Genetic Variations of Three Kazakhstan Strains of the SARS-CoV-2 Virus
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection
2.2. RNA Extraction
2.3. cDNA Synthesis
2.4. Primer Design and Synthesis
2.5. Polymerase Chain Reaction (PCR) Setup
2.6. Determination of Nucleotide Sequences
2.7. Lineage Determination and Mutation Identification of the Studied Isolates
2.8. Analysis of Non-Synonymous Mutation Function
2.9. Phylogenetic Analysis of Nucleotide Sequences
3. Results
3.1. PCR Amplification of SARS-CoV-2 Virus Strains
3.2. Characteristics of the Genomes of the Studied SARS-CoV-2 Virus Strains
3.3. Impact of Mutations on Biological Function of Proteins in the Studied SARS-CoV-2 Samples
3.4. Phylogenetic Analysis
4. Discussion
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Protein | Data for Strain: | Amino Acid Change | ||||||||
---|---|---|---|---|---|---|---|---|---|---|
Wuhan-Hu-1 a | KAZ/Britain/2021 | KAZ/B1.1/2021 | KAZ/Delta020/2021 | Type of Mutation | ||||||
Position | Variant | Variant | Position | Variant | Position | Variant | Position | |||
5′ UTR b | 106 | C | – | – | T | 29 | – | – | – | 106 |
210 | G | – | – | – | – | T | 184 | – | 210 | |
241 | C | T | 215 | T | 164 | T | 215 | – | 241 | |
ORF1ab | 344 | C | - | - | T | 267 | – | – | SNP | L27F |
913 | C | T | 887 | – | – | – | – | SNP_silent | S36S | |
1048 | G | – | – | – | – | T | 1022 | SNP | K81N c | |
1688 | A | C | 1662 | – | – | – | – | SNP | I295L | |
1899 | G | – | – | – | – | T | 1873 | SNP | R365L | |
2110 | C | T | 2084 | – | – | – | – | SNP_silent | N435N | |
2530 | A | – | – | G | 2453 | – | – | SNP_silent | E575E | |
3037 | C | T | 3011 | T | 2960 | T | 3011 | SNP_silent | F106F | |
3267 | C | T | 3241 | – | – | – | – | SNP | T183I | |
4181 | G | – | – | – | – | T | 4155 | SNP | A488S | |
4449 | C | – | – | A | 4372 | – | – | SNP | T577N | |
4455 | C | – | – | T | 4378 | – | – | SNP | A579V | |
4475 | C | – | – | T | 4398 | – | – | SNP | R586C | |
5388 | C | A | 5362 | – | – | – | – | SNP | A890D | |
5829 | A | – | – | C | 5752 | – | – | SNP | K1037T | |
5986 | C | T | 5960 | – | – | – | – | SNP_silent | F1089F | |
6402 | C | – | – | – | – | T | 6376 | SNP | P1228L | |
6954 | T | C | 6928 | – | – | – | – | SNP | I1412T | |
7042 | G | T | 7016 | – | – | – | – | SNP | M1441I | |
7124 | C | – | – | – | – | T | 7098 | SNP | P1469S | |
8986 | C | – | – | – | – | T | 8960 | SNP_silent | D144D | |
9053 | G | – | – | – | – | T | 9027 | SNP | V167L | |
9749 | A | – | – | G | 9672 | – | – | SNP | K399E | |
9867 | T | – | – | G | 9790 | – | – | SNP | L438R | |
10,029 | C | – | – | – | – | T | 10,003 | SNP | T492I | |
10,198 | C | – | – | T | 10,121 | – | – | SNP_silent | D48D | |
11,195 | C | T | 11,169 | – | – | – | – | SNP | L75F | |
11,201 | A | – | – | – | – | G | 11,175 | SNP | T77A | |
11,288 | TCTGGTTTT | del | 11,261 | del | 11,210 | – | – | SNP_stop | S106 | |
11,332 | A | – | – | G | 11,306 | SNP_silent | V120V | |||
14,120 | C | T | 14,085 | – | – | SNP | P218L | |||
14,408 | C | T | 14,373 | T | 14,322 | T | 14,382 | SNP | P314L | |
14,676 | C | T | 14,641 | – | – | – | – | SNP_silent | P403P | |
15,017 | C | – | – | T | 14,931 | – | – | SNP | A517V | |
15,279 | C | T | 15,244 | – | – | – | – | SNP_silent | H604H | |
