Iranian Journal of Medical Sciences

Iranian Journal of Medical Sciences

Current Issue

By Issue

By Author

By Subject

Author Index

Keyword Index

About Journal

Aims and Scope

Journal Team

Publication Ethics

Indexing and Abstracting

Related Links

Peer Review Process

Journal Metrics

Disappearance of Imported Cases of Omicron Lineage BA.2.40 in West Kalimantan, Indonesia

Document Type : Original Article(s)

Authors

1 Department of Microbiology, School of Medicine, Universitas Tanjungpura, Pontianak, Indonesia

2 Department of Biochemistry and Biomolecular, School of Medicine, Universitas Tanjungpura, Pontianak, Indonesia

10.30476/ijms.2023.97513.2935

Abstract

Background: The World Health Organization has declared Omicron as the fifth variant of concern with more than 50 mutations, particularly in the spike protein. Given increased viral infectivity due to mutations, worldwide genomic surveillance and detection of severe acute respiratory syndrome 2 (SARS-CoV-2) is essential. The present study aimed to track Omicron lineage BA.2.40 in West Kalimantan, Indonesia.
Methods: In May-August 2022, nasopharyngeal swab samples (n=3,642) were collected from international travelers to West Kalimantan (active surveillance), and patients hospitalized due to SARS-CoV-2 infection (baseline surveillance). The samples were tested for Omicron lineages based on ORF1ab, N, and HV69-70del genes, followed by whole-genome sequencing. The sequences were then identified using two genomic databases, aligned against the reference genome (Wuhan/Hu-1/2019), and then compared with BA.2.40 lineage detected across the world. Phylogenetic analysis between the samples and other SARS-CoV-2 isolates was performed using molecular evolutionary genetics analysis software.
Results: Based on the genomic databases, 10 isolates were identified as BA.2.40. All samples tested positive for the ORF1ab and N genes, but negative for the HV69-70del gene, which is a marker to detect the Omicron variant. Phylogenetic analysis showed the isolates were closely related to an isolate from Malaysia, an area dominated by BA.2.40. 
Conclusion: Omicron lineage BA.2.40 has no HV69-70 deletion in the spike protein, a marker used to screen for the Omicron variant. BA.2.40 showed a high similarity to an isolate from Malaysia and was detected only during certain periods, indicating the effect of internationally imported cases.

Keywords

References
  1. Organization WH. World Health Organization tracking SARS-CoV-2 variants. Geneva: World Health Organization; 2022.
  2. Meo SA, Meo AS, Al-Jassir FF, Klonoff DC. Omicron SARS-CoV-2 new variant: global prevalence and biological and clinical characteristics. Eur Rev Med Pharmacol Sci. 2021;25:8012-8. doi: 10.26355/eurrev_202112_27652. PubMed PMID: 34982465.
  3. Organization WH [Internet]. Statement on the update of WHO’s working definitions and tracking system for SARS-CoV-2 variants of concern and variants of interest. [cited 24 April 2023]. Available from: https://www.who.int/news/item/16-03-2023-statement-on-the-update-of-who-s-working-definitions-and-tracking-system-for-sars-cov-2-variants-of-concern-and-variants-of-interest
  4. Organization WH [Internet]. Statement on Omicron sublineage BA.2. [cited 22 February 2022]. Available from: https://www.who.int/news/item/22-02-2022-statement-on-omicron-sublineage-ba.2
  5. Mollaei HR, Afshar AA, Kalantar-Neyestanaki D, Fazlalipour M, Aflatoonian B. Comparison five primer sets from different genome region of COVID-19 for detection of virus infection by conventional RT-PCR. Iran J Microbiol. 2020;12:185-93. PubMed PMID: 32685113; PubMed Central PMCID: PMCPMC7340604.
  6. Ke Z, Oton J, Qu K, Cortese M, Zila V, McKeane L, et al. Structures and distributions of SARS-CoV-2 spike proteins on intact virions. Nature. 2020;588:498-502. doi: 10.1038/s41586-020-2665-2. PubMed PMID: 32805734; PubMed Central PMCID: PMCPMC7116492.
  7. Norz D, Grunwald M, Olearo F, Fischer N, Aepfelbacher M, Pfefferle S, et al. Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with built-in screening functionality for del-HV69/70- and N501Y variants such as B.1.1.7. J Clin Virol. 2021;141:104894. doi: 10.1016/j.jcv.2021.104894. PubMed PMID: 34182299; PubMed Central PMCID: PMCPMC8196477.
  8. Andrew R. Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations. Virological. 2020.
  9. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772-80. doi: 10.1093/molbev/mst010. PubMed PMID: 23329690; PubMed Central PMCID: PMCPMC3603318.
  10. Khare S, Gurry C, Freitas L, Schultz MB, Bach G, Diallo A, et al. GISAID’s Role in Pandemic Response. China CDC Wkly. 2021;3:1049-51. doi: 10.46234/ccdcw2021.255. PubMed PMID: 34934514; PubMed Central PMCID: PMCPMC8668406.
  11. GISAID EpiFlu™ Database. GISAID: Munich; 2011.
  12. Organization WH. Enhancing Response to Omicron SARS-CoV-2 variant. Geneva: World Health Organization; 2022.
  13. Parums DV. Editorial: The XBB.1.5 (‘Kraken’) Subvariant of Omicron SARS-CoV-2 and its Rapid Global Spread. Med Sci Monit. 2023;29:e939580. doi: 10.12659/MSM.939580. PubMed PMID: 36722047; PubMed Central PMCID: PMCPMC9901170.
  14. Shrestha LB, Foster C, Rawlinson W, Tedla N, Bull RA. Evolution of the SARS-CoV-2 omicron variants BA.1 to BA.5: Implications for immune escape and transmission. Rev Med Virol. 2022;32:e2381. doi: 10.1002/rmv.2381. PubMed PMID: 35856385; PubMed Central PMCID: PMCPMC9349777.
  15. Ghafari C, Benusic M, Prystajecky N, Sbihi H, Kamelian K, Hoang L. Epidemiological analysis of the emergence and disappearance of the SARS-CoV-2 Kappa variant within a region of British Columbia, Canada. Can Commun Dis Rep. 2022;48:22-6. doi: 10.14745/ccdr.v48i01a04. PubMed PMID: 35273466; PubMed Central PMCID: PMCPMC8856721.
  16. Russell TW, Wu JT, Clifford S, Edmunds WJ, Kucharski AJ, Jit M, et al. Effect of internationally imported cases on internal spread of COVID-19: a mathematical modelling study. Lancet Public Health. 2021;6:e12-e20. doi: 10.1016/S2468-2667(20)30263-2. PubMed PMID: 33301722; PubMed Central PMCID: PMCPMC7801817.
  17. Zhang L, Yang H, Wang K, Zhan Y, Bian L. Measuring imported case risk of COVID-19 from inbound international flights --- A case study on China. J Air Transp Manag. 2020;89:101918. doi: 10.1016/j.jairtraman.2020.101918. PubMed PMID: 32904487; PubMed Central PMCID: PMCPMC7455240.
  18. Yang B, Tsang TK, Wong JY, He Y, Gao H, Ho F, et al. The differential importation risks of COVID-19 from inbound travellers and the feasibility of targeted travel controls: A case study in Hong Kong. Lancet Reg Health West Pac. 2021;13:100184. doi: 10.1016/j.lanwpc.2021.100184. PubMed PMID: 34179860; PubMed Central PMCID: PMCPMC8214928.
  19. Harvey WT, Carabelli AM, Jackson B, Gupta RK, Thomson EC, Harrison EM, et al. SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol. 2021;19:409-24. doi: 10.1038/s41579-021-00573-0. PubMed PMID: 34075212; PubMed Central PMCID: PMCPMC8167834.
  20. Groves DC, Rowland-Jones SL, Angyal A. The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. Biochem Biophys Res Commun. 2021;538:104-7. doi: 10.1016/j.bbrc.2020.10.109. PubMed PMID: 33199022; PubMed Central PMCID: PMCPMC7643658.
  21. Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, et al. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell. 2020;182:812-27. doi: 10.1016/j.cell.2020.06.043. PubMed PMID: 32697968; PubMed Central PMCID: PMCPMC7332439.
