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. 2024 Nov 12;13(12):e00789-24. doi: 10.1128/mra.00789-24

Genomic surveillance of SARS-CoV-2 in Nepal

Binod Khadka 1, Rajindra Napit 1,2, Kathie A Mihindukulasuriya 3,4,5, Smita Shrestha 1, Ramanuj Rauniyar 1, Eans T Tuladhar 1,6, Lindsay Droit 3,4, Anne M Paredes 4, Runa Jha 7, Roji Raut 1,2, Bimalesh K Jha 7, Scott A Handley 4,5, Annie Elong-Ngono 8, Sujan Shresta 8, David Wang 3, Krishna D Manandhar 1,✉
Editor: John J Dennehy9
PMCID: PMC11636318  PMID: 39530702

ABSTRACT

During the COVID-19 pandemic, Nepal, like other countries, faced emerging SARS-CoV-2 variants. To evaluate the circulating variants, 278 samples collected between September 2021 and March 2022 were sequenced in the country. From these, 229 high-quality genomes were obtained (82.97% Omicron and 17.03% Delta) highlighting the genomic diversity of SARS-CoV-2 in Nepal.

KEYWORDS: COVID-19, whole-genome sequencing, coronavirus, Illumina

ANNOUNCEMENT

During the COVID-19 pandemic caused by SARS-CoV-2, a positive-sense, single-stranded RNA virus of the family Coronaviridae and genus Betacoronavirus (1), the availability of complete, high-quality viral genome sequence data was limited in Nepal (2, 3).

A total of 278 nasopharyngeal swab samples from the government approved National Public Health laboratory (collected from different parts of the country) and KM-TU Biotech Covid Lab (collected from Kathmandu) from September 2021 to March 2022 were studied. The samples were stored at −80°C until use. RNA was extracted using Chemagic Prime Viral RNA kit (CMG-1449) on a Perkin Elmer Chemagic 360 instrument. Real Time Multiplex RT-PCR was performed using the Liferiver Novel Coronavirus (2019-nCoV) Real Time Multiplex RT-PCR Kit (Ref no.: RR-0479-02), and SARS-CoV-2-positive samples with Ct values less than 30 were used for sequencing.

Following Illumina COVIDSeq protocol (#1000000126053-04), the SARS-CoV-2 genome of each sample was amplified using CPP1 and CPP2 ARTIC v3 pools of primers (https://github.com/artic-network/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv). Amplicons from each of the two PCR reactions per sample were pooled and indexed with “IDT for Illumina-PCR Indexes” (unique index per sample) using on-bead tagmentation. Each indexed sample was then pooled for the final library, followed by quality check with Agilent Bioanalyzer (Kit Cat. 50671504) and quantified with Qubit 3.0 (Kit Cat. Q32851). The final library was diluted to 4 nM and denatured. The sample was loaded on the sequencer at 10 pmol. Sequencing was done on Illumina MiSeq with the 2 × 300 bp paired-end protocol using MiSeqV3 reagent kit (MS-102–3003) at the IVDRL, Tribhuvan University, Nepal.

The 229 high-quality genomic sequences (Table 1) were analyzed using the CDC SARS-CoV-2 BFX-UT_ARTIC_Illumina pipeline (https://github.com/CDCgov/SARS-CoV-2_Sequencing/tree/master/protocols/BFX-UT_ARTIC_Illumina). The Illumina reads were mapped (bwa-mem version 0.7.17-r1188) to the SARS-CoV-2 reference genome (MN908947.3), sorted, and unmapped reads were removed using samtools (version 1.17 using htslib 1.18). The total number of reads and the average sequencing depth (201–4,766) per genome are listed in Table 1. Primers were trimmed, and the consensus genome (39 complete and 190 nearly complete coding sequence) was generated using iVar version 1.4.2 (4). Variants were called with iVar version 1.4.2 followed by LoFreq version 2.1.5 (5), then annotated with snpEff version 5.1f and snpSift version 4.3t (6). The sequences were concatenated, and lineages were assigned using Pangolin version 1.1.14 (7) and NextClade version 2.14.0 (8), combined in R version 4.2.2. Sequences with more than 3,000 Ns compared to the reference genome were excluded. Full genomes were aligned using MAFFT version 0.7 (9), and a phylogenetic tree was generated with Augur version 17.7.0 from Nextstrain (10). The tree was visualized and edited in iTOL version 5 (11), with clade labels added in Microsoft Preview. Default settings were used for all these software unless otherwise specified.

TABLE 1.

