the impact of the emerging B.1.1.7. variant. The viral load in the wastewater peaked at almost 9 × 108 viral fragments per person equivalent (PE) and day on October 25, and showed a second peak on December 22 reaching a viral ...
SSRN Electronic Journal, 2022
A real-time RT-PCR assay was designed for the rapid detection of the Omicron variant. • 737 sewage samples collected throughout Italy (11 Nov-25 Dec 2021) were tested. • The first occurrence of Omicron was on 7 December 2021, in Veneto, North Italy. • Omicron detection in sewage increased rapidly, raising from 1.0% to 65.9% in 3 weeks. • In the same period, the variant spread over the country, spreading from one Region to 17.
Science of The Total Environment
SARS-CoV-2 major VOCs/lineages can be tracked in wastewater (WW) overtime. • Estimations of the relative abundance of VOCs in WW based on NGS and RT-ddPCR correlate. • WW NGS can be used to detect and track mutations that were not detected by clinical surveillance. • WW genomic surveillance can detect differences in viral diversity at a spatiotemporal level, even within the same city.
2022
The COVID-19 pandemic represents an unprecedented global crisis necessitating novel approaches for, amongst others, early detection of emerging variants relating to the evolution and spread of the virus. Recently, the detection of SARS-CoV-2 RNA in wastewater has emerged as a useful tool to monitor the prevalence of the virus in the community. Here, we propose a novel methodology, called lineagespot, for the monitoring of mutations and the detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing (NGS). Our proposed method was tested and evaluated using NGS data produced by the sequencing of 14 wastewater samples from the municipality of Thessaloniki, Greece, covering a 6-month period. The results showed the presence of SARS-CoV-2 variants in wastewater data. lineagespot was able to record the evolution and rapid domination of the Alpha variant (B.1.1.7) in the community, and allowed the correlation between the mutations evident through our approach and the mutations observed in patients from the same area and time periods. lineagespot is an open-source tool, implemented in R, and is freely available on GitHub and registered on bio.tools. Nearly a year after the first report of SARS-CoV-2 in Wuhan, China, the virus has spread at an unprecedented pace causing a global pandemic. The predominant transmission process of SARS-CoV-2 is through droplets and contact between people, and whether a person is infected can be identified by rapid molecular strategies. SARS-CoV-2 genotyping for epidemiological investigations/to understand its molecular epidemiology relies on PCR-based methods, affordable for most laboratories. However, these methods are not easily scalable, especially in large urban areas, where a high number of individuals have to be tested to assess virus and variant spread among the population, or when new variant/mutation screening is needed, which can be attained only by sequencing methods. Interestingly, the viral RNA can also be detected in wastewater, with SARS-CoV-2 RNA levels in wastewater correlating with the COVID-19 epidemiology 1-3. Indeed, in the previous work of Petala et al. 3. normalized viral copy levels in Thessaloniki wastewater agreed with the epidemiological conditions in the city. Thessaloniki is the second largest city in Greece with around 1 million inhabitants. The city is a chief