Tracing COVID-19 Trails in Wastewater: A Systematic Review of SARS-CoV-2 Surveillance with Viral Variants
Abstract
:1. Introduction
2. Theoretical Background: The Emergence of SARS-CoV-2 Variants
2.1. Alpha (B.1.1.7 and Q Lineages)
2.2. Delta (B.1.617.2 and AY Lineages)
2.3. Omicron (B.1.1.529 and BA Lineages)
2.4. Other Variants
3. Methodology
4. Results
4.1. Geospatial Distribution
4.2. Sampling Techniques
4.3. Concentration Methods
4.4. Analytical Methods to Detect Variants
4.5. Detected Variants
5. Discussion
6. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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WHO Label/Pango Lineage | Country First Detected | Spike Mutations of Interest | Outbreak Countries | Major Outbreak Peaks | Classification (WHO) during November 2022 | Outbreak Condition during November 2022 |
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Alpha/B.1.1.7 | United Kingdom, September 2020 | N501Y, D614G, P681H | At least 189 countries, predominant in the US, India, Sweden, France, Spain, Australia, Nigeria, and so on (1.2 million cases globally reported). | November 2020 to August 2021 | VOC: 29 December 2020 VBM: 21 September 2021 PVOC: 9 March 2022 | Drastically reduced circulation globally, with almost no reporting at the time of writing the manuscript. |
Delta/B.1.617.2 | India, October 2020 | L452R, T478K, D614G, P681R | At least 208 countries, predominant in the US, UK, Japan, Italy, India, Germany, Canada, Denmark, France, and so on (4.4 million cases globally). | May 2021–January 2022 | VOC: 15 June 2021 VBM: 14 April 2022, PVOC: 7 June 2022 | Abundance is very low at the time of writing the manuscript. |
Beta/B.1.351 | South Africa, May 2020 | K417N, E484K, N501Y, D614G, A701V | At least 127 countries, predominant in South Africa, the US, India, Sweden, France, Spain, Australia, Nigeria, Iran, and so on (43,000 cases globally). | November 2020 to August 2021 | VOC: 29 December 2020 VBM: 21 September 2021, PVOC: 9 March 2022 | Drastically reduced circulation globally, with almost no reporting at the time of writing the manuscript. |
Gamma/P.1 | Brazil, November 2020 | K417T, E484K, N501Y, D614G, H655Y | At least 93 countries, predominant in the US, Canada, Brazil, Argentina, Chile, Italy, Peru, Mexico, Sweden, South Korea, Venezuela, and so on (74,300 cases globally). | Feb 2021–November 2021 | VOC: 29 December 2020 VBM: 21 September 2021 PVOC: 9 March 2022 | No longer detected or detected at extremely low levels globally. |
Epsilon/B.1.427, B.1429 | California USA, July 2020 | I4205V and D1183Y in the ORF1ab gene, and S13I, W152C, L452R in the spike protein’s S-gene | At least 45 countries. | November 2020–March 2021 | VOC, March 2021. VBM-September 2021. Previously circulating VOI: March 2022 (WHO), | After an initial increase, its prevalence rapidly decreased from February 2021 and was outcompeted by the more transmissible Alpha variant. |
Lambda/C.37 | Peru, August 2020 | Virus’s spike protein code: G75V, T76I, Δ246–252, L452Q, F490S, D614G and T859N | At least 45 countries (predominant in Peru, Chile, US). Total global cases of less than 10,000. | November 2020–November 2021 | VOI June 2021 | No longer reported. |
Omicron/BA.2, BA.4, BA.5, BA.2.75, BQ.1, XBB | South Africa and Botswana November, 2021 | BA.2 (y*), BA.4 (L452R, F486V, R493Q), BA.5 (L452R, F486V, R493Q). BA.2.75 (z**), BQ.1 (K444T, N460K), XBB (N460K, F490S) | At least 208 countries, predominant in the US, UK, Denmark, Canada, India, Japan, Germany, France, and so on (6.2 million cases globally, 14 December 2022). | November 2021-Currently circulating lineages: BA.2, BA.4, BA.5, and their recombinants and sub-lineages | BA.2, BA.4, and BA.5 are VOC, and BA.2.75, BQ.1, XBB are current VOI at the time of drafting the manuscript, December 2022. | Many lineages are currently going around the world (83,046 in the last four weeks of 14 December 2022). |
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Tiwari, A.; Adhikari, S.; Zhang, S.; Solomon, T.B.; Lipponen, A.; Islam, M.A.; Thakali, O.; Sangkham, S.; Shaheen, M.N.F.; Jiang, G.; et al. Tracing COVID-19 Trails in Wastewater: A Systematic Review of SARS-CoV-2 Surveillance with Viral Variants. Water 2023, 15, 1018. https://doi.org/10.3390/w15061018
Tiwari A, Adhikari S, Zhang S, Solomon TB, Lipponen A, Islam MA, Thakali O, Sangkham S, Shaheen MNF, Jiang G, et al. Tracing COVID-19 Trails in Wastewater: A Systematic Review of SARS-CoV-2 Surveillance with Viral Variants. Water. 2023; 15(6):1018. https://doi.org/10.3390/w15061018
Chicago/Turabian StyleTiwari, Ananda, Sangeet Adhikari, Shuxin Zhang, Tamunobelema B. Solomon, Anssi Lipponen, Md. Aminul Islam, Ocean Thakali, Sarawut Sangkham, Mohamed N. F. Shaheen, Guangming Jiang, and et al. 2023. "Tracing COVID-19 Trails in Wastewater: A Systematic Review of SARS-CoV-2 Surveillance with Viral Variants" Water 15, no. 6: 1018. https://doi.org/10.3390/w15061018