Exploration of Medicine

From: Figuring the characteristics of the Delta variant SARS-CoV-2 gene mutations in an Indonesian hospital: a descriptive study

Table 1. Patient characteristics

Variable	Delta variant distribution
Variable	B.1.617.2 (n = 3; 6.12%)	AY.23 (n = 34; 69.39%)	AY.24 (n = 11; 22.45%)	AY.75 (n = 1; 2.04%)	Total (n = 49)
Age
6–18 years	0 (0%)	1 (2.94%)	3 (27.27%)	0 (0%)	4 (8.16%)
19–30 years	1 (33.33%)	13 (38.24%)	1 (9.09%)	0 (0%)	15 (30.61)
31–45 years	2 (66.67%)	10 (29.41%)	4 (36.36%)	1 (100%)	17 (34.69%)
46–59 years	0 (0%)	8 (23.53%)	2 (18.18%)	0 (0%)	10 (20.41%)
≥ 60 years	0 (0%)	2 (5.88%)	1 (9.09%)	0 (0%)	3 (6.13%)
Gender
Male	0 (0%)	12 (35.29%)	5 (45.45%)	0 (0%)	17 (34.69%)
Female	3 (100%)	22 (64.71%)	6 (54.55%)	1 (100%)	32 (65.31%)
Vaccination status
Unvaccinated	1 (33.33%)	9 (26.48%)	1 (9.09%)	1 (100%)	12 (24.49%)
One dose	1 (33.33%)	4 (11.76%)	3 (27.28%)	0 (0%)	8 (16.33%)
Two doses	1 (33.33%)	21 (61.76%)	7 (63.63%)	0 (0%)	29 (59.18%)
Clinical manifestation
Fever	2 (66.67%)	27 (79.41%)	10 (90.91%)	0 (0%)	39 (79.60%)
Cough	2 (66.67%)	24 (70.59%)	7 (63.63%)	1 (100%)	34 (69.39%)
Runny nose	2 (66.67%)	21 (61.76%)	10 (90.91%)	1 (100%)	34 (69.39%)
Sore throat	1 (33.33%)	22 (64.71%)	7 (63.63%)	1 (100%)	31 (63.27%)
Malaise	3 (100%)	27 (79.41%)	9 (81.82%)	0 (0%)	39 (79.60%)
Fatigue	2 (66.7%)	21 (61.76%)	6 (54.54%)	0 (0%)	29 (59.18%)
Abdominal pain	0 (0%)	7 (20.59%)	2 (18.18%)	0 (0%)	9 (18.37%)
Diarrhea	0 (0%)	6 (17.65%)	2 (18.18%)	0 (0%)	8 (16.33%)
Pneumonia	0 (0%)	7 (20.59%)	2 (18.18%)	0 (0%)	9 (18.37%)
Anosmia	0 (0%)	14 (41.17%)	6 (54.54%)	0 (0%)	20 (40.82%)
Ageusia	0 (0%)	12 (35.29%)	1 (9.09%)	0 (0%)	13 (26.53%)
Shortness of breath	1 (33.33%)	14 (41.17%)	4 (36.36%)	1 (100%)	20 (40.82%)
Nausea or vomiting	1 (33.33%)	15 (44.12%)	3 (27.28%)	0 (0%)	19 (38.78%)
Severity
Mild	3 (100%)	26 (76.48%)	9 (81.82%)	1 (100%)	39 (79.60%)
Moderate	0 (0%)	4 (11.76%)	1 (9.09%)	0 (0%)	5 (10.20%)
Severe	0 (0%)	4 (11.76%)	1 (9.09%)	0 (0%)	5 (10.20%)

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Declarations

Author contributions

PL: Conceptualization, Methodology, Software, Validation, Formal analysis, Investigation, Resources, Data curation, Writing—original draft, Supervision. MAM: Software, Formal analysis, Investigation, Data curation, Writing—original draft. ER: Methodology, Formal analysis, Resources, Data curation, Supervision. RPP: Methodology, Resources, Data curation, Supervision. KYR: Methodology, Data curation, Writing—original draft, Supervision. NAS: Validation, Resources, Data curation. TPU: Software, Validation, Writing—review & editing, Visualization. All authors have read and approved the final version of the manuscript.

Conflicts of interest

The authors declare that they have no conflicts of interest.

Ethical approval

The Faculty of Medicine, Universitas Sriwijaya Ethics Review Committee granted ethical clearance for the investigation (approval number: 242-2022).

Consent to participate

Informed consent was not needed due to the retrospective nature of this study; therefore, it was exempted by the Faculty of Medicine, Universitas Sriwijaya Ethics Review Committee.

Consent to publication

Not applicable.

Availability of data and materials

Data are available upon reasonable request from the corresponding author.

Funding

Not applicable.

Copyright

References

Farahat RA, Abdelaal A, Umar TP, El-Sakka AA, Benmelouka AY, Albakri K, et al. The emergence of SARS-CoV-2 Omicron subvariants: current situation and future trends. Infez Med. 2022;30:480–94. [DOI] [PubMed] [PMC]

Jain N, Hung IC, Kimura H, Goh YL, Jau W, Huynh KLA, et al. The global response: How cities and provinces around the globe tackled Covid-19 outbreaks in 2021. Lancet Reg Health Southeast Asia. 2022;4:100031. [DOI] [PubMed] [PMC]

WHO coronavirus (COVID-19) dashboard [Internet]. Geneva: World Health Organization; c2023 [cited 2023 Jun 3]. Available from: https://covid19.who.int/

Umar TP, Kadir AKMS, Mohammed YA, Setti MO. Healthcare system preparedness for the next pandemic beyond COVID-19 situation. J Prev Med Hyg. 2022;63:E493–4. [DOI] [PubMed] [PMC]

Farahat RA, Baklola M, Umar TP. Omicron B.1.1.529 subvariant: brief evidence and future prospects. Ann Med Surg (Lond). 2022;83:104808. [DOI] [PubMed] [PMC]

Roy B, Dhillon JK, Habib N, Pugazhandhi B. Global variants of COVID-19: current understanding. J Biomed Sci. 2021;8:8–11. [DOI]

Wang C, Liu B, Zhang S, Huang N, Zhao T, Lu QB, et al. Differences in incidence and fatality of COVID-19 by SARS-CoV-2 Omicron variant versus Delta variant in relation to vaccine coverage: a world-wide review. J Med Virol. 2023;95:e28118. [DOI] [PubMed] [PMC]

Alimohamadi Y, Tola HH, Abbasi-Ghahramanloo A, Janani M, Sepandi M. Case fatality rate of COVID-19: a systematic review and meta-analysis. J Prev Med Hyg. 2021;62:E311–20. [DOI] [PubMed] [PMC]

Dyer O. Covid-19: Indonesia becomes Asia’s new pandemic epicentre as delta variant spreads. BMJ. 2021;374:n1815. [DOI] [PubMed]

10.

Heinz FX, Stiasny K. Distinguishing features of current COVID-19 vaccines: knowns and unknowns of antigen presentation and modes of action. NPJ Vaccines. 2021;6:104. [DOI] [PubMed] [PMC]

11.

Understanding vaccination process 2023 [Internet]. Baltimore: Johns Hopkins University; c2023 [cited 2023 Feb 25]. Available from: https://coronavirus.jhu.edu/vaccines/international

12.

Cahyani I, Putro EW, Ridwanuloh AM, Wibowo S, Hariyatun H, Syahputra G, et al. Genome profiling of SARS-CoV-2 in Indonesia, ASEAN and the neighbouring East Asian countries: features, challenges and achievements. Viruses. 2022;14:778. [DOI] [PubMed] [PMC]

13.

Azami NAM, Perera D, Thayan R, AbuBakar S, Sam IC, Salleh MZ, et al. SARS-CoV-2 genomic surveillance in Malaysia: displacement of B.1.617.2 with AY lineages as the dominant Delta variants and the introduction of Omicron during the fourth epidemic wave. Int J Infect Dis. 2022;125:216–26. [DOI] [PubMed] [PMC]

14.

Taboada B, Zárate S, García-López R, Muñoz-Medina JE, Sanchez-Flores A, Herrera-Estrella A, et al. Dominance of three sublineages of the SARS-CoV-2 Delta variant in Mexico. Viruses. 2022;14:1165. [DOI] [PubMed] [PMC]

15.

Dhawan M, Sharma A, PriyankaThakur N, Rajkhowa TK, Choudhary OP. Delta variant (B.1.617.2) of SARS-CoV-2: mutations, impact, challenges and possible solutions. Hum Vaccin Immunother. 2022;18:2068883. [DOI] [PubMed] [PMC]

16.

Suratekar R, Ghosh P, Niesen MJM, Donadio G, Anand P, Soundararajan V, et al. High diversity in Delta variant across countries revealed by genome-wide analysis of SARS-CoV-2 beyond the Spike protein. Mol Syst Biol. 2022;18:e10673. [DOI] [PubMed] [PMC]

17.

Khan MI, Baig MH, Mondal T, Alorabi M, Sharma T, Dong JJ, et al. Impact of the double mutants on spike protein of SARS-CoV-2 B.1.617 lineage on the human ACE2 receptor binding: a structural insight. Viruses. 2021;13:2295. [DOI] [PubMed] [PMC]

18.

Rochman ND, Faure G, Wolf YI, Freddolino PL, Zhang F, Koonin EV. Epistasis at the SARS-CoV-2 receptor-binding domain interface and the propitiously boring implications for vaccine escape. mBio. 2022;13:e0013522. [DOI] [PubMed] [PMC]

19.

Johnson BA, Zhou Y, Lokugamage KG, Vu MN, Bopp N, Crocquet-Valdes PA, et al. Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis. PLoS Pathog. 2022;18:e1010627. [DOI] [PubMed] [PMC]

20.

Moghaddar M, Radman R, Macreadie I. Severity, pathogenicity and transmissibility of delta and lambda variants of SARS-CoV-2, toxicity of spike protein and possibilities for future prevention of COVID-19. Microorganisms. 2021;9:2167. [DOI] [PubMed] [PMC]

21.

El-Shabasy RM, Nayel MA, Taher MM, Abdelmonem R, Shoueir KR, Kenawy ER. Three wave changes, new variant strains, and vaccination effect against COVID-19 pandemic. Int J Biol Macromol. 2022;204:161–8. [DOI] [PubMed] [PMC]

22.

Kumar S, Thambiraja TS, Karuppanan K, Subramaniam G. Omicron and Delta variant of SARS-CoV-2: a comparative computational study of spike protein. J Med Virol. 2022;94:1641–9. [DOI] [PubMed]

23.

Liu Y, Liu J, Johnson BA, Xia H, Ku Z, Schindewolf C, et al. Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. Cell Rep. 2022;39:110829. [DOI] [PubMed] [PMC]