15,451 | G | – | - | – | – | A | 15,425 | SNP | G662S | |
16,176 | T | C | 16,141 | – | – | – | – | SNP | T903T | |
16,466 | C | – | – | – | – | T | 16,440 | SNP | P77L | |
18,271 | G | – | – | – | – | A | 18,245 | SNP | E78K | |
18,337 | G | – | – | – | – | T | 18,311 | SNP | A100S | |
19,220 | C | – | – | – | – | T | 19,194 | SNP | A394V | |
20,405 | C | T | 20,370 | – | – | – | – | SNP | P262L | |
20,759 | C | – | – | T | 20,673 | – | – | SNP | A34V | |
21,080 | A | – | – | G | 20,994 | – | – | SNP | K141R | |
21,215 | A | G | 21,180 | – | – | – | – | SNP | H186R | |
21,446 | A | – | – | G | 21,360 | – | – | SNP | K263R | |
3′ UTR | 27,389 | C | – | – | T | 27,303 | – | – | – | 27,389 |
29,733 | – | – | – | TA | 29,648 | – | – | – | 29,733 | |
29,742 | G | – | – | – | – | T | 29,716 | – | 29,742 | |
29,755 | – | – | – | C | 29,672 | – | – | – | 29,755 | |
29,790 | – | – | – | T | 29,708 | – | – | – | 29,790 |
Protein | Data for Strain: | |||||||
---|---|---|---|---|---|---|---|---|
Wuhan-Hu-1 a | KAZ/Britain/2021 | KAZ/B1.1/2021 | KAZ/Delta020/2021 | |||||
Position | Variant | Variant | Position | Variant | Position | Variant | Position | |
S | 21,618 | C | – | – | – | – | G | 21592 |
21,646 | C | – | – | T | 21,560 | – | – | |
21,648 | C | – | – | T | 21,562 | – | – | |
21,765 | TACATG | del | 21,729 | – | – | – | – | |
21,766 | A | – | – | – | – | del | 21,739 | |
21,784 | T | – | – | A | 21,698 | – | – | |
21,789 | C | – | – | T | 21,703 | – | – | |
21,846 | C | – | – | T | 21,760 | – | – | |
21,987 | G | – | – | – | – | A | 21,961 | |
21,993 | ATT | del | 21,951 | – | – | – | – | |
22,185 | C | – | – | – | – | T | 22,159 | |
22,407 | A | – | – | – | – | T | 22,381 | |
22,917 | T | – | – | – | – | G | 22,891 | |
22,995 | C | – | – | – | – | A | 22,969 | |
23,014 | A | – | – | C | 22,928 | – | – | |
23,063 | A | T | 23,019 | – | – | – | – | |
23,271 | C | A | 32,227 | – | – | – | – | |
23,403 | A | G | 23,359 | G | 23,317 | G | 23,377 | |
23,520 | C | - | – | T | 23,434 | – | – | |
23,604 | C | A | 23,560 | – | – | G | 23,578 | |
23,709 | C | T | 23,665 | – | – | – | – | |
23,751 | C | – | – | T | 23,665 | – | – | |
23,997 | C | – | – | T | 23,911 | – | – | |
24,000 | G | – | – | T | 23,914 | – | – | |
24,410 | G | – | – | – | – | A | 24,384 | |
24,506 | T | G | 24,462 | – | – | – | – | |
24,538 | A | – | – | T | 24,452 | – | – | |
24,914 | G | C | 24,870 | – | – | – | – |
Protein | Data for Strain: | Amino Acid Change | ||||||||
---|---|---|---|---|---|---|---|---|---|---|
Wuhan-Hu-1 a | KAZ/Britain/2021 | KAZ/B1.1/2021 | KAZ/Delta020/2021 | Type of Mutation | ||||||
Position | Variant | Variant | Position | Variant | Position | Variant | Position | |||
ORF3a | 25,459 | C | – | – | – | – | T | 25,443 | SNP | S26L b |
25,688 | C | – | – | T | 25,602 | – | – | SNP | A99V | |
25,838 | G | T | 25,794 | – | – | – | – | SNP | W149L | |
26,110 | C | – | – | T | 26,024 | – | – | SNP | P240S | |
M | 26,767 | T | – | – | – | – | C | 26,741 | SNP | I82T |
26,895 | C | – | – | T | 26,809 | – | – | SNP | H125Y | |
27,008 | G | – | – | T | 26,922 | – | – | SNP | K162N | |
ORF6 | 27,281 | GG | AA | 27,237 | – | – | – | – | SNP_stop | W27 |
27,285 | TC | AT | 27,241 | – | – | – | – | SNP | NL28KF | |
ORF7a | 27,527 | C | – | – | – | – | T | 27,501 | SNP | P45L |
