Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India
Abstract
:1. Introduction
2. Materials and Methods
3. Results
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Addressable Wells | Chip-1 (9 Samples) | Chip-2 (11 Samples) | ||||
---|---|---|---|---|---|---|
37,849,615 | 37,849,615 | |||||
With ISPs | 33,700,206 | 89.00% | 32,798,330 | 86.70% | ||
Live | 33,698,044 | 100.00% | 32,749,088 | 99.80% | ||
Test Fragments | 680,001 | 2.00% | 657,319 | 2.00% | ||
Library | 33,018,043 | 98.00% | 32,091,769 | 98.00% | ||
Library ISPs | 33,018,043 | 32,091,769 | ||||
Filtered: Polyclonal | 8,159,862 | 24.70% | 7,284,699 | 22.70% | ||
Filtered: Low Quality | 22,21,791 | 6.70% | 1,630,141 | 5.10% | ||
Filtered: Adapter Dimer | 56,745 | 0.20% | 158,413 | 0.50% | ||
Final Library ISPs | 22,579,645 | 68.40% | 23,018,516 | 71.70% | ||
Total Reads | 22,391,814 | 22,825,334 | ||||
Aligned Reads | 21,175,935 | 94.60% | 22,067,308 | 96.70% | ||
Unaligned Reads | 1,215,879 | 5.40% | 758,026 | 3.30% | ||
Alignment Quality | AQ17 | AQ20 | Perfect | AQ17 | AQ20 | Perfect |
Total Number of Bases [Mbp] | 3.83 G | 3.68 G | 2.96 G | 4.18 G | 4.02 G | 3.25 G |
Mean Length [bp] | 193 | 189 | 158 | 197 | 192 | 160 |
Longest Alignment [bp] | 377 | 376 | 359 | 343 | 343 | 332 |
Mean Coverage Depth | 57.1 | 54.8 | 44.1 | 62.3 | 59.8 | 48.4 |
S.No. | Patient ID | Qbit 4.O Reading ng/ul-RNA Sample | GenBank Accession No. | GISAID Accession No. | No. of Mapped Reads | Total Assigned Amplicon Reads | % on Target Reads | Average Read per Amplicon | Mean Depth | %Uniformity | Assembly Length (bp) | PANGO Lineage | Emerging Clade | GISAID Clade |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | NCOV/AB/21/FL407 | 3.02 | MZ562746 | EPI_ISL_1972141 | 1,378,010 | 1,364,626 | 99.03 | 5758 | 7503 | 74.30% | 29,837 | B.1.617.1 | 21B (Kappa) | G |
2 | NCOV/AB/21/FL409 | 8.87 | MZ562747 | EPI_ISL_1972134 | 3,733,707 | 3,732,055 | 99.96 | 15,747 | 25,230 | 97.89% | 29,833 | B.1.617.1 | 21B (Kappa) | G |
3 | NCOV/AB/21/FL901 | 5.92 | MZ562748 | EPI_ISL_1972135 | 2,389,121 | 2,388,613 | 99.98 | 10,079 | 15,986 | 97.03% | 29,834 | B.1.617.1 | 21B (Kappa) | G |
4 | NCOV/AB/21/FL902 | 5.53 | MZ562749 | EPI_ISL_1972136 | 2,725,685 | 2,694,642 | 98.86 | 11,370 | 18,478 | 99.29% | 29,840 | B.1.617.1 | 21B (Kappa) | G |
5 | NCOV/AB/21/FL832 | 6.73 | MZ562750 | EPI_ISL_1972130 | 661,367 | 144,412 | 21.84 | 609.3 | 936.4 | 99.28% | 29,816 | B.1.1.7 | 20I/501Y.V1 | GRY |
6 | NCOV/AB/21/FL405 | 3.72 | MZ562751 | EPI_ISL_1972142. | 3,581,768 | 3,544,684 | 98.96 | 14,956 | 22,246 | 97.10% | 29,826 | B.1.36 | 20A | GH |
7 | NCOV/AB/21/EX986 | 3.24 | MZ723921 | EPI_ISL_3305853 | 394,294 | 371,849 | 94.31 | 1569 | 2,473 | 97.28% | 29,800 | B.1.36 | 20A | GH |
8 | NCOV/AB/20/CA052 | 5.65 | MZ562752 | EPI_ISL_1972143 | 4,349,146 | 4,289,977 | 98.64 | 18,101 | 28,961 | 99.54% | 29,834 | B.1.36 | 20A | GH |