  22. Plante JA, Liu Y, Liu J, Xia H, Johnson BA, Lokugamage KG, et al. Spike mutation D614G alters SARS-CoV-2 fitness. Nature. 2021;592:116-21. doi: 10.1038/s41586-020-2895-3. PubMed PMID: 33106671; PubMed Central PMCID: PMCPMC8158177.
  23. Weissman D, Alameh MG, de Silva T, Collini P, Hornsby H, Brown R, et al. D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. Cell Host Microbe. 2021;29:23-31. doi: 10.1016/j.chom.2020.11.012. PubMed PMID: 33306985; PubMed Central PMCID: PMCPMC7707640.
  24. Zhou B, Thao TTN, Hoffmann D, Taddeo A, Ebert N, Labroussaa F, et al. SARS-CoV-2 spike D614G change enhances replication and transmission. Nature. 2021;592:122-7. doi: 10.1038/s41586-021-03361-1. PubMed PMID: 33636719.
  25. Papanikolaou V, Chrysovergis A, Ragos V, Tsiambas E, Katsinis S, Manoli A, et al. From delta to Omicron: S1-RBD/S2 mutation/deletion equilibrium in SARS-CoV-2 defined variants. Gene. 2022;814:146134. doi: 10.1016/j.gene.2021.146134. PubMed PMID: 34990799; PubMed Central PMCID: PMCPMC8725615.
  26. Lan J, Ge J, Yu J, Shan S, Zhou H, Fan S, et al. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature. 2020;581:215-20. doi: 10.1038/s41586-020-2180-5. PubMed PMID: 32225176.
  27. Selvavinayagam ST, Yong YK, Joseph N, Hemashree K, Tan HY, Zhang Y, et al. Low SARS-CoV-2 viral load among vaccinated individuals infected with Delta B.1.617.2 and Omicron BA.1.1.529 but not with Omicron BA.1.1 and BA.2 variants. Front Public Health. 2022;10:1018399. doi: 10.3389/fpubh.2022.1018399. PubMed PMID: 36211690; PubMed Central PMCID: PMCPMC9540788.
  28. Cao Y, Wang J, Jian F, Xiao T, Song W, Yisimayi A, et al. Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Nature. 2022;602:657-63. doi: 10.1038/s41586-021-04385-3. PubMed PMID: 35016194; PubMed Central PMCID: PMCPMC8866119
  29. Kullappan M, Mary U, Ambrose JM, Veeraraghavan VP, Surapaneni KM. Elucidating the role of N440K mutation in SARS-CoV-2 spike - ACE-2 binding affinity and COVID-19 severity by virtual screening, molecular docking and dynamics approach. J Biomol Struct Dyn. 2023;41:912-29. doi: 10.1080/07391102.2021.2014973. PubMed PMID: 34904526.
  30. Rani PR, Imran M, Lakshmi JV, Jolly B, Jain A, Surekha A, et al. Symptomatic reinfection of SARS-CoV-2 with spike protein variant N440K associated with immune escape. J Med Virol. 2021;93:4163-5. doi: 10.1002/jmv.26997. PubMed PMID: 33818797; PubMed Central PMCID: PMCPMC8250729.
  31. Kannan SR, Spratt AN, Cohen AR, Naqvi SH, Chand HS, Quinn TP, et al. Evolutionary analysis of the Delta and Delta Plus variants of the SARS-CoV-2 viruses. J Autoimmun. 2021;124:102715. doi: 10.1016/j.jaut.2021.102715. PubMed PMID: 34399188; PubMed Central PMCID: PMCPMC8354793.
  32. Cao Y, Yisimayi A, Jian F, Song W, Xiao T, Wang L, et al. BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection. Nature. 2022;608:593-602. doi: 10.1038/s41586-022-04980-y. PubMed PMID: 35714668; PubMed Central PMCID: PMCPMC9385493
  33. Saifi S, Ravi V, Sharma S, Swaminathan A, Chauhan NS, Pandey R. SARS-CoV-2 VOCs, Mutational diversity and clinical outcome: Are they modulating drug efficacy by altered binding strength? Genomics. 2022;114:110466. doi: 10.1016/j.ygeno.2022.110466. PubMed PMID: 36041637; PubMed Central PMCID: PMCPMC9419439.
  34. Pastorio C, Zech F, Noettger S, Jung C, Jacob T, Sanderson T, et al. Determinants of Spike infectivity, processing, and neutralization in SARS-CoV-2 Omicron subvariants BA.1 and BA.2. Cell Host Microbe. 2022;30:1255-68. doi: 10.1016/j.chom.2022.07.006. PubMed PMID: 35931073; PubMed Central PMCID: PMCPMC9289044.
  35. Cherian S, Potdar V, Jadhav S, Yadav P, Gupta N, Das M, et al. SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. Microorganisms. 2021;9. doi: 10.3390/microorganisms9071542. PubMed PMID: 34361977; PubMed Central PMCID: PMCPMC8307577.
  36. Zhang Z, Wan X, Li X, Cai S, Wan C. Enhancing the Immunogenicity of RBD Protein Variants through Amino Acid E484 Mutation in SARS-CoV-2. Viruses. 2022;14. doi: 10.3390/v14092020. PubMed PMID: 36146826; PubMed Central PMCID: PMCPMC9506138.
  37. Shishir TA, Jannat T, Naser IB. An in-silico study of the mutation-associated effects on the spike protein of SARS-CoV-2, Omicron variant. PLoS One. 2022;17:e0266844. doi: 10.1371/journal.pone.0266844. PubMed PMID: 35446879; PubMed Central PMCID: PMCPMC9022835.
  38. Tegally H, Moir M, Everatt J, Giovanetti M, Scheepers C, Wilkinson E, et al. Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa. Nat Med. 2022;28:1785-90. doi: 10.1038/s41591-022-01911-2. PubMed PMID: 35760080; PubMed Central PMCID: PMCPMC9499863 Lancet Laboratories.
Iranian Journal of Medical Sciences

Articles InPress, Corrected Proof
Available Online from 28 October 2023
Files
History
  • Received: 21 December 2022
  • Revised: 23 February 2023
  • Accepted: 29 March 2023
  • First Publish Date: 28 October 2023
Share
How to cite
Statistics