Details of SARS-CoV-2 samples, sequence analysis, and hyperlinks of the study

S. No. Sample name Collection_Date Hyperlinked SRA accession ID GenBank accession ID GC content (%) Lineage (Nextclade) clade_who Length qc.overallScore (Nextclade) Genome coverage (%) (Nextclade) Number of reads Sequencing depth
1 BB466 2021-12 SRR29872869 PP825474 39 BA.1.17.2 Omicron 29,760 60.61 91.6 139,487 605.13
2 qc5158 2022-01 SRR29872868 PP825475 39.80 BA.2 Omicron 29,805 11.56 95.7 236,261 1,470.6
3 qc8160 2022-02 SRR29872857 PP825476 39.40 BA.2 Omicron 29,648 18.46 94.4 141,771 725.48
4 qc8213 2022-02 SRR29872846 PP825477 39 BA.2.10 Omicron 29,636 14.08 94.8 278,256 1,550.1
5 qc8215 2022-02 SRR29872835 PP825478 38.70 BA.2 Omicron 29,797 36.76 93.3 255,107 1,525
6 qc8219 2022-02 SRR29872824 PP825479 39.40 BA.2.10 Omicron 29,621 19.43 94.2 245,897 1,388.8
7 qc8220 2022-02 SRR29872823 PP825480 38.50 BA.2.10 Omicron 29,781 5.58 96.6 182,429 1,242.1
8 qc8221 2022-02 SRR29872822 PP825481 39 BA.2 Omicron 29,640 4.92 96.2 256,586 1,565.4
9 qc8228 2022-02 SRR29872821 PP825482 41.30 BA.2 Omicron 29,755 64.59 91.3 176,481 905.09
10 qc8249 2022-01 SRR29872820 PP825483 38.80 BA.2 Omicron 29,708 94.81 89.6 169,426 925.52
11 qc8258 2022-02 SRR29872867 PP825484 38.80 BA.2 Omicron 29,778 13.55 95.3 190,765 1,127.2
12 qc8260 2022-02 SRR29872866 PP825485 37.90 BA.2.10 Omicron 29,602 54.21 91.4 225,175 1,652.3
13 qc8261 2022-02 SRR29872865 PP825486 38.20 BA.2.10 Omicron 29,703 15.12 94.9 284,906 1,597.7
14 qc8273 2022-01 SRR29872864 PP825487 38.80 BA.2 Omicron 29,678 16.84 94.6 177,154 1,098.1
15 qc8274 2022-01 SRR29872863 PP825488 39.10 BA.2 Omicron 29,747 44.49 92.5 134,298 751.64
16 qc8280 2022-01 SRR29872862 PP825489 37.90 BA.2.10 Omicron 29,638 16.72 94.5 281,714 1,847.9
17 qc8281 2022-01 SRR29872861 PP825490 39.40 BA.2.2 Omicron 29,805 12.99 95.5 321,001 1,749.7
18 qc8317 2022-02 SRR29872860 PP825491 38.80 BA.2.10 Omicron 29,637 17.36 94.4 130,560 714.6
19 qc8319 2022-02 SRR29872859 PP825492 38.40 BA.2 Omicron 29,774 17.48 95 175,423 1,061.8
20 qc8321 2022-02 SRR29872858 PP825493 37.90 BA.2 Omicron 29,799 60.72 91.7 238,459 1,453.1
21 qc8322 2022-02 SRR29872856 PP825494 39 BA.2.2 Omicron 29,631 17.53 94.6 162,709 1,035.8
22 qc8323 2022-02 SRR29872855 PP825495 39.30 BA.2 Omicron 29,697 18.02 94.6 169,050 951.75
23 qc8324 2022-02 SRR29872854 PP825496 41.80 BA.2 Omicron 29,647 9.86 95.4 347,504 1,853.2
24 qc8326 2022-02 SRR29872853 PP825497 41.10 BA.2 Omicron 29,642 8.09 95.6 398,228 2,255.1
25 qc8327 2022-02 SRR29872852 PP825498 39 BA.2 Omicron 29,660 71.68 90.6 247,540 1,428.3
26 qc8338 2022-02 SRR29872851 PP825499 39.80 BA.2.10 Omicron 29,713 61.01 91.4 239,720 1,205.3
27 qc8342 2022-02 SRR29872850 PP825500 40.90 BA.2 Omicron 29,578 49.26 91.7 236,197 1,134.4
28 qc8344 2022-02 SRR29872849 PP825501 38.60 BA.2 Omicron 29,634 8.13 95.6 271,237 1,608.3
29 QC8512 2022-03 SRR29872848 PP825502 38.70 BA.2 Omicron 29,729 0.69 99.6 154,684 1,217.7
30 QC8514 2022-03 SRR29872847 PP825503 41.30 BA.2 Omicron 29,722 30.41 93.6 77,197 456.37
31 QC8516 2022-03 SRR29872845 PP825504 39.30 BA.2.10 Omicron 29,729 0 98.7 152,397 1,006
32 QC8532 2022-03 SRR29872844 PP825505 42.20 BA.2 Omicron 29,774 14.1 95.4 170,158 999.32
33 QC8534 2022-03 SRR29872843 PP825506 39.40 BA.2.2 Omicron 29,776 0.98 97.9 108,161 718.66
