In a recent study published in the journal Nature, researchers evaluated the transmission of coronavirus 2 (SARS-CoV-2) from severe acute respiratory syndrome by sequencing wastewater.
“Prior to wastewater sequencing, the only way to do this was through clinical trials, which are not feasible on a large scale, especially in areas with limited resources, public participation, or the ability to perform sufficient testing and sequencing. . We have shown that wastewater sequencing can successfully follow regional infection dynamics with fewer limitations and biases than clinical trials for the benefit of almost any community. ”
Timely detection of emerging variants of SARS-CoV-2 is essential for public health interventions. Detection of SARS-CoV-2 ribonucleic acid (RNA) in wastewater may provide an effective indicator of regional viral dynamics, although clinical evidence for the inference of predominant viral lineages is unviable at scale.
Study: Wastewater sequencing reveals transmission of the early cryptic variant of SARS-CoV-2. Image credit: w.tab / Shutterstock
About the study
In the present study, the team reported a high-resolution approach to assess community-based SARS-CoV-2 transmission by monitoring genomic profiles of wastewater and estimating viral concentration.
The team sequenced the SARS-CoV-2 genome from wastewater samples obtained daily from nearly 131 wastewater samples at 360 campus buildings. Epidemiological transmission links were identified by sequencing of all wastewater and clinical samples that tested positive for SARS-CoV-2 by amplicon sequencing. The team also obtained and tested 21,383 wastewater samples, of which 19,944 were from the University of California at San Diego (UCSD) campus and 1,475 were from the greater San Diego region. Sequences obtained from a total of 600 campus wastewater samples were compared with 759 genomes from on-campus clinical swabs. The team used a building-level wastewater monitoring system enabled by a Geographic Information System (GIS) that covered 360 buildings present on the UCSD campus.
“Sewage sampling allowed us to essentially ‘scrub each person’s noses’ upstream of the collector on a daily basis and use this information to concentrate viral detection efforts on an individual level.”
The team also analyzed the effectiveness of genomic surveillance of wastewater to assess viral spread within a community. This was achieved by collecting almost complete viral genomes corresponding to wastewater samples with high cycle quantification (Cq) values. In addition, the team captured the viral diversity present in the community biospecimens by developing a tool called Freyja that assessed the relative abundance of viral lineages present in mixed samples. Freyja could effectively recover relative lineage abundance in mixed samples and perform site-specific weighting to explain the non-constant variance of the estimated single nucleotide variant (SNV) frequency between sites.
Freyja was validated by sequencing synthetic tip mixtures obtained with five primary SARS-CoV-2 lineages, i.e. lineage A, Beta, Delta, Epsilon and Gamma at different concentrations ranging from 5% to 100% per sample. In addition, the team assessed whether wastewater could facilitate early detection of the new viral lineage by using Freyja in the wastewater sequencing data. The team subsequently compared the collection dates corresponding to positive samples with the dates on which the clinical samples were collected.
In addition, the effectiveness of wastewater monitoring was tested to detect new viral variants by aggregating all data related to wastewater sequencing. These data were used more to predict the temporal profile correlated with the prevalence of community lineages.
Results
The results of the study showed that the SARS-CoV-2 positivity of the wastewater samples was strongly associated with the number of positive clinical samples. This indicated that wastewater samples could effectively represent the dynamics of community infection according to the total viral load. In addition, the team found that the genetic diversity of SARS-CoV-2 was significantly greater among the wastewater samples compared to the clinical samples. This indicated that several viral lineages were present in the wastewater samples, which were removed from different people, while the clinical samples comprised only a single viral lineage.
Freyja validation revealed that Freyja consistently recovered the estimated lineage abundances for all sample mixtures. The team also noted that Freyja robustly identified the same lineages detected in the quantitative polymerase chain reaction (qPCR) tests and also recognized additional lineages that had SNV. Taken together, this demonstrated that Freyja robustly assessed viral lineage abundance from samples comprising mixed lineages.
The team noted that the Alpha and Delta lineages were detected in the wastewater samples up to 14 days before they were first detected in the genomic clinical samples. In addition, wastewater and clinical genomic monitoring could effectively control changes in lineage abundance, while an increase in the frequency of lineage detection was first found in wastewater samples.
Interestingly, the team found that estimates of viral lineage abundance in wastewater samples facilitated early detection of variants and emerging lineages, including lineages that were rarely detected through clinical surveillance. This was especially noticeable when the SARS-CoV-2 Mu variant was detected by wastewater monitoring on 27 July, while its first detection was reported in clinical samples on 23 August. However, despite the constant detection of the Mu variant in July and August in wastewater samples, the team did not detect the variant in either clinical or wastewater samples in September, which indicates that transmission of the Mu variant to the local community did not continue.
Overall, the study findings showed that improved viral detection in wastewater samples along with a new approach to identify multiple SARS-CoV-2 variants present in a mixed sample effectively detected viral lineage. prevalent in the community. In addition, the method also allowed the timely detection of new viral lineages, which can subsequently improve the accuracy and effectiveness of interventions.