27,638 | T | – | – | – | – | C | 27,612 | SNP | V82A | |
27,630 | C | – | – | T | 27,544 | – | – | SNP_silent | A79A | |
27,667 | G | – | – | A | 27,581 | – | – | SNP | E92K | |
27,739 | C | – | – | T | 27,653 | – | – | SNP | L116F | |
27,752 | C | – | – | – | T | 27,726 | SNP | T120I | ||
ORF7b | 27,874 | C | – | – | – | – | T | 27,848 | SNP | T40I |
ORF8 | 27,919 | T | – | – | – | – | C | 27,893 | SNP | I9T |
27,972 | C | T | 27,928 | – | – | – | – | SNP_stop | Q27 | |
28,048 | G | T | 28,004 | – | – | – | – | SNP | R52I | |
28,095 | A | T | 28,051 | – | – | – | – | SNP_stop | K68 | |
28,111 | A | G | 28,067 | – | – | – | – | SNP | Y73C | |
28,251 | T | – | – | – | – | C | 28,225 | SNP | F120L | |
28,253 | C | – | – | – | – | A | 28,227 | SNP | F120L | |
28,255 | T | – | – | – | – | A | 28,229 | SNP | I121N | |
28,258 | A | – | – | – | – | G | 28,232 | SNP_silent | 122 * | |
N | 28,280 | GAT | CTA | 28,236 | – | – | – | – | SNP | D3L |
28,461 | A | – | – | – | G | 28,435 | SNP | D63G | ||
28,881 | GGG | AAC | 28,837 | AAC | 28,837 | – | – | SNP | RG203KR | |
28,881 | G | – | – | – | – | T | 28,855 | SNP | R203M | |
28,916 | G | – | – | – | – | T | 28,890 | SNP | G215C | |
28,977 | C | T | 28,933 | – | – | – | – | SNP | S235F | |
29,236 | C | – | – | – | – | T | 29,210 | SNP_silent | G312G | |
29,402 | G | – | – | – | – | T | 29,376 | SNP | D377Y | |
29,436 | A | – | – | T | 29,350 | – | – | SNP | K388I |
Protein | KAZ/Britain/2021 | KAZ/B1.1/2021 | KAZ/Delta020/2021 | ||||||
---|---|---|---|---|---|---|---|---|---|
Amino Acid Change | PROVEAN Assessment | The Effect of Variation on Protein | Amino Acid Change | PROVEAN Assessment | The Effect of Variation on Protein | Amino Acid Change | PROVEAN Assessment | The Effect of Variation on Protein | |
ORF1ab | I295L | 0.232 | Neutral | L27F | −0.047 | Neutral | K81N | −0.070 | Neutral |
T183I | 0.216 | Neutral | A579V | 0.011 | Neutral | R365L | −0.939 | Neutral | |
T577N | 0.240 | Neutral | R586C | −0.727 | Neutral | A488S | −0.061 | Neutral | |
A890D | −1.749 | Neutral | K1037T | −1.196 | Neutral | P1228L | −1.038 | Neutral | |
I1412T | −0.370 | Neutral | K399E | −1.877 | Neutral | P1469S | 0.338 | Neutral | |
M1441I | 0.263 | Neutral | L438R | 0.659 | Neutral | V167L | −0.696 | Neutral | |
L75F | −2.290 | Neutral | P314L | −0.446 | Neutral | T492I | 1.435 | Neutral | |
P218L | −5.021 | Deleterious | A517V | −1.291 | Neutral | T77A | −0.878 | Neutral | |
P314L | −0.446 | Neutral | A34V | 1.158 | Neutral | P314L | −0.446 | Neutral | |
P262L | −0.014 | Neutral | K141R | −0.221 | Neutral | G662S | −2.475 | Neutral | |
H186R | −0.267 | Neutral | K263R | −1.344 | Neutral | P77L | −6.845 | Deleterious | |
– | – | – | E78K | −1.123 | Neutral | ||||
– | – | – | – | – | – | A100S | 1.338 | Neutral | |
– | – | – | – | – | – | A394V | −1.523 | Neutral | |
S | H69del | 0.260 | Neutral | Y28Y | 0.000 | Neutral | T19R | −0.839 | Neutral |
Y145del | 0.853 | Neutral | T29I | −1.538 | Neutral | I68del | −0.821 | Neutral | |
N501Y | −0.090 | Neutral | N74K | −1.309 | Neutral | G142D | −0.277 | Neutral | |
A570D | −0.682 | Neutral | T76I | −0.115 | Neutral | T208M | −0.314 | Neutral | |
D614G | 0.598 | Neutral | T95I | −1.214 | Neutral | N282I | −3.717 | Deleterious | |