34 QC8538 2022-03 SRR29872842 PP825507 39.90 BA.2 Omicron 29,729 36.22 93.2 171,852 1,127.5
35 QC8598 2022-03 SRR29872841 PP825508 38.40 BA.2 Omicron 29,775 0 99.4 140,043 1,101.9
36 QC8629 2022-03 SRR29872840 PP825509 39.90 BA.2 Omicron 29,781 1.56 99.7 139,410 956.51
37 QC8630 2022-03 SRR29872839 PP825510 44.30 BA.2.10 Omicron 29,441 80.47 89.5 88,085 381.77
38 QC8636 2022-03 SRR29872838 PP825511 38.80 BA.2 Omicron 29,779 0 99 124,409 956.03
39 QC8638 2022-03 SRR29872837 PP825512 43.80 BA.2 Omicron 29,635 70 90.7 83,769 398.32
40 QC8641 2022-03 SRR29872836 PP825513 40.20 BA.2.10 Omicron 29,698 9.96 95.6 73,226 497.95
41 QC8644 2022-03 SRR29872834 PP825514 43.20 BA.2 Omicron 29,682 17.39 94.7 117,215 591.27
42 QC8651 2022-03 SRR29872833 PP825515 39.80 BA.2 Omicron 29,771 38.81 93.1 131,622 945.49
43 QC8661 2022-03 SRR29872832 PP825516 39.70 BA.2 Omicron 29,776 5.02 98 83,146 577.5
44 QC8663 2022-03 SRR29872831 PP825517 43.90 BA.2 Omicron 29,741 39.46 92.9 70,942 291.18
45 QC8664 2022-03 SRR29872830 PP825518 39.40 BA.2 Omicron 29,723 2.48 97.4 145,775 1,031.2
46 QC8665 2022-03 SRR29872829 PP825519 40.20 BA.2 Omicron 29,729 1.02 97.7 137,181 929.15
47 QC8667 2022-03 SRR29872828 PP825520 44.40 BA.2.10.1 Omicron 29,755 31.57 93.5 112,736 433.42
48 QC8668 2022-03 SRR29872827 PP825521 40.50 BA.2.10 Omicron 29,739 0 99.5 100,208 657.97
49 QC8710 2022-03 SRR29872826 PP825522 41 BA.2 Omicron 29,779 51.57 92.3 106,539 740.48
50 QC8711 2022-03 SRR29872825 PP825523 40.20 BA.2 Omicron 29,781 1.37 97.7 137,732 998.91
51 QC8712 2022-03 SRR29874965 PP825524 39.90 BA.2 Omicron 29,709 55.25 91.8 183,189 1,347.3
52 QC8714 2022-03 SRR29874964 PP825525 44 BA.2 Omicron 29,568 58.27 91.2 88,203 345.46
53 QC8731 2022-03 SRR29874934 PP825526 38.60 BA.2.10 Omicron 29,789 0 99.8 180,103 1,353.3
54 QC8732 2022-03 SRR29874923 PP825527 39.10 BA.2 Omicron 29,773 0 99.2 134,732 998.56
55 QC8733 2022-03 SRR29874959 PP825528 39.70 BA.2 Omicron 29,744 0.02 98.5 62,387 437.29
56 QC8734 2022-03 SRR29874948 PP825529 43.40 BA.2 Omicron 29,779 1.6 97.6 63,998 361.41
57 QC8735 2022-03 SRR29874947 PP825530 50.20 BA.2 Omicron 29,755 77.51 90.6 61,243 276.08
58 QC8736 2022-03 SRR29874946 PP825531 40.50 BA.2 Omicron 29,779 0 99.7 110,527 745.68
59 QC8737 2022-03 SRR29874945 PP825532 38.40 BA.2.3 Omicron 29,729 0 99.2 106,569 831.41
60 QC8738 2022-03 SRR29874943 PP825533 38.20 BA.2 Omicron 29,776 0.09 98.5 97,165 770.57
61 QC8768 2022-03 SRR29874963 PP825534 38.80 BA.2 Omicron 29,773 13.36 95.4 83,925 639.71
62 QC8803 2022-02 SRR29874944 PP825535 38.20 BA.2 Omicron 29,729 0 98.8 150,622 1,178.4
63 QC8812 2022-02 SRR29874942 PP825536 39.10 BA.2 Omicron 29,726 22.54 94.3 103,461 742.99
64 QC8837 2022-02 SRR29874941 PP825537 38.50 BA.2 Omicron 29,745 0 98.8 106,001 808.3
65 QC8844 2022-03 SRR29874940 PP825538 38.70 BA.2 Omicron 29,769 5.57 96.6 60,147 455.91
66 QC8845 2022-03 SRR29874939 PP825539 41.50 BA.2 Omicron 29,729 11.64 95.5 76,449 440.91
67 QC8847 2022-03 SRR29874938 PP825540 40 BA.2.10 Omicron 29,790 7.23 96.4 79,020 542.74
68 QC8849 2022-03 SRR29874937 PP825541 40.10 BA.2 Omicron 29,729 8.11 96 122,295 813.73
69 QC8850 2022-03 SRR29874936 PP825542 38.20 BA.2 Omicron 29,766 2.75 97.2 97,401 769.71
70 QC8851 2022-03 SRR29874935 PP825543 38.40 BA.2.10 Omicron 29,792 3.72 97.1 80,651 648.05
