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

Main Article Content

Ahmad Ghiffari
Chairil Anwar
Indri Ramayanti
Hamzah Hasyim
Iskhaq Iskandar
Muhammad Totong Kamaluddin
Legiran Legiran
Zulkhair Ali


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


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


Download data is not yet available.
Abstract 1 |


(1) C. Wang, P. W. Horby, F. G. Hayden, and G. F. Gao, “A novel coronavirus outbreak of global health concern,” Lancet, vol. 6736, no. 20, pp. 1–4, 2020, doi: 10.1016/S0140-6736(20)30185-9.
(2) D. Cucinotta and M. Vanelli, “WHO declares COVID-19 a pandemic,” Acta Biomed., vol. 91, no. 1, pp. 157–160, 2020, doi: 10.23750/abm.v91i1.9397.
(3) World Health Organization (WHO), “WHO Coronavirus (COVID-19) Dashboard,” 2021.
(4) D. N. Aisyah, C. A. Mayadewi, H. Diva, Z. Kozlakidis, S. Siswanto, and W. Adisasmito, “A spatial-temporal description of the SARS-CoV-2 infections in Indonesia during the first six months of outbreak,” PLoS One, vol. 15, no. 12 December, pp. 1–14, 2020, doi: 10.1371/journal.pone.0243703.
(5) R. Tosepu, D. S. Effendy, and L. O. A. I. Ahmad, “The first confirmed cases of COVID-19 in Indonesian citizens,” Public Heal. Indones., vol. 6, no. 2, pp. 70–71, 2020.
(6) E. Petersen 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., vol. 94, pp. 88–90, 2020, doi: 10.1016/j.ijid.2020.04.029.
(7) N. G. Davies et al., “Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England,” Science (80-. )., vol. 372, no. 149, p. eabg3055, 2021, doi: 10.1126/science.abg3055.
(8) B. K. Kupferschmidt and M. Wadman, “Delta variant triggers dangerous new phase in the pandemic,” Science, 2021.
(9) J. A. Plante et al., “Spike mutation D614G alters SARS-CoV-2 fitness,” Nature, vol. 592, no. September 2020, 2020, doi: 10.1038/s41586-020-2895-3.
(10) F. K. Yoshimoto, “The proteins of Severe Acute Respiratory Syndrome Coronavirus‑2 (SARS CoV‑2 or n‑COV19), the cause of COVID‑19,” Protein J., vol. 39, no. 3, pp. 198–216, 2020, doi: 10.1007/s10930-020-09901-4.
(11) C. Pattabiraman et al., “Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka,” PLoS One, vol. 15, no. 12, pp. 1–15, 2020, doi: 10.1371/journal.pone.0243412.
(12) E. Retnaningsih, N. Nuryanto, R. Oktarina, O. Komalasari, and S. Maryani, “The effect of knowledge and attitude toward Coronavirus Disease-19 transmission prevention practice in South Sumatera Province, Indonesia,” Open Access Maced. J. Med. Sci., vol. 8, no. T1, pp. 198–202, 2020, doi: 10.3889/oamjms.2020.5184.
(13) GISAID, “Novel variant 501Y.V2 with triple spike receptor binding site substitutions,” p. 2021, 2021, [Online]. Available:
(14) Dinas Kesehatan Kota Palembang, “Spot kasus COVID-19 di kota Palembang periode 1 Februari 2020 - 27 Juli 2021,”, 2021. .
(15) M. Kearse et al., “Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data,” Bioinformatics, vol. 28, no. 12, pp. 1647–1649, 2012, doi: 10.1093/bioinformatics/bts199.
(16) P. R. Krause et al., “SARS-CoV-2 Variants and Vaccines,” N. Engl. J. Med., vol. 385, no. 2, pp. 179–186, 2021.
(17) Centers for Disease Control and Prevention, “SARS-CoV-2 variant classifications and definitions,” CDC, 2021. (accessed Jul. 13, 2021).
(18) Alaa Abdel Latif et al., “SARS-CoV-2 (hCoV-19) Mutation Report,” 2021.
(19) World Health Organization, “Tracking SARS-CoV-2 variants,” 2021. [Online]. Available:
(20) S. Guo, K. Liu, and J. Zheng, “The genetic variant of SARS-CoV-2 : would it matter for controlling the devastating pandemic?,” Int. J. Biol. Sci., vol. 17, no. 6, pp. 1476–1485, 2021, doi: 10.7150/ijbs.59137.
