A Global Mutational Profile of SARS-CoV-2: A Systematic Review and Meta-Analysis of 368,316 COVID-19 Patients
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Design and Protocol
2.2. Literature Review
2.3. Inclusion and Exclusion Criteria for Studies
2.4. Quality Assessment
2.5. Data Extraction
2.6. Data Synthesis and Analysis
3. Results
3.1. Search Result and Eligible Studies
3.2. Characteristics of the Eligible Studies
3.3. The Pooled Prevalence of SARS-CoV-2 Variants
3.4. Subgroup Meta-Analysis
3.5. Meta-Regression
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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No | Study ID (Ref) | Country of Study | Period of Study | No. of Participant | No. of Mutated Cases | Mutation Detection Method | Regions of Mutation |
---|---|---|---|---|---|---|---|
1 | Akter et al., 2020 [13] | Bangladesh | May–June 2020 | 3 | 3 | Whole-genome sequencing | ORF1ab, N and S gene |
2 | Andrés et al., 2020 [14] | Spain | March 2020 | 18 | 18 | Deep sequencing of S gene | S gene |
3 | Badua et al., 2020 [15] | Multiple countries | January–May 2020 | 151 | 151 | NGS | ORF1ab, ORF8, ORF3a, 5′UTR, 3′UTR, ORF6, ORF7a, ORF10, S, E, M and N gene. |
4 | Barret et al., 2020 [16] | USA | December 2019–May 2020 | 119 | 119 | NGS | 5′UTR, ORF1ab, S gene |
5 | Bartolini et al., 2020 [17] | Italy | February–March 2020 | 9 | 9 | NGS (SARS-CoV-2 panel) | ORF1ab, UTR, S, N and M gene, |
6 | Becerra-Flores 2020 [18] | Worldwide | March–April 2020 | NR | NR | NGS | S gene |
7 | Benvenuto et al., 2020 [19] | Italy | January–April 2020 | 79 | 79 | NGS | S and N gene |
8 | Chang et al., 2020 [20] | Multiple countries | NR | 10 | 10 | NGS | ORF1ab, ORF8, S and E gene |
9 | Chen et al., 2020 [21] | China | January–February 2020 | 10 | 10 | qRT-PCR on ORF1ab and N gene; RNA sequencing | ORF1ab, ORF3a, ORF8, ORF10, S and N gene |
10 | Cusi et al., 2020 [22] | Italy | March 2020 | 1 | 1 | Direct RNA and amplicon sequencing | S gene |
11 | Demİr et al., 2020 [23] | Turkey | March–May 2020 | 63 | 63 | NGS | ORF1ab, ORF3a, 3′UTR, 5′UTR, S, N and M gene |
12 | Devendran et al., 2021 [24] | India | as of April 2020 | 10 | 10 | NGS/WGS | ORF1ab, ORF8, S and N gene |
13 | Du et al., 2020 [25] | China | January–April 2020 | 102 | 102 | qRT-PCR, meta-transcriptomic sequencing | 5′UTR, ORF1ab, S, ORF3a, ORF8, N gene |
14 | Elizondo et al., 2020 [26] | Uruguay | March–May 2020 | 44 | 44 | qRT-PCR, NGS | ORF8, ORF3a, ORF1ab |
15 | Eskier et al., 2020 [27] | USA and UK | January–March 2020 | 11,701 | 11,701 | NGS | Whole genome |
16 | Gómez-Carballa et al., 2020 [28] | Spain | as of June 2020 | 922 | 922 | NGS | Whole genome |
17 | Gong et al., 2020 [29] | Taiwan | January–March 2020 | 20 | 19 | RT-PCR & WGS | ORF1ab, ORF8, ORF3a, S gene, N gene |
18 | Gupta 2020 [30] | Worldwide | January–April 2020 | 87 | 87 | NGS | ORF1ab, ORF3a, ORF7a, ORF8, N, S and M gene |
19 | Hartley et al., 2021 [31] | USA | March–June 2020 | 200 | 173 | NGS | ORF1ab, S gene |
20 | Hassan et al., 2020 [32] | India | as of May 2020 | 128 | 128 | NGS | ORF1, ORF3a, ORF8, ORF7a, S, M and N gene |
21 | Yang et al., 2020 [33] | Worldwide | December 2019–June 2020 | 46,414 | 46,414 | NGS | Whole genome |
22 | Ip et al., 2020 [34] | Hong Kong | January–March 2020 | 12 | 1 | Sanger sequencing, Nanopore and Illumina sequencing | S gene |
23 | Islam et al., 2020 [35] | Multiple countries | as of May 2020 | 444 | 404 | NGS | ORF1ab, N, E, M, S |