71 QC8852 2022-03 SRR29874933 PP825544 39.40 BA.2 Omicron 29,777 2.81 97.2 163,295 1,178.1
72 QC8853 2022-03 SRR29874932 PP825545 38.10 BA.2 Omicron 29,805 85.87 90.4 83,370 630.61
73 QC8854 2022-03 SRR29874931 PP825546 38.50 BA.2 Omicron 29,781 40.68 93 112,793 856.61
74 QC8856 2022-03 SRR29874930 PP825547 38.40 BA.2 Omicron 29,778 93.59 90 66,083 500.9
75 QC8858 2022-03 SRR29874929 PP825548 38.90 BA.2 Omicron 29,781 91.52 90.1 97,493 710.69
76 QC8868 2022-03 SRR29874928 PP825549 41.20 BA.2 Omicron 29,779 7.8 96.2 147,903 909.59
77 QC8870 2022-03 SRR29874927 PP825550 38.40 BA.2 Omicron 29,781 13.31 95.5 106,570 770.01
78 QC8911 2022-03 SRR29874926 PP825551 39.40 BA.2 Omicron 29,781 8.28 96.2 127,597 948.84
79 QC8912 2022-03 SRR29874925 PP825552 42.60 BA.2 Omicron 29,744 94.02 89.9 63,355 366.15
80 QC8913 2022-03 SRR29874924 PP825553 40.70 BA.2 Omicron 29,729 80.67 90.5 82,204 584.12
81 QC8914 2022-03 SRR29874922 PP825554 40.50 BA.2 Omicron 29,781 3.78 97 89,511 637.07
82 QC8916 2022-03 SRR29874921 PP825555 39.30 BA.2 Omicron 29,805 42.35 92.9 106,977 761.39
83 QC8917 2022-03 SRR29874920 PP825556 42.50 BA.2 Omicron 29,770 69.31 91.1 114,848 615.2
84 QC8920 2022-03 SRR29874919 PP825557 41.30 BA.2 Omicron 29,773 71.31 91.1 112,709 765.84
85 QC8927 2022-03 SRR29874918 PP825558 38.20 BA.2 Omicron 29,755 78.81 90.6 95,313 751.59
86 QC8938 2022-03 SRR29874917 PP825559 41 BA.2 Omicron 29,768 30.54 93.7 103,909 672.93
87 QC8944 2022-03 SRR29874916 PP825560 39.80 BA.2.31.1 Omicron 29,771 30.54 93.7 131,260 973.09
88 QC8946 2022-03 SRR29874962 PP825561 41 BA.2 Omicron 29,779 7.7 96.3 150,787 1,019
89 QC8948 2022-03 SRR29874961 PP825562 40.30 BA.2 Omicron 29,770 91.03 90 66,787 490.69
90 QC8957 2022-03 SRR29874960 PP825563 40.50 BA.2 Omicron 29,781 3.93 97 251,044 1,876.1
91 QC8958 2022-03 SRR29874958 PP825564 42.60 BA.2 Omicron 29,771 22.33 94.5 252,585 1,414
92 QC8965 2022-03 SRR29874957 PP825565 39.20 BA.2 Omicron 29,787 4.43 98.5 276,743 2,243.1
93 QC8966 2022-03 SRR29874956 PP825566 40.50 BA.2.50 Omicron 29,814 0.02 98.7 237,570 1,813.3
94 QC8967 2022-03 SRR29874955 PP825567 40.50 BA.2.12.1 Omicron 29,781 6.7 96.4 343,467 2,534.5
95 QC8968 2022-03 SRR29874954 PP825568 40.70 BA.2.50 Omicron 29,781 12.46 95.6 110,853 818.2
96 QC8969 2022-03 SRR29874953 PP825569 40.40 BA.2 Omicron 29,781 0 98.9 175,990 1,358
97 QC8975 2022-03 SRR29874952 PP825570 41.20 BA.2 Omicron 29,779 19.43 94.8 124,140 897.66
98 QC8979 2022-03 SRR29874951 PP825571 38.90 BA.2 Omicron 29,760 82.54 90.4 110,570 895.92
99 QC8981 2022-03 SRR29874950 PP825572 39.60 BA.2.3 Omicron 29,744 19.62 94.6 213,190 1,735.1
100 QC9031 2022-03 SRR29874949 PP825573 38.40 BA.2.3 Omicron 29,776 1.49 97.6 120,816 1,087.3
101 QC9032 2022-03 SRR29875192 PP825574 38.30 BA.2.3 Omicron 29,763 10.7 95.7 139,954 1,237.8
102 QC9033 2022-03 SRR29875191 PP825575 38.60 BA.2.3 Omicron 29,781 0 98.8 139,818 1,228.1
103 QC9034 2022-03 SRR29875180 PP825576 38.30 BA.2.9 Omicron 29,799 36.58 93.3 164,730 1,474.4
104 QC9035 2022-03 SRR29875169 PP825577 39.20 BA.2 Omicron 29,779 9.66 96 174,932 1,504.9
105 QC9036 2022-03 SRR29875158 PP825578 40.50 BA.2 Omicron 29,781 0.01 98.7 190,449 1,516.8
106 QC9037 2022-03 SRR29875147 PP825579 42.10 BA.2 Omicron 29,779 12.22 95.6 258,998 1,845.1
107 QC9038 2022-03 SRR29875146 PP825580 39.90 BA.2 Omicron 29,781 2.74 97.3 237,240 1,990.9
108 QC9039 2022-03 SRR29875145 PP825581 40.80 BA.2 Omicron 29,775 0.1 98.5 154,325 1,211.5
109 QC9051 2022-03 SRR29875144 PP825582 38.20 BA.2 Omicron 29,734 0.17 99.6 183,635 1,857.9
110 QC9052 2022-03 SRR29875143 PP825583 38.40 BA.2 Omicron 29,734 0.54 97.9 256,284 2,459.7
111 QC9053 2022-03 SRR29875190 PP825584 40.20 BA.2 Omicron 29,729 0 99.1 218,645 1,753.8
112 QC9055 2022-03 SRR29875189 PP825585 42.60 BA.2 Omicron 29,729 0.42 98 190,770 1,236.4
113 QC9056 2022-03 SRR29875188 PP825586 40.20 BA.2 Omicron 29,786 17.36 99.6 271,489 2,311
114 QC9057 2022-03 SRR29875187 PP825587 39.30 BA.2 Omicron 29,729 0.68 97.8 187,485 1,645.5
115 QC9058 2022-03 SRR29875186 PP825588 41.80 BA.2 Omicron 29,729 19.16 94.6 204,331 1,099.9
116 QC9059 2022-03 SRR29875185 PP825589 40.90 BA.4.2 Omicron 29,714 22.06 94.4 101,473 604.09
117 QC9081 2022-03 SRR29875184 PP825590 38.20 BA.2 Omicron 29,729 0.04 98.4 159,177 1,571.5
118 QC9097 2022-03 SRR29875183 PP825591 38.50 BA.2 Omicron 29,675 9.77 95.6 229,436 1,808.7
119 QC9116 2022-03 SRR29875182 PP825592 39.30 BA.2 Omicron 29,809 0.62 98.1 234,880 2,084.3
120 QC9117 2022-03 SRR29875181 PP825593 40.70 BA.2.10 Omicron 29,781 13.23 95.5 132,163 1,049
121 SQ1513 2021-11 SRR29875179 PP825594 38.90 B.1.617.2 Delta 29,821 68.38 91.4 177,005 789.19
122 SQ1529 2021-12 SRR29875178 PP825595 39 B.1.617.2 Delta 29,855 46.04 94.4 518,055 2,193.2
123 SQ1537 2021-12 SRR29875177 PP825596 38.60 B.1.617.2 Delta 29,806 16.6 95.2 198,401 891.36
124 sq1539 2021-12 SRR29875176 PP825597 38.40 B.1.617.2 Delta 29,454 51.05 91.1 140,714 597.45
125 SQ1580 2021-12 SRR29875175 PP825598 38.60 B.1.617.2 Delta 29,821 60.8 91.8 455,614 2,032.7
126 SQ1635 2021-12 SRR29875174 PP825599 39 B.1.617.2 Delta 29,614 56.11 91.4 113,343 498.8
127 sq1637 2021-12 SRR29875173 PP825600 38.40 B.1.617.2 Delta 29,819 1.72 97.6 171,968 766.33
128 sq1640 2021-12 SRR29875172 PP825601 38.40 B.1.617.2 Delta 29,860 58.85 92 313,925 1,327.5
129 SQ1651 2021-12 SRR29875171 PP825602 39.50 B.1.617.2 Delta 29,785 40.97 93.2 179,134 769.07
130 sq1654 2021-12 SRR29875170 PP825603 38.70 B.1.617.2 Delta 29,814 16.75 96.2 145,600 1,070.6
131 sq1655 2021-12 SRR29875168 PP825604 39.40 B.1.617.2 Delta 29,794 3.39 97.5 254,578 1,110.5
132 SQ1665 2021-12 SRR29875167 PP825605 38.50 B.1.617.2 Delta 29,819 10.78 96.5 133,604 603.22
133 SQ1667 2021-12 SRR29875166 PP825606 39.20 B.1.617.2 Delta 29,806 23.02 96 115,505 495.66
134 sq1672 2021-12 SRR29875165 PP825607 38 B.1.617.2 Delta 29,492 1.64 97.4 207,546 912.01
135 SQ1680 2021-11 SRR29875164 PP825608 39.90 B.1.617.2 Delta 29,806 42.7 93.3 139,687 585.89
136 SQ1682 2021-11 SRR29875163 PP825609 39.70 B.1.617.2 Delta 29,798 72.56 91.1 207,047 873.18
137 SQ1689 2021-11 SRR29875162 PP825610 39 B.1.617.2 Delta 29,820 21.81 94.8 206,476 900.04
138 sq1690 2021-11 SRR29875161 PP825611 38.40 AY.4 Delta 29,691 88.05 90.2 81,881 348.81
139 sq1702 2021-11 SRR29875160 PP825612 38.80 AY.75 Delta 29,817 30.92 96.6 346,627 1,501.6
140 sq1703 2021-11 SRR29875159 PP825613 38.50 B.1.617.2 Delta 29,735 81.46 90.4 81,599 348.63
141 sq1705 2021-11 SRR29875157 PP825614 38.80 B.1.617.2 Delta 29,821 22.86 94.7 185,534 810.47
142 SQ1707 2021-11 SRR29875156 PP825615 39.80 B.1.617.2 Delta 29,811 38.93 95.9 145,128 616.64