(21) E. Alm et al., “Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020,” Eurosurveillance, vol. 25, no. 32, pp. 1–8, 2020, doi: 10.2807/1560-7917.ES.2020.25.32.2001410.
(22) A. Rambaut et al., “A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology,” Nat. Microbiol., vol. 5, pp. 1403–1407, 2020, doi: 10.1101/2020.04.17.046086.
(23) N. G. Davies et al., “Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7,” Nature, vol. 593, no. 7858, pp. 270–274, 2021, doi: 10.1038/s41586-021-03426-1.
(24) C. Li et al., “The impact of receptor-binding domain natural mutations on antibody recognition of SARS-CoV-2,” Signal Transduct. Target. Ther., vol. 6, no. 132, pp. 1–3, 2021, doi: 10.1038/s41392-021-00536-0.
(25) M. Ramanathan, I. D. Ferguson, W. Miao, and P. A. Khavari, “SARS-CoV-2 B.1.1.7 and B.1.351 spike variants bind human ACE2 with increased affinity,” Lancet Infect. Dis., vol. 21, no. 8, p. 1070, 2021, doi: 10.1016/S1473-3099(21)00262-0.
(26) Pango lineages, “Global report investigating novel coronavirus haplotypes,”, 2021. .
(27) S. S. A. Karim and T. de Oliveira, “New SARS-CoV-2 variants-Clinical, public health, and vaccine implications,” N. Engl. J. Med., vol. 384, no. 19, pp. 1866–1868, 2021.
(28) T. K. Burki, “News lifting of COVID-19 restrictions in the UK and the Delta variant,” Lancet Respir., vol. 2600, no. 21, p. 1, 2021, doi: 10.1016/S2213-2600(21)00328-3.
(29) A. A. Latif et al., “Indonesia Mutation Report,”, 2021. .
(30) J. Wise, “Covid-19: The E484K mutation and the risks it poses,” BMJ, no. February, pp. 1–2, 2021, doi: 10.1136/bmj.n359.
(31) D. A. Collier et al., “Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies,” Nature, vol. 593, no. January, pp. 136–141, 2021, doi: 10.1038/s41586-021-03412-7.
(32) E. C. Wall et al., “Neutralising antibody activity against SARS-CoV-2 VOCs B.1.617.2 and B.1.351 by BNT162b2 vaccination,” Lancet, vol. 397, no. 10292, pp. 2331–2333, 2021, doi: 10.1016/S0140-6736(21)01290-3.
(33) C. Liu et al., “Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum,” Cell, vol. 184, no. 16, pp. 4220-4236.e13, 2021, doi: 10.1016/j.cell.2021.06.020.
(34) R. Januar et al., “Transmission dynamics of novel coronavirus–SARS-CoV-2 in South Sumatera, Indonesia,” Clin. Epidemiol. Glob. Heal., vol. 11, no. November 2020, p. 100777, 2021, doi: 10.1016/j.cegh.2021.100777.
(35) P. Nouvellet et al., “Reduction in mobility and COVID-19 transmission,” Nat. Commun., vol. 12, pp. 1–9, 2021, doi: 10.1038/s41467-021-21358-2.
(36) K. Deforche, J. Vercauteren, V. Müller, and A. M. Vandamme, “Behavioral changes before lockdown and decreased retail and recreation mobility during lockdown contributed most to controlling COVID-19 in Western countries,” BMC Public Health, vol. 21, no. 1, pp. 1–11, 2021, doi: 10.1186/s12889-021-10676-1.
(37) B. P. Y. Loo, K. H. Tsoi, P. P. Y. Wong, and P. C. Lai, “Identification of superspreading environment under COVID-19 through human mobility data,” Sci. Rep., vol. 11, no. 1, pp. 1–9, 2021, doi: 10.1038/s41598-021-84089-w.
(38) U. K. Mukherjee et al., “Evaluation of reopening strategies for educational institutions during COVID-19 through agent based simulation,” Sci. Rep., vol. 11, no. 1, pp. 1–24, 2021, doi: 10.1038/s41598-021-84192-y.
(39) M. Yechezkel, A. Weiss, I. Rejwan, E. Shahmoon, S. Ben-Gal, and D. Yamin, “Human mobility and poverty as key drivers of COVID-19 transmission and control,” BMC Public Health, vol. 21, no. 1, pp. 1–13, 2021, doi: 10.1186/s12889-021-10561-x.
