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Volume 27, Number 5—May 2021
Research

Monitoring SARS-CoV-2 Circulation and Diversity through Community Wastewater Sequencing, the Netherlands and Belgium

Ray Izquierdo-Lara, Goffe Elsinga, Leo Heijnen, Bas B. Oude Munnink, Claudia M.E. Schapendonk, David Nieuwenhuijse, Matthijs Kon, Lu Lu, Frank M. Aarestrup, Samantha Lycett, Gertjan Medema1, Marion P.G. Koopmans1, and Miranda de Graaf1Comments to Author 
Author affiliations: Erasmus University Medical Center, Rotterdam, the Netherlands (R. Izquierdo-Lara, B.B. Oude Munnink, C.M.E. Schapendonk, D. Nieuwenhuijse, M. Kon, M.P.G. Koopmans, M. de Graaf); KWR Water Research Institute, Nieuwegein, the Netherlands (G. Elsinga, L. Heijnen, G. Medema); University of Edinburgh, Edinburgh, Scotland, UK (L. Lu, S. Lycett); Technical University of Denmark, Kongens Lyngby, Denmark (F.M. Aarestrup)

Main Article

Table 2

Summary of LFVs detected in wastewater samples determined by Illumina sequencing in study of SARS-CoV-2 circulation and diversity through community wastewater sequencing, the Netherlands and Belgium*

Position† Sample MV LFV LFV, % Total depth Feature AA MV AA LFV Frequency, %‡
NL BE Global
1440 NL/Schiphol-92506-I G A 13.2 53 ORF1a G N 1.619 4.167 1.903
3549 NL/Franeker-92719-I GACCA
CTTA –§ 46.8 201 ORF1a GPLK E 0 0 0
4497 NL/Beverwijk-92721-I T C 42.6 479 ORF1a I T 0 0 0.000
10514
 NL/AmsterdamWest-92852-I
 T
 C
 12.5
 1,656
 ORF1a
 Y
 H
 0
 0
 0
10933
 BE/Aartselaar-93030-I C T 18.0 50 ORF1a P P 100.000 100.000 99.996
NL/Tilburg-94339-I
 T
 C
 11.1
 63
 ORF1a
 P
 P
 0
 0
 0.004
11083
 BE/Properinge-92949-I G T 12.1 58 ORF1a L F 5.635 7.320 11.007
BE/Aartselaar-93030-I T G 26.4 129 ORF1a F L 94.430 92.680 88.069
NL/Tilburg-94339-I
 G
 T
 12.7
 150
 ORF1a
 L
 F
 5.635
 7.320
 11.007
11109
 NL/AmsterdamWest-92852-I C T 48.3 230 ORF1a A V 15.220 0.338 0.534
NL/Tilburg-94339-I
 C
 T
 21.2
 66
 ORF1a
 A
 V
 15.220
 0.338
 0.534
11484
 NL/Beverwijk-92721-I
 C
 T
 44.0
 84
 ORF1a
 A
 V
 0
 0
 0
11494
 NL/Franeker-92719-I C T 13.5 104 ORF1a N N 0 0 0.002
BEAartselaar-93030-I C T 43.5 370 ORF1a N N 0 0 0.002
NL/Tilburg-94339-I
 C
 T
 13.8
 247
 ORF1a
 N
 N
 0
 0
 0.002
13046 BE/Aartselaar-93030-I C A 36.7 98 ORF1a P T 0 0 0
13426 BE/Gent-93032-I C T 22.6 115 ORF1a R R 0 0 0.038
16538 BE/Gent-93032-I – ATA 27.6 348 ORF1b – N 100.000 100.000 100.000
16777 NL/Schiphol-92851-I G T 30.2 404 ORF1b V F 0 0 0
16806 NL/Tilburg-94339-I C A 22.1 77 ORF1b N K 0 0 0.016
16823 BE/Aartselaar-93030-I G T 12.0 192 ORF1b G V 0 0 0
24862 NL/Katwoude-92722-I A G 34.0 53 S T T 8.614 0.338 0.463
28115 NL/Delft-92965-I T C 47.8 67 ORF8 I I 100.000 100.000 99.993
28139 NL/Tilburg-94339-I C A 36.0 136 ORF8 S S 0.130 0.113 0.007
28375
 NL/Tilburg-94339-I
 G
 A
 30.8
 146
 N
 G
 G
 0
 0
 0.002
28394
 NL/AmsterdamWest-92852-I C T 31.5 54 N R W 0 0 0.004
BE/Properinge-92949-I C T 16.7 60 N R W 0 0 0.004
NL/Tilburg-94339-I
 C
 T
 13.6
 191
 N
 R
 W
 0
 0
 0.004
28736 BE/Leuven-93034-I A G 22.0 363 N A T 100.000 100.000 100.000

*BE, Belgium; LFV, low-frequency variant; MV, major variant; NL, Netherlands; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.
†Positions are given with respect to Wuhan-Hu-1 (GenBank accession no. MN908947).
‡Frequency of the LFV of sample against GISAID database (as of July 8, 2020) of the Netherlands, Belgium, and global samples.
§Dashes represent a gap at the given region, either as a MV or LFV.

Main Article

1These senior authors contributed equally to this article.

Page created: March 02, 2021
Page updated: April 20, 2021
Page reviewed: April 20, 2021
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