143 SQ1713 2021-11 SRR29875155 PP825616 41.20 B.1.617.2 Delta 29,785 52.98 92.2 190,191 749.53
144 SQ1720 2021-12 SRR29875154 PP825617 39.30 B.1.617.2 Delta 29,889 12.46 97.2 1,097,224 4,765.7
145 sq1723 2021-12 SRR29875153 PP825618 38.80 B.1.617.2 Delta 29,827 58.95 91.8 223,543 954.62
146 sq1729 2021-12 SRR29875152 PP825619 38.30 B.1.617.2 Delta 29,738 91.99 92.6 117,549 499.5
147 sq1742 2021-12 SRR29875151 PP825620 38.20 B.1.617.2 Delta 29,636 13.05 95.1 265,739 1,152.6
148 SQ1752 2021-12 SRR29875150 PP825621 38.90 B.1.617.2 Delta 29,878 76.47 94.9 355,941 1,565.4
149 SQ1755 2021-12 SRR29875149 PP825622 39.20 B.1.617.2 Delta 29,885 10.48 96.1 808,264 3,431.5
150 sq1780 2021-12 SRR29875148 PP825623 38.10 B.1.617.2 Delta 29,315 90.31 88.9 110,417 470.77
151 sq1819 2021-12 SRR29876922 PP825624 38.20 B.1.617.2 Delta 29,573 70.81 90.5 46,018 200.75
152 SQ1841 2021-12 SRR29876921 PP825625 38.90 B.1.617.2 Delta 29,887 21.63 95.4 960,625 4,271
153 SQ1868 2021-12 SRR29876862 PP825626 38.90 B.1.617.2 Delta 29,748 58.66 91.9 138,073 599.77
154 SQ1871 2021-12 SRR29876851 PP825627 42.60 B.1.617.2 Delta 29,871 67.18 91.5 546,357 1,719.4
155 SQ1874 2021-12 SRR29876916 PP825628 38.70 B.1.617.2 Delta 29,819 47.9 93.8 154,688 680.96
156 SQ5043 2021-09 SRR29876905 PP825629 38.50 B.1.617.2 Delta 29,819 3.82 97.4 974,178 4,394.8
157 sq5149 2022-01 SRR29876894 PP825630 41.40 BA.2 Omicron 29,584 88.01 89.5 163,335 744.84
158 sq5150 2022-01 SRR29876883 PP825631 39 BA.2 Omicron 29,755 23.47 94.2 218,801 1,082.5
159 sq5151 2022-01 SRR29876873 PP825632 39.40 BA.2.2 Omicron 29,781 5.98 96.6 173,514 1,000.1
160 sq5152 2022-01 SRR29876871 PP825633 38.90 BA.2.2 Omicron 29,802 6.61 96.4 210,124 1,004
161 sq5153 2022-01 SRR29876920 PP825634 39.10 AY.76 Delta 29,598 160.68 89.1 182,923 914.95
162 sq5154 2022-01 SRR29876872 PP825635 39.40 BA.2 Omicron 29,755 25.15 94.1 154,101 892.92
163 sq5157 2022-01 SRR29876870 PP825636 39.60 BA.2.10 Omicron 29,755 38.85 93 208,367 869.91
164 sq5207 2022-01 SRR29876869 PP825637 38.60 BA.1.1 Omicron 29,752 69.2 91.1 237,055 1,295.5
165 sq5208 2022-01 SRR29876868 PP825638 38.60 BA.1.1 Omicron 29,727 74.73 90.7 126,607 583.6
166 sq5209 2022-01 SRR29876867 PP825639 38.10 BA.1.1 Omicron 29,752 46.34 92.4 253,489 1,285.2
167 sq5215 2022-01 SRR29876866 PP825640 38.50 BA.2.10 Omicron 29,632 31.53 93.1 210,497 1,052.7
168 sq5218 2022-01 SRR29876865 PP825641 38.40 BA.2.10 Omicron 29,807 4.39 96.9 278,136 1,430.4
169 sq5220 2022-01 SRR29876864 PP825642 38.10 BA.1.1 Omicron 29,752 23.83 94.3 253,216 1,516.1
170 sq5224 2022-01 SRR29876863 PP825643 38 BA.2.10 Omicron 29,792 14.72 95.3 229,726 1,252.5
171 sq5226 2022-01 SRR29876861 PP825644 38.60 BA.2.10 Omicron 29,772 15.97 95 348,822 2,029.8
172 sq5230 2022-01 SRR29876860 PP825645 39 BA.2.10 Omicron 29,704 28.13 93.6 347,876 1,944.6
173 sq5234 2022-01 SRR29876859 PP825646 38 BA.2.10 Omicron 29,772 6.07 96.4 289,439 1,610.9
174 sq5236 2022-01 SRR29876858 PP825647 39 BA.2.10 Omicron 29,755 32.79 93.4 146,310 768.35
175 sq5240 2022-01 SRR29876857 PP825648 38.10 BA.2.10 Omicron 29,755 24.41 94.1 266,493 1,470.9
176 sq5248 2022-01 SRR29876856 PP825649 38.50 BA.2.10 Omicron 29,699 4.71 96.4 233,513 1,462.2
177 sq5254 2022-01 SRR29876855 PP825650 39 BA.2 Omicron 29,742 11.56 95.5 200,688 1,111.9