24 | Jacob et al., 2020 [36] | India | until June 2020 | >600 | NR | NGS/WGS | S gene |
25 | Jary et al., 2021 [37] | France | January–February 2020 | 1 | 1 | NGS | ORF3a, ORF7a, ORF6, ORF7b, ORF8, ORF10, N, M and E gene |
26 | Jenjaroenpun et al., 2021 [38] | USA | July 2020 | 2 | 2 | Oxford Nanopore Technologies (ONT) MinION sequencing technology | ORF1ab, ORF3a, ORF14 and S gene |
27 | Khailany et al., 2020 [39] | Worldwide | December 2019–April 2020 | 95 | 71 | NGS/WGS | ORF1ab, ORF8, ORF3a, ORF10, S, N and M gene |
28 | Kim et al., 2020 [40] | Worldwide | NR | 178 | 178 | NGS | ORF1ab, ORF3, ORF6, ORF7a, ORF7b, ORF8, ORF10 S, M, E and N gene |
29 | Kim et al., 2020 [41] | Korea | NR | 4 | 4 | qRT-PCR and Sanger sequencing | S gene |
30 | Koyama et al., 2020 [42] | Worldwide | February–May 2020 | 15,755 | 10,022 | NGS | Whole genome |
31 | Kozlovskaya et al., 2020 [43] | Russia | March–April 2020 | 220 | 220 | NGS | ORF1ab, S and N gene |
32 | Kumar et al., 2020 [44] | Multiple countries | December 2019–March 2020 | 95 | 95 | NGS/WGS | Whole genome |
33 | Laamarti et al., 2020 [45] | Morocco | NR | 6 | 6 | Oxford NanoporeTechnologies [ONT] | ORF1ab, S gene, 5′UTR |
34 | Leung et al., 2021 [46] | Hong Kong | as of February 2020 | 50 | 50 | Nanopore and NGS | ORF3a, ORF1ab, S gene |
35 | Ling et al., 2020 [47] | Sweden | February–May 2020 | 348 | 348 | NGS | 5′-UTR, ORF1ab, S, ORF3a, M and N gene |
36 | McNamara et al., 2020 [48] | USA | March–May 2020 | 175 | 175 | NGS | S and 3′UTR |
37 | Micheli et al., 2020 [49] | Italy | February–April 2020 | 20 | 20 | NGS | M and N gene |
38 | Nagy et al. 2021 [50] | Worldwide | December 2019–September 2020 | 149,061 | 149,061 | NGS | ORF1ab, ORF3a, ORF8, ORF6, N and S gene |
39 | Pachetti et al., 2020 [51] | Worldwide | December 2019–March 2020 | 220 | 215 | NGS/WGS | Whole genome |
40 | Parvez et al., 2021 [52] | Bangladesh | as of August 2020 | 311 | 311 | NGS/WGS | ORF1a, S and N gene |
41 | Raghav et al., 2020 [53] | India | March–June 2020 | 202 | 202 | NGS | ORF1ab, 5′-UTR, ORF3a, ORF6, ORF7b, ORF84, ORF10, M, N and S |
42 | Rito et al., 2020 [54] | Worldwide | May–20 | 26,869 | 20,163 | NGS/WGS | Whole genome |
43 | Saha et al., 2020 [55] | India | NR | 566 | 566 | NGS | 5′UTR, ORF1ab, ORF3a, S, M and N |
44 | Saha et al., 2020 [56] | Bangladesh | April–July 2020 | 41 | 41 | NGS | ORF1ab, ORF3a, ORF6, ORF7a, ORF8, Matrix (M gene), S and N gene |
45 | San et al., 2021 [57] | South Africa | March–June 2020 | 109 | 109 | NGS | ORF1ab, ORF3a, ORF6, ORF7a, ORF7b, ORF8, ORF10, S, E, M and N gene |
46 | Skums et al., 2020 [58] | Worldwide | NR | 319 | 274 | NGS/WGS | Whole genome |
47 | Soliman et al., 2021 [59] | Egypt | June 2020 | 1 | 1 | NGS | ORF1ab and S gene |
48 | Soratto et al., 2020 [2] | Sweden | April 2020 | 4 | 4 | NGS | ORF1ab, ORF3a, ORF7a, S and N gene |
49 | Sun et al., 2020 [60] | China | NR | 1 | 1 | RT-PCR | E gene |
50 | Surleac et al., 2020 [61] | Romania | January–February 2020 | 25 | 25 | NGS | ORF1ab, S and N gene |
51 | Taboada et al., 2020 [62] | Mexico | February–March 2020 | 17 | 17 | NGS | ORF1ab, ORF8 and S gene |
52 | Toyoshima et al., 2020 [63] | Multiple countries | As of May 2020 | 12,343 | 12,343 | NGS | ORF1ab, ORF3a, ORF8, S, N and M gene |
53 | Velasco et al., 2020 [64] | The Phillipines | April–July 2020 | 23 | 23 | NGS | ORF1ab, ORF6, ORF7a, OORF7b, ORF8, ORF10, S, N and M gene |
