Volume 28, Number 6—June 2022
Synopsis
Detection of SARS-CoV-2 B.1.351 (Beta) Variant through Wastewater Surveillance before Case Detection in a Community, Oregon, USA
, Tyler S. Radniecki, Devrim Kaya, Dana Alegre, Matthew Geniza, Anne-Marie Girard, Katherine Carter, Mark Dasenko, Justin L. Sanders, Paul R. Cieslak, Christine Kelly, and Brett M. Tyler
Table
SARS-CoV-2 variant B.1.351 mutations detected in clinical specimens and wastewater samples in Linn County, Oregon, and surrounding jurisdictions, March-May 2021
| Sample* | Collection site† | Date | Mutations specific to‡ |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| B.1.351 |
Clade 1 |
Subclade§ |
||||||||||
| + | – | ? | + | – | ? | 1a | 1b | |||||
| Clinical specimens | ||||||||||||
| EPI_ISL_1866415 | Linn Co. | 2021 Mar 29¶ | 9 | 0 | 0 | 5 | 1 | 0 | – | – | ||
| EPI_ISL_1736521 | Linn Co. | 2021 Apr 5 | 9 | 0 | 0 | 6 | 0 | 0 | + | – | ||
| EPI_ISL_1736532 | Linn Co. | 2021 Apr 5 | 9 | 0 | 0 | 6 | 0 | 0 | + | – | ||
| EPI_ISL_1737841 | Linn Co. | 2021 Apr 7 | 9 | 0 | 0 | 0# | 0 | 0 | – | – | ||
| EPI_ISL_1964160 | Linn Co. | 2021 Apr 9 | 8 | 0 | 1 | 6 | 0 | 0 | – | + | ||
| EPI_ISL_1999265 | Linn Co. | 2021 Apr 12 | 9 | 0 | 0 | 5 | 1 | 0 | – | – | ||
| EPI_ISL_2202145 | Linn Co. | 2021 Apr 16 | 8 | 0 | 1 | 4 | 0 | 2 | + | – | ||
| EPI_ISL_2139637 | Linn Co. | 2021 Apr 26 | 9 | 0 | 0 | 6 | 0 | 0 | + | – | ||
| EPI_ISL_2139638 | Linn Co. | 2021 Apr 26 | 9 | 0 | 0 | 6 | 0 | 0 | + | – | ||
| EPI_ISL_2139639 | Linn Co. | 2021 Apr 26 | 9 | 0 | 0 | 6 | 0 | 0 | + | – | ||
| EPI_ISL_2139644 | Linn Co. | 2021 Apr 27 | 9 | 0 | 0 | 6 | 0 | 0 | + | – | ||
| EPI_ISL_2250177 | Linn Co. | 2021 Apr 27 | 8 | 0 | 1 | 6 | 0 | 0 | – | + | ||
| EPI_ISL_2086679 | Linn Co. | 2021 Apr 28 | 9 | 0 | 0 | 6 | 0 | 0 | + | – | ||
| EPI_ISL_2086678 | Linn Co. | 2021 Apr 28 | 9 | 0 | 0 | 6 | 0 | 0 | + | – | ||
| EPI_ISL_2139636 | Linn Co. | 2021 Apr 30 | 9 | 0 | 0 | 6 | 0 | 0 | + | – | ||
| EPI_ISL_2086694 | Linn Co. | 2021 Apr 30 | 9 | 0 | 0 | 6 | 0 | 0 | + | – | ||
| EPI_ISL_2339336 | Linn Co. | 2021 May 10 | 9 | 0 | 0 | 6 | 0 | 0 | + | – | ||
| EPI_ISL_2382524 | Linn Co. | 2021 May 12 | 9 | 0 | 0 | 6 | 0 | 0 | + | – | ||
| EPI_ISL_2382527 |
Linn Co. |
2021 May 14 |
9 |
0 |
0 |
6 |
0 |
0 |
+ |
– |
||
| Wastewater samples | ||||||||||||
| ALB-Inf-03-26-21-A | Albany, Linn Co. | 2021 Mar 26 | 7 | 1 | 1 | 3 | 1 | 2 | – | + | ||
| ALB-Inf-03-31-21-A | Albany, Linn Co. | 2021 Mar 31 | 9 | 0 | 0 | 5 | 0 | 1 | + | + | ||
| COR-25th-04-04-21-A | Corvallis, Benton Co. | 2021 Apr 4 | 9 | 0 | 0 | 6 | 0 | 0 | + | – | ||
| COR-26th-04-04-21-A | Corvallis, Benton Co. | 2021 Apr 4 | 6 | 2 | 1 | 5 | 0 | 1 | – | – | ||
| ALB-Inf-04-07-21-A | Albany, Linn Co. | 2021 Apr 7 | 8 | 1 | 0 | 6 | 0 | 0 | + | + | ||
| DAL-Inf-04-19-21-A | Dallas, Polk Co. | 2021 Apr 19 | 9 | 0 | 0 | 6 | 0 | 0 | – | + | ||
| ALB-Inf-04-21-21-A | Albany, Linn Co. | 2021 Apr 21 | 5 | 3 | 1 | 2 | 3 | 1 | – | – | ||
*Sequences from individual clinical specimens are identified by their GISAID accession numbers (https://www.gisaid.org). Wastewater sequences are identified by their field collection identifier. Co., County; +, mutation detected; –, mutation not detected; ?, inadequate sequence data for a determination. †Cities where individual clinical specimens were collected are not provided to reduce identifiability of case-patients. ‡Number of mutations matched by the sequences from each sample. Mutations specific to B.1.351 are G174T, A2692T, G5230T, A21801C, 22283∆9, G22813T, C25904T, C26456T, and C28253T. Mutations specific to clade 1 are A1763G, C5100T, G13045A, C19524T, 28027∆129, and C29741T. §A single mutation defines each of clades 1a (A11875G) and 1b (C15928T). Absence of both mutations defines clade 1c in the case of individual specimens; in the case of wastewater samples, determining whether a mutation is truly absent from the RNA molecules present, or if the mutations have simply not been detected, is not possible. ¶This sample was retrospectively identified as B.1.351 late in April 2021 after routine sequencing of historical specimens. #This specimen falls into clade 2 (Figure 1).