Fig 1.
Gel electrophoresis of primer combinations (P1-P22) used for amplification and sequencing.
L = 100 bp ladder, P1 = NIMR_CoV1, P2 = NIMR_CoV2, P3 = NIMR_CoV3, P4 = NIMR_CoV4, P5 = NIMR_CoV5, P6 = NIMR_CoV6, P7 = NIMR_CoV7, P8 = NIMR_CoV8, P9 = NIMR_CoV9, P10 = NIMR_CoV10, P11 = NIMR_CoV11, P12 = NIMR_CoV12, P13 = NIMR_CoV13, P14 = NIMR_CoV14, P15 = NIMR_CoV15, P16 = NIMR_CoV16, P17 = NIMR_CoV17, P18 = NIMR_CoV18, P19 = NIMR_CoV19, P20 = NIMR_CoV20, P21 = NIMR_CoV21, P22 = NIMR_CoV22. Note: P10 on the first gel image (Fig 1 above) with band size of about 350bp was not used in the sequencing process; instead, the P10 on the second gel was used. The gel images were obtained from sample NGN57752 with accession number: MT576584.1.
Table 1.
Amplification and sequencing primers.
Fig 2.
a & b: Snapshots of N-region and ORF1ab region of the assembled individual sequence chromatograms.
Table 2.
Comparison of the level of identity of the sequence generated (MT576584.1) against isolates across other regions.
Fig 3.
a–Nucleotide variation at position 201 (5’ NCR). b—Nucleotide variation at position 2997 (ORF1ab–region). c-Nucleotide variation at position 23363 (Spike-gene). d—Nucleotides variation at position 28841–28843 (N-region).
Table 3.
Variation analysis of nucleotide bases and amino acids of the sequence (MT576584.1) as against the reference strain.
Fig 4.
Pairwise with dots alignment of reference protein (YP_009724390.1) and analysed sequence protein (QKK12863.1) showing point (614) of protein variation.
Fig 5.
Pairwise with dots alignment of reference protein (YP 009724397.2) and analysed sequence protein (QKK12871.1) showing point (203–204) of protein variation.
Fig 6.
Phylogenetic tree showing the relationships of the sequences from Nigeria with others.