54 | Volz et al., 2021 [65] | UK | January–June 2020 | 26,986 | 21,231 | NGS | S gene |
55 | Wang et al., 2020 [66] | USA | July 2020 | 24,715 | 24,715 | NGS | ORF1ab, ORF3a, ORF8 and S gene |
56 | Wang et al., 2020 [67] | Multiple countries | as of October 2020 | 75,775 | 75,775 | NGS | ORF1ab |
57 | Wang et al., 2020 [68] | Worldwide | as of June 2020 | 15,140 | 15,140 | NGS | Whole genome |
58 | Yap et al., 2020 [69] | Multiple countries | January–April 2020 | 142 | 112 | NGS | ORF1ab, ORF8, S and N gene |
59 | Yuan et al., 2020 [70] | Worldwide | January–May 2020 | 11,183 | 11,183 | NGS | Whole genome |
60 | Zhang et al., 2020 [71] | China | June–July 2020 | 6 | 6 | NGS | ORF1ab gene, S and N gene |
61 | Ziegler et al., 2020 [72] | Germany | July 2020 | 1 | 1 | qRT-PCR, PCR & Sanger sequencing | N gene |
62 | Zuckerman et al., 2020 [73] | Isreal | March 2020 | 8 | 8 | qRT-PCR, NGS | 5-UTR, ORF1ab, S, ORF3a and N gene |
Country of Study | Number of Studies | Prevalence (%) | 95% CI | I2 (%) | Q | Heterogeneity Test | |
---|---|---|---|---|---|---|---|
DF | p | ||||||
Bangladesh | 3 | 98.7 | 91.9–99.8 | 57.445 | 4.700 | 2 | 0.095 |
China | 3 | 97.5 | 85.1–99.6 | 5.356 | 2.113 | 2 | 0.348 |
Hong Kong | 2 | 60.3 | 15.9–92.5 | 93.675 | 15.811 | 1 | 0.000 |
India | 4 | 99.6 | 97.8–99.9 | 28.063 | 4.170 | 3 | 0.244 |
Israel | 1 | 94.4 | 37.4–99.8 | - | - | - | 1.000 |
Italy | 3 | 98.1 | 88.2–99.7 | 0.000 | 1.129 | 2 | 0.569 |
Korea | 1 | 90.0 | 22.9–99.6 | - | - | - | 1.000 |
Mexico | 1 | 97.2 | 56.0–99.9 | - | - | - | 1.000 |
Morocco | 1 | 92.9 | 30.9–99.7 | - | - | - | 1.000 |
Multiple countries | 6 | 98.2 | 95.3–99.3 | 95.168 | 103.483 | 5 | 0.000 |
Romania | 1 | 98.1 | 65.2–99.9 | - | - | - | 1.000 |
Russia | 1 | 99.8 | 94.3–100.0 | - | - | - | 1.000 |
Spain | 2 | 99.6 | 96.3–100.0 | 73.466 | 3.769 | 1 | 0.052 |
Sweden | 2 | 98.8 | 89.0–99.9 | 77.667 | 4.478 | 1 | 0.034 |
Taiwan | 1 | 95.0 | 56.8–99.6 | - | - | - | 1.000 |
The Philippines | 1 | 97.9 | 63.3–99.9 | - | - | - | 1.000 |
Turkey | 1 | 99.2 | 82.5–100.0 | - | - | - | 1.000 |
UK | 1 | 78.7 | 78.2–79.2 | - | - | - | 1.000 |
Uruguay | 1 | 98.9 | 76.7–100.0 | - | - | - | 1.000 |
USA | 5 | 98.4 | 94.8–99.5 | 92.301 | 51.954 | 4 | 0.000 |
Worldwide | 10 | 90.3 | 82.6–94.8 | 99.747 | 3553.894 | 9 | 0.000 |
Total | 51 | 97.4 | 94.4–98.8 | 98.952 | 4772.621 | 50 | 0.000 |
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Yusof, W.; Irekeola, A.A.; Wada, Y.; Engku Abd Rahman, E.N.S.; Ahmed, N.; Musa, N.; Khalid, M.F.; Rahman, Z.A.; Hassan, R.; Yusof, N.Y.; et al. A Global Mutational Profile of SARS-CoV-2: A Systematic Review and Meta-Analysis of 368,316 COVID-19 Patients. Life 2021, 11, 1224. https://doi.org/10.3390/life11111224
Yusof W, Irekeola AA, Wada Y, Engku Abd Rahman ENS, Ahmed N, Musa N, Khalid MF, Rahman ZA, Hassan R, Yusof NY, et al. A Global Mutational Profile of SARS-CoV-2: A Systematic Review and Meta-Analysis of 368,316 COVID-19 Patients. Life. 2021; 11(11):1224. https://doi.org/10.3390/life11111224
Chicago/Turabian StyleYusof, Wardah, Ahmad Adebayo Irekeola, Yusuf Wada, Engku Nur Syafirah Engku Abd Rahman, Naveed Ahmed, Nurfadhlina Musa, Muhammad Fazli Khalid, Zaidah Abdul Rahman, Rosline Hassan, Nik Yusnoraini Yusof, and et al. 2021. "A Global Mutational Profile of SARS-CoV-2: A Systematic Review and Meta-Analysis of 368,316 COVID-19 Patients" Life 11, no. 11: 1224. https://doi.org/10.3390/life11111224