(40) R. F. Savaris, G. Pumi, J. Dalzochio, and R. Kunst, “Stay-at-home policy is a case of exception fallacy: an internet-based ecological study,” Sci. Rep., vol. 11, no. 1, pp. 1–13, 2021, doi: 10.1038/s41598-021-84092-1.
(41) S. Ando, Y. Matsuzawa, H. Tsurui, T. Mizutani, D. Hall, and Y. Kuroda, “Stochastic modelling of the effects of human-mobility restriction and viral infection characteristics on the spread of COVID-19,” Sci. Rep., vol. 11, no. 1, pp. 1–10, 2021, doi: 10.1038/s41598-021-86027-2.
(42) D. Meidan et al., “Alternating quarantine for sustainable epidemic mitigation,” Nat. Commun., vol. 12, no. 1, pp. 1–12, 2021, doi: 10.1038/s41467-020-20324-8.
(43) C. C. Kerr et al., “Controlling COVID-19 via test-trace-quarantine,” Nat. Commun., vol. 12, no. 1, pp. 1–12, 2021, doi: 10.1038/s41467-021-23276-9.
(44) S. H. Hodgson, K. Mansatta, G. Mallett, V. Harris, K. R. W. Emary, and A. J. Pollard, “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., vol. 21, no. 2, pp. e26–e35, 2021, doi: 10.1016/S1473-3099(20)30773-8.
(45) I. McDonald, S. M. Murray, C. J. Reynolds, D. M. Altmann, and R. J. Boyton, “Comparative systematic review and meta-analysis of reactogenicity, immunogenicity and efficacy of vaccines against SARS-CoV-2,” npj Vaccines, vol. 6, no. 74, pp. 1–14, 2021, doi: 10.1038/s41541-021-00336-1.
(46) H. Chemaitelly 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., no. July 9, pp. 1–17, 2021, doi: 10.1038/s41591-021-01446-y.
(47) E. C. Thomson, L. E. Rosen, J. G. Shepherd, D. Corti, D. L. Robertson, and G. Snell, “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,” pp. 1171–1187, 2021, doi: 10.1016/j.cell.2021.01.037.
(48) E. C. Thomson et al., “Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity,” Cell, vol. 184, no. 5, pp. 1171-1187.e20, 2021, doi: 10.1016/j.cell.2021.01.037.
(49) D. Planas et al., “Reduced sensitivity of infectious SARS-CoV-2 variant Delta to antibody neutralization,” Nature, no. July, pp. 1–20, 2021, [Online]. Available:
(50) D. Planas et al., “Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies,” Nat. Med., vol. 27, no. 5, pp. 917–924, 2021, doi: 10.1038/s41591-021-01318-5.
(51) C. K. Wibmer et al., “SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma,” Nat. Med., vol. 27, no. April, pp. 622–625, 2021, doi: 10.1038/s41591-021-01285-x.
(52) P. Wang et al., “Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization,” Cell Host Microbe, vol. 29, no. 5, pp. 747-750.e5, 2021, doi: 10.1016/j.chom.2021.04.007.
(53) A. Nugroho, “UGM Expert: Having an efficacy rate of 65.3 percent, Sinovac vaccine remains safe,”, 2021. .
(54) Dinas Kesehatan Kota Palembang, “Update 8 Agustus 2021 Vaksinasi COVID-19 Kota Palembang,”, 2021. .
(55) A. Pormohammad et al., “Efficacy and safety of COVID-19 vaccines: A systematic review and meta-analysis of randomized clinical trials,” Vaccines, vol. 9, no. 467, pp. 1–21, 2021, doi: 10.1007/s40265-019-01114-z.
(56) J. L. Bernal et al., “Effectiveness of COVID-19 vaccines against the B.1.617.2 (Delta) variant,” N. Engl. J. Med., no. July, pp. 1–10, 2021, doi: DOI: 10.1056/NEJMoa2108891.
(57) H. Harapan et al., “Willingness-to-pay for a COVID-19 vaccine and its associated determinants in Indonesia,” Hum. Vaccines Immunother., vol. 00, no. 00, pp. 1–7, 2020, doi: 10.1080/21645515.2020.1819741.
(58) 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. .