9 | NCOV/AB/21/FA012 | 6.69 | MZ562753 | EPI_ISL_1972144 | 1,506,394 | 1,446,477 | 96.02 | 6103 | 9750 | 99.49% | 29,848 | B.1.36 | 20A | GH |
10 | NCOV/AB/21/FB757 | 3.73 | MZ562754 | EPI_ISL_1972145 | 4,124,452 | 4,104,495 | 99.52 | 17,319 | 26,603 | 96.98% | 29,834 | B.1.36 | 20A | GH |
11 | NCOV/AB/21/FD308 | 3.88 | MZ562755 | EPI_ISL_1972146 | 80,774 | 79,290 | 98.16 | 334.6 | 534.7 | 99.12% | 29,834 | B.1.36 | 20A | GH |
12 | NCOV/AB/21/FF663 | 3.38 | MZ562756 | EPI_ISL_1972137 | 393,314 | 275,581 | 70.07 | 1163 | 1,842 | 98.12% | 29,833 | B.1.617.1 | 21B (Kappa) | G |
13 | NCOV/AB/21/FF945 | 4.34 | MZ562757 | EPI_ISL_1972138 | 2,080,768 | 2,058,700 | 98.94 | 8686 | 13,990 | 98.64% | 29,836 | B.1.617.1 | 21B (Kappa) | G |
14 | NCOV/AB/21/EQ324 | 5.32 | MZ562758 | EPI_ISL_1972139 | 917,154 | 899,993 | 98.13 | 3797 | 5,763 | 97.97% | 29,832 | B.1.617.1 | 21B (Kappa) | G |
15 | NCOV/AB/21/FG788 | 3.34 | MZ562759 | EPI_ISL_1972140 | 3,939,432 | 3,917,148 | 99.43 | 16,528 | 26,628 | 98.21% | 29,835 | B.1.617.1 | 21B (Kappa) | G |
16 | NCOV/AB/21/FK354 | 7.18 | MZ562760 | EPI_ISL_1972147 | 1,945,720 | 1,901,249 | 97.71 | 8022 | 12,758 | 99.11% | 29,853 | B.1.36 | 20A | GH |
17 | NCOV/AB/21/FL862 | 4.35 | MZ723922 | EPI_ISL_1972132 | 3,313,340 | 3,203,191 | 96.68 | 13,516 | 21,669 | 97.89% | 29,823 | B.1.1.7 | 20I/501Y.V1 | GRY |
18 | NCOV/AB/21/FK940 | 4.94 | MZ562761 | EPI_ISL_1972133 | 2,262,299 | 2,261,261 | 99.95 | 9541 | 14,961 | 99.10% | 29,840 | B.1.617.1 | 21B (Kappa) | G |
19 | NCOV/AB/21/FL880 | 5.27 | MZ562762 | EPI_ISL_1972131 | 2,668,661 | 2,667,095 | 99.94 | 11,254 | 18,319 | 99.06% | 29,817 | B.1.1.7 | 20I/501Y.V1 | GRY |
20 | NCOV/AB/21/FL414 | 6.54 | MZ734487 | EPI_ISL_3316398 | 238,608 | 125,526 | 52.61 | 529.6 | 848 | 92.73% | 29,834 | B.1.306 | 20B | GR |
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Singh, J.; Malhotra, A.G.; Biswas, D.; Shankar, P.; Lokhande, L.; Yadav, A.K.; Raghuvanshi, A.; Kale, D.; Nema, S.; Saigal, S.; et al. Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India. Genes 2021, 12, 1803. https://doi.org/10.3390/genes12111803
Singh J, Malhotra AG, Biswas D, Shankar P, Lokhande L, Yadav AK, Raghuvanshi A, Kale D, Nema S, Saigal S, et al. Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India. Genes. 2021; 12(11):1803. https://doi.org/10.3390/genes12111803
Chicago/Turabian StyleSingh, Jitendra, Anvita Gupta Malhotra, Debasis Biswas, Prem Shankar, Leena Lokhande, Ashvini Kumar Yadav, Arun Raghuvanshi, Dipesh Kale, Shashwati Nema, Saurabh Saigal, and et al. 2021. "Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India" Genes 12, no. 11: 1803. https://doi.org/10.3390/genes12111803
APA StyleSingh, J., Malhotra, A. G., Biswas, D., Shankar, P., Lokhande, L., Yadav, A. K., Raghuvanshi, A., Kale, D., Nema, S., Saigal, S., & Singh, S. (2021). Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India. Genes, 12(11), 1803. https://doi.org/10.3390/genes12111803