SARS-CoV-2 Variants of Concern Increased Transmission and Decrease Vaccine Efficacy in the COVID-19 Pandemic in Palembang Indonesia

SARS-CoV-2 Variants of Concern Increased Transmission and Decrease Vaccine Efficacy in the COVID-19 Pandemic in Palembang Indonesia


  • Ahmad Ghiffari Univ
  • Chairil Anwar
  • Hamzah Hasyim
  • Iskhaq Iskandar
  • Muhammad Totong Kamaluddin


outbreak, contagious, immunity, temporal analysis, variant of interest


Background and aim: The number of COVID-19 cases surging despite the large scale of health promotion campaigns. This study aimed to find disease transmissibility and affected vaccine efficacy associated with the mutation of the SARS-CoV-2 variant of concern.

Methods: The study was a descriptive temporal survey design with secondary ecological data: the whole-genome sequence (WGS) from the Global Initiative on Sharing Avian Influenza (GISAID) and COVID-19 data from the Palembang City Health Office website. Bioinformatics software was used to detect mutations.

Results: Palembang submitted 43 whole genome sequences, 13 of which were Pangoline sequences classifications.

Conclusions: The two concern variations, Alpha and Delta, were associated with increased transmissions and decreased vaccination efficacy using temporal analysis. Regulations governing the relaxation of mobility restrictions should be based on high rates of testing and tracing, and universal vaccination programs should require that all received two doses of any vaccines as fast as possible.


Wang C, Horby PW, Hayden FG, Gao GF. A novel coronavirus outbreak of global health concern. Lancet. 2020;6736(20):1–4.

Cucinotta D, Vanelli M. WHO declares COVID-19 a pandemic. Acta Biomed. 2020;91(1):157–60.

World Health Organization (WHO). WHO Coronavirus (COVID-19) Dashboard. 2021.

Aisyah DN, Mayadewi CA, Diva H, Kozlakidis Z, Siswanto S, Adisasmito W. A spatial-temporal description of the SARS-CoV-2 infections in Indonesia during the first six months of outbreak. PLoS One. 2020;15(12 December):1–14.

Tosepu R, Effendy DS, Ahmad LOAI. The first confirmed cases of COVID-19 in Indonesian citizens. Public Heal Indones. 2020;6(2):70–1.

Petersen E, McCloskey B, Hui DS, Kock R, Ntoumi F, Memish ZA, et al. COVID-19 travel restrictions and the International Health Regulations – Call for an open debate on easing of travel restrictions. Int J Infect Dis. 2020;94:88–90.

Davies NG, Abbott S, Barnard RC, Jarvis CI, Kucharski AJ, Munday JD, et al. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science (80- ). 2021;372(149):eabg3055.

Kupferschmidt BK, Wadman M. Delta variant triggers dangerous new phase in the pandemic. Science [Internet]. 2021; Available from:

Plante JA, Liu Y, Liu J, Xia H, Johnson BA, Lokugamage KG, et al. Spike mutation D614G alters SARS-CoV-2 fitness. Nature. 2020;592(September 2020):116–21.

Yoshimoto FK. The proteins of Severe Acute Respiratory Syndrome Coronavirus‑2 (SARS CoV‑2 or n‑COV19), the cause of COVID‑19. Protein J. 2020;39(3):198–216.

Pattabiraman C, Habib F, Harsha PK, Rasheed R, Prasad P, Reddy V, et al. Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka. PLoS One. 2020;15(12):1–15.

Retnaningsih E, Nuryanto N, Oktarina R, Komalasari O, Maryani S. The effect of knowledge and attitude toward Coronavirus Disease-19 transmission prevention practice in South Sumatera Province, Indonesia. Open Access Maced J Med Sci. 2020;8(T1):198–202.

GISAID. Novel variant 501Y.V2 with triple spike receptor binding site substitutions. 2021;2021. Available from:

Dinas Kesehatan Kota Palembang. Spot kasus COVID-19 di kota Palembang periode 1 Februari 2020 - 27 Juli 2021. 2021. p. 1.

Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, et al. Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012;28(12):1647–9.

Krause PR, Fleming TR, Longini IM, Peto R, Briand S, Heymann DL, et al. SARS-CoV-2 Variants and Vaccines. N Engl J Med. 2021;385(2):179–86.