178 sq5257 2022-01 SRR29876854 PP825651 38.90 BA.2.10 Omicron 29,797 30.99 93.7 131,641 824.97
179 sq5260 2022-01 SRR29876853 PP825652 38.60 BA.2.10 Omicron 29,584 25.15 93.5 271,286 1,550.4
180 sq5303 2022-01 SRR29876852 PP825653 38.40 BA.2 Omicron 29,773 1.11 97.7 384,010 2,044.3
181 sq5304 2022-01 SRR29876850 PP825654 38.50 BA.1.1 Omicron 29,752 8.26 96 267,500 1,395.2
182 sq5373 2022-01 SRR29876849 PP825655 38.70 BA.1 Omicron 29,798 632.37 96.3 259,655 1,661
183 sq5379 2022-01 SRR29876848 PP825656 39.30 BA.2 Omicron 2,9652 28.48 93.4 281,980 1,290.9
184 sq5392 2022-01 SRR29876847 PP825657 39 BA.2 Omicron 29,781 0.15 98.4 308,318 1,936.6
185 sq5400 2022-01 SRR29876846 PP825658 38.20 BA.2 Omicron 29,805 0.68 98 220,174 1,302.4
186 sq5406 2022-01 SRR29876845 PP825659 39 BA.2 Omicron 29,805 5.32 96.7 322,155 1,746.6
187 sq5408 2022-01 SRR29876844 PP825660 38.70 BA.2 Omicron 29,803 11.53 95.7 215,785 1,091.3
188 sq5452 2022-01 SRR29876919 PP825661 38.50 BA.1.1 Omicron 29,804 0.67 98 293,342 1,820
189 sq5476 2022-01 SRR29876918 PP825662 38.30 BA.2.10 Omicron 29,664 6.74 95.9 166,667 864.34
190 sq5489 2022-01 SRR29876917 PP825663 37.90 BA.2 Omicron 29,807 2.85 97.2 243,357 1,375.1
191 sq5498 2022-01 SRR29876915 PP825664 38.60 BA.2 Omicron 29,755 34.81 93.3 308,560 1,624.5
192 sq5502 2022-01 SRR29876914 PP825665 38.90 BA.1 Omicron 29,611 32.75 93 193,930 1,104.5
193 sq5509 2022-01 SRR29876913 PP825666 37.90 B.1.617.2 Delta 29,769 13.83 97.1 239,876 1,447.8
194 sq5514 2022-01 SRR29876912 PP825667 38.40 BA.2 Omicron 29,799 3.53 97 367,112 2,013.3
195 sq5519 2022-01 SRR29876911 PP825668 38.50 BA.2.10 Omicron 29,755 81.47 90.4 249,932 1,436.6
196 sq5526 2022-01 SRR29876910 PP825669 39.60 BA.2 Omicron 29,755 32.79 93.4 216,286 990.24
197 sq6155 2022-02 SRR29876909 PP825670 38.90 BA.2 Omicron 29,626 14.64 94.7 230,171 1,574.4
198 sq6157 2022-02 SRR29876908 PP825671 39.70 BA.2.10 Omicron 29,660 15.04 94.8 266,996 1,628.6
199 sq6158 2022-02 SRR29876907 PP825672 41 BA.2.10 Omicron 29,653 15.38 94.7 171,948 939.71
200 sq6164 2022-02 SRR29876906 PP825673 41.30 BA.2.10 Omicron 29,701 9.16 95.7 228,609 1,208.5
201 sq6167 2022-02 SRR29876904 PP825674 39.20 BA.2 Omicron 29,704 12.46 95.2 232,901 1,288.5
202 sq6168 2022-02 SRR29876903 PP825675 39.30 BA.2.10 Omicron 29,806 12.17 95.6 309,913 1,877.6
203 sq6218 2022-02 SRR29876902 PP825676 38.80 BA.2 Omicron 29,628 12.04 95 307,585 1,864.9
204 sq6220 2022-02 SRR29876901 PP825677 38.30 BA.2 Omicron 29,584 13.31 94.7 175,806 1,171.7
205 sq6224 2022-02 SRR29876900 PP825678 39.10 BA.2 Omicron 29,805 11.76 95.7 345,097 2,066.6
206 sq6227 2022-02 SRR29876899 PP825679 38.80 BA.2 Omicron 29,779 19.85 94.6 257,662 1,601.1
207 SQ6292 2022-03 SRR29876898 PP825680 38.90 BA.2.12.1 Omicron 29,780 4.06 96.9 234,714 1,846
208 SQ6294 2022-04 SRR29876897 PP825681 39.50 BA.2 Omicron 29,780 13.34 95.5 265,917 1,967
209 SQ6296 2022-04 SRR29876896 PP825682 41.50 BA.2.43 Omicron 29,728 35.51 93.2 96,169 609.25
210 SQ6297 2022-04 SRR29876895 PP825683 40.50 BA.2.78 Omicron 29,779 6.38 96.5 222,689 1,663.5
211 SQ6298 2022-04 SRR29876893 PP825684 38.50 BA.2.43 Omicron 29,775 2.64 97.3 222,151 1,798.6
212 SQ6299 2022-04 SRR29876892 PP825685 39.70 BA.2.43 Omicron 29,771 0 99.3 366,263 2,817.3
213 SQ6301 2022-04 SRR29876891 PP825686 39.10 BA.2 Omicron 29,772 20.85 94.6 327,061 2,558.5