P681H | 0.060 | Neutral | E484D | −0.210 | Neutral | L452R | 0.559 | Neutral | |
T716I | −3.293 | Deleterious | D614G | 0.598 | Neutral | T478K | −0.524 | Neutral | |
S982A | −1.505 | Neutral | A653V | −0.715 | Neutral | D614G | 0.598 | Neutral | |
D1118H | −1.142 | Neutral | S730T | −0.040 | Neutral | P681R | 0.741 | Neutral | |
– | – | – | P812L | −0.868 | Neutral | D950N | −1.631 | Neutral | |
– | – | – | S813I | −2.867 | Deleterious | – | – | – | |
– | – | – | Q992H | −4.059 | Deleterious | – | – | – | |
ORF3a | – | – | – | – | – | – | S26L | −2.314 | Neutral |
A99V | −1.962 | Neutral | – | – | – | ||||
W149L | −9.419 | Deleterious | – | – | – | – | – | ||
– | – | – | P240S | −1.495 | Neutra | – | – | – | |
M | – | – | – | I82T | −3.853 | Deleterious | |||
– | – | – | H125Y | 0.799 | Neutral | – | – | – | |
– | – | – | K162N | 0.501 | Neutral | – | – | – | |
ORF7a | – | – | – | – | – | – | P45L | −10.000 | Deleterious |
– | – | – | – | – | – | V82A | −2.667 | Deleterious | |
– | – | – | A79A | 0.000 | Neutral | – | – | – | |
– | – | – | E92K | −1.842 | Neutral | – | – | – | |
– | – | – | L116F | −1.263 | Neutral | – | – | – | |
– | – | – | – | – | – | T120I | −1.789 | Neutral | |
ORF7b | – | – | – | – | – | – | T40I | −2.000 | Neutral |
ORF8 | – | – | – | I9T | −1.333 | Neutral | |||
R52I | −6.417 | Deleterious | – | – | – | – | – | – | |
Y73C | −4.500 | Deleterious | – | – | – | – | – | – | |
– | – | – | – | – | – | F120L | −2.667 | Deleterious | |
– | – | – | – | – | – | F120L | −2.667 | Deleterious | |
– | – | – | – | – | – | I121N | −0.667 | Neutral | |
N | D3L | −0.230 | Neutral | – | – | – | |||
– | – | – | – | – | – | D63G | −0.929 | Neutral | |
– | – | – | – | – | – | R203M | −3.304 | Deleterious | |
– | – | – | – | – | – | G215C | −0.953 | Neutral | |
– | – | – | – | – | – | S235F | −1.738 | Neutral | |
– | – | – | – | – | – | D377Y | −1.779 | Neutral | |
– | – | – | K388I | −1.204 | Neutral | – | – | – |
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Usserbayev, B.; Sultankulova, K.T.; Burashev, Y.; Melisbek, A.; Shirinbekov, M.; Myrzakhmetova, B.S.; Zhunushov, A.; Smekenov, I.; Kerimbaev, A.; Nurabaev, S.; et al. Genetic Variations of Three Kazakhstan Strains of the SARS-CoV-2 Virus. Viruses 2025, 17, 415. https://doi.org/10.3390/v17030415
Usserbayev B, Sultankulova KT, Burashev Y, Melisbek A, Shirinbekov M, Myrzakhmetova BS, Zhunushov A, Smekenov I, Kerimbaev A, Nurabaev S, et al. Genetic Variations of Three Kazakhstan Strains of the SARS-CoV-2 Virus. Viruses. 2025; 17(3):415. https://doi.org/10.3390/v17030415
Chicago/Turabian StyleUsserbayev, Bekbolat, Kulyaisan T. Sultankulova, Yerbol Burashev, Aibarys Melisbek, Meirzhan Shirinbekov, Balzhan S. Myrzakhmetova, Asankadir Zhunushov, Izat Smekenov, Aslan Kerimbaev, Sergazy Nurabaev, and et al. 2025. "Genetic Variations of Three Kazakhstan Strains of the SARS-CoV-2 Virus" Viruses 17, no. 3: 415. https://doi.org/10.3390/v17030415
APA StyleUsserbayev, B., Sultankulova, K. T., Burashev, Y., Melisbek, A., Shirinbekov, M., Myrzakhmetova, B. S., Zhunushov, A., Smekenov, I., Kerimbaev, A., Nurabaev, S., Chervyakova, O., Kozhabergenov, N., & Kutumbetov, L. B. (2025). Genetic Variations of Three Kazakhstan Strains of the SARS-CoV-2 Virus. Viruses, 17(3), 415. https://doi.org/10.3390/v17030415