Centers for Disease Control and Prevention. SARS-CoV-2 variant classifications and definitions [Internet]. CDC. 2021 [cited 2021 Jul 13]. p. 1–11. Available from:

Alaa Abdel Latif, Mullen JL, Alkuzweny M, Tsueng G, Cano M, Haag E, et al. SARS-CoV-2 (hCoV-19) Mutation Report. 2021.

World Health Organization. Tracking SARS-CoV-2 variants [Internet]. 2021. Available from:

Guo S, Liu K, Zheng J. The genetic variant of SARS-CoV-2 : would it matter for controlling the devastating pandemic? Int J Biol Sci. 2021;17(6):1476–85.

Alm E, Broberg EK, Connor T, Hodcroft EB, Komissarov AB, Maurer-Stroh S, et al. Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020. Eurosurveillance [Internet]. 2020;25(32):1–8. Available from:

Rambaut A, Holmes EC, O’Toole A, Hill V, McCrone JT, Ruis C, et al. A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology. Nat Microbiol. 2020;5:1403–1407.

Davies NG, Jarvis CI, van Zandvoort K, Clifford S, Sun FY, Funk S, et al. Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7. Nature. 2021;593(7858):270–4.

Li C, Tian X, Jia X, Wan J, Lu L, Jiang S, et al. The impact of receptor-binding domain natural mutations on antibody recognition of SARS-CoV-2. Signal Transduct Target Ther. 2021;6(132):1–3.

Ramanathan M, Ferguson ID, Miao W, Khavari PA. SARS-CoV-2 B.1.1.7 and B.1.351 spike variants bind human ACE2 with increased affinity. Lancet Infect Dis. 2021;21(8):1070.

Pango lineages. Global report investigating novel coronavirus haplotypes. 2021.

Karim SSA, Oliveira T de. New SARS-CoV-2 variants-Clinical, public health, and vaccine implications. N Engl J Med. 2021;384(19):1866–8.

Burki TK. News lifting of COVID-19 restrictions in the UK and the Delta variant. Lancet Respir. 2021;2600(21):1.

Latif AA, Mullen JL, Alkuzweny M, Tsueng G, Cano M, Haag E, et al. Indonesia Mutation Report. 2021.

Wise J. Covid-19: The E484K mutation and the risks it poses. BMJ. 2021;(February):1–2.

Collier DA, Marco A De, Ferreira IATM, Meng B, Silacci-fregni C, Bianchi S, et al. Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. Nature. 2021;593(January):136–41.

Wall EC, Wu M, Harvey R, Kelly G, Warchal S, Sawyer C, et al. Neutralising antibody activity against SARS-CoV-2 VOCs B.1.617.2 and B.1.351 by BNT162b2 vaccination. Lancet. 2021;397(10292):2331–3.

Liu C, Ginn HM, Dejnirattisai W, Supasa P, Wang B, Tuekprakhon A, et al. Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum. Cell. 2021;184(16):4220-4236.e13.

Januar R, Wathan I, Ridwan H, Wibisono H, Nuraini L, Yusri Y, et al. Transmission dynamics of novel coronavirus–SARS-CoV-2 in South Sumatera, Indonesia. Clin Epidemiol Glob Heal. 2021;11(November 2020):100777.

Nouvellet P, Bhatia S, Cori A, Ainslie KEC, Baguelin M, Bhatt S, et al. Reduction in mobility and COVID-19 transmission. Nat Commun. 2021;12:1–9.

Deforche K, Vercauteren J, Müller V, Vandamme AM. Behavioral changes before lockdown and decreased retail and recreation mobility during lockdown contributed most to controlling COVID-19 in Western countries. BMC Public Health. 2021;21(1):1–11.

Loo BPY, Tsoi KH, Wong PPY, Lai PC. Identification of superspreading environment under COVID-19 through human mobility data. Sci Rep. 2021;11(1):1–9.

Mukherjee UK, Bose S, Ivanov A, Souyris S, Seshadri S, Sridhar P, et al. Evaluation of reopening strategies for educational institutions during COVID-19 through agent based simulation. Sci Rep. 2021;11(1):1–24.

Yechezkel M, Weiss A, Rejwan I, Shahmoon E, Ben-Gal S, Yamin D. Human mobility and poverty as key drivers of COVID-19 transmission and control. BMC Public Health. 2021;21(1):1–13.

Savaris RF, Pumi G, Dalzochio J, Kunst R. Stay-at-home policy is a case of exception fallacy: an internet-based ecological study. Sci Rep. 2021;11(1):1–13.