214 SQ6303 2022-04 SRR29876890 PP825687 41.20 BA.2 Omicron 29,734 28.76 93.8 238,759 1,743.1
215 SQ6307 2022-04 SRR29876889 PP825688 38.30 B.1.617.2 Delta 29,821 25 99.5 196,880 1,737.3
216 SQ6308 2022-04 SRR29876888 PP825689 43.30 BA.2.3 Omicron 29,576 46.49 91.9 154,097 789.96
217 SQ6310 2022-04 SRR29876887 PP825690 45.60 BA.2.3 Omicron 29,738 87.73 90.2 229,620 893.29
218 SQ6311 2022-04 SRR29876886 PP825691 40.80 BA.1.1 Omicron 29,819 7.47 97.8 324,671 2,308.9
219 SQ6316 2022-01 SRR29876885 PP825692 39.10 BA.2.38 Omicron 29,775 1.53 97.9 313,996 2,449.5
220 SQ6321 2022-05 SRR29876884 PP825693 44.40 BA.2 Omicron 29,426 65.25 90.3 132,006 498.47
221 SQ6324 2022-04 SRR29876882 PP825694 39.80 BA.2 Omicron 29,679 18.49 94.5 289,957 2,361.7
222 SQ6325 2022-04 SRR29876881 PP825695 38.80 BA.2 Omicron 29,729 5.85 96.4 210,095 1,540.1
223 SQ6330 2022-05 SRR29876880 PP825696 40 BA.2.12.1 Omicron 29,665 8.82 95.7 207,454 1,653.4
224 SQ6339 2022-05 SRR29876879 PP825697 38.40 BA.2 Omicron 29,789 12.72 96.5 361,239 3,407.8
225 SQ6360 2022-05 SRR29876878 PP825698 39.20 BA.2 Omicron 29,441 41.44 91.8 189,082 1,360.9
226 SQ6364 2022-05 SRR29876877 PP825699 39.70 BA.2.9 Omicron 29,441 52.91 91.1 208,067 1,797.8
227 SQ6366 2022-05 SRR29876876 PP825700 39.30 BA.2 Omicron 29,435 84.23 89.4 170,110 1,201.8
228 SQ6400 2022-02 SRR29876875 PP825701 43 BA.2.38 Omicron 29,657 17.08 94.6 566,559 3,000.6
229 ssq5500 2022-01 SRR29876874 PP825702 38.30 BA.1.17.2 Omicron 29,804 44.2 92.8 244,823 1,697.3
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Among the samples, 82.97% were Omicron with BA.2 and its sub-lineages (94.21%, n = 179/190) and 17.03% were Delta with B.1.617.2 (92.3%, n = 36/39). The phylogenetic tree showed the SARS-CoV-2 genomic diversity in Nepal (Fig. 1). This study provides insights and contributes valuable data for genomic surveillance in understanding and monitoring SARS-CoV-2 variants in Nepal.

Fig 1.

Fig 1

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Phylogenetic analysis of complete SARS-CoV-2 genome sequences using GTR substitution model. The phylogenetic analysis showed a distinct clustering pattern among the circulating variants where the tree shows distinct clustering of Delta (red) and Omicron (blue).

ACKNOWLEDGMENTS

This work was funded by the United States National Institutes of Health (grant U01AI151810).

Contributor Information

Krishna D. Manandhar, Email: krishna.manandhar@gmail.com.

John J. Dennehy, Queens College Department of Biology, Queens, New York, USA

DATA AVAILABILITY

The GenBank accession numbers of the 229 sequences from this study are provided in Table 1. The raw reads are available in the SRA database under the BioProject number PRJNA1137145, and the accession IDs for these raw reads are also available in Table 1.

ETHICS APPROVAL

Ethical approval was obtained from Nepal Health Research Council (NHRC) (Regd.: 274/2020).

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

The GenBank accession numbers of the 229 sequences from this study are provided in Table 1. The raw reads are available in the SRA database under the BioProject number PRJNA1137145, and the accession IDs for these raw reads are also available in Table 1.

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