Ando S, Matsuzawa Y, Tsurui H, Mizutani T, Hall D, Kuroda Y. Stochastic modelling of the effects of human-mobility restriction and viral infection characteristics on the spread of COVID-19. Sci Rep. 2021;11(1):1–10.

Meidan D, Schulmann N, Cohen R, Haber S, Yaniv E, Sarid R, et al. Alternating quarantine for sustainable epidemic mitigation. Nat Commun. 2021;12(1):1–12.

Kerr CC, Mistry D, Stuart RM, Rosenfeld K, Hart GR, Núñez RC, et al. Controlling COVID-19 via test-trace-quarantine. Nat Commun. 2021;12(1):1–12.

Hodgson SH, Mansatta K, Mallett G, Harris V, Emary KRW, Pollard AJ. What defines an efficacious COVID-19 vaccine? A review of the challenges assessing the clinical efficacy of vaccines against SARS-CoV-2. Lancet Infect Dis. 2021;21(2):e26–35.

McDonald I, Murray SM, Reynolds CJ, Altmann DM, Boyton RJ. Comparative systematic review and meta-analysis of reactogenicity, immunogenicity and efficacy of vaccines against SARS-CoV-2. npj Vaccines. 2021;6(74):1–14.

Chemaitelly H, Yassine HM, Benslimane FM, Al Khatib HA, Tang P, Hasan MR, et al. mRNA-1273 COVID-19 vaccine effectiveness against the B.1.1.7 and B.1.351 variants and severe COVID-19 disease in Qatar. Nat Med. 2021;(July 9):1–17.

Thomson EC, Rosen LE, Shepherd JG, Corti D, Robertson DL, Snell G. Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity ll Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. 2021;1171–87.

Thomson EC, Rosen LE, Shepherd JG, Spreafico R, da Silva Filipe A, Wojcechowskyj JA, et al. Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Cell. 2021;184(March 4):1171–87.

Planas D, Veyer D, Baidaliuk A, Staropoli I, Guivel-Benhassine F, Rajah MM, et al. Reduced sensitivity of infectious SARS-CoV-2 variant Delta to antibody neutralization. Nature. 2021;(July):1–20.

Planas D, Bruel T, Grzelak L, Guivel-Benhassine F, Staropoli I, Porrot F, et al. Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies. Nat Med. 2021;27(5):917–24.

Wibmer CK, Ayres F, Hermanus T, Madzivhandila M, Kgagudi P, Oosthuysen B, et al. SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma. Nat Med. 2021;27(April):622–5.

Wang P, Casner RG, Nair MS, Wang M, Yu J, Cerutti G, et al. Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization. Cell Host Microbe. 2021;29(5):747-750.e5.

Nugroho A. UGM Expert: Having an efficacy rate of 65.3 percent, Sinovac vaccine remains safe. Vol. January, 2021. p. 1–3.

Dinas Kesehatan Kota Palembang. Update 8 Agustus 2021 Vaksinasi COVID-19 Kota Palembang. 2021.

Pormohammad A, Zarei M, Ghorbani S, Mohammadi M, Razizadeh MH, Turner DL, et al. Efficacy and safety of COVID-19 vaccines: A systematic review and meta-analysis of randomized clinical trials. Vaccines. 2021;9(467):1–21.

Bernal JL, Andrews N, Gower C, Gallagher E, Simmons R, Thelwall S, et al. Effectiveness of COVID-19 vaccines against the B.1.617.2 (Delta) variant. N Engl J Med. 2021;(July):1–10.

Harapan H, Wagner AL, Yufika A, Winardi W, Anwar S, Gan AK, et al. Willingness-to-pay for a COVID-19 vaccine and its associated determinants in Indonesia. Hum Vaccines Immunother. 2020;00(00):1–7.

Minister of Health of Indonesia. Regulation of the Minister of Health of the Republic of Indonesia number 10 year 2021 on the Implementation of vaccination in order to combat pandemics. 2021. p. 1–33.







How to Cite

Ghiffari A, Anwar C, Hasyim H, Iskandar I, Kamaluddin MT. SARS-CoV-2 Variants of Concern Increased Transmission and Decrease Vaccine Efficacy in the COVID-19 Pandemic in Palembang Indonesia. Acta Biomed [Internet]. 2022 Mar. 14 [cited 2024 Jul. 21];93(1):e2022018. Available from: