1887

Microbial Genomics logo

Volume 8, Issue 7

Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021 Open Access

Abstract

The COVID-19 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Eastern Mediterranean Region. Lebanon experienced its largest wave of COVID-19 infections from January to April 2021. Limited genomic surveillance was undertaken, with just 26 SARS-CoV-2 genomes available for this period, nine of which were from travellers from Lebanon detected by other countries. Additional genome sequencing is thus needed to allow surveillance of variants in circulation. In total, 905 SARS-CoV-2 genomes were sequenced using the ARTIC protocol. The genomes were derived from SARS-CoV-2-positive samples, selected retrospectively from the sentinel COVID-19 surveillance network, to capture diversity of location, sampling time, sex, nationality and age. Although 16 PANGO lineages were circulating in Lebanon in January 2021, by February there were just four, with the Alpha variant accounting for 97 % of samples. In the following 2 months, all samples contained the Alpha variant. However, this had changed dramatically by June and July 2021, when all samples belonged to the Delta variant. This study documents a ten-fold increase in the number of SARS-CoV-2 genomes available from Lebanon. The Alpha variant, first detected in the UK, rapidly swept through Lebanon, causing the country's largest wave to date, which peaked in January 2021. The Alpha variant was introduced to Lebanon multiple times despite travel restrictions, but the source of these introductions remains uncertain. The Delta variant was detected in Gambia in travellers from Lebanon in mid-May, suggesting community transmission in Lebanon several weeks before this variant was detected in the country. Prospective sequencing in June/July 2021 showed that the Delta variant had completely replaced the Alpha variant in under 6 weeks.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): bioinformatics , genomic epidemiology , SARS-CoV-2 and sequencing
Funding
This study was supported by the:
  • World Health Organization (Award #01047)
    • Principle Award Recipient: SimaTokajian
  • Biotechnology and Biological Sciences Research Council (Award BB/CCG1860/1)
    • Principle Award Recipient: NotApplicable
  • Biotechnology and Biological Sciences Research Council (Award BBS/E/F/000PR10352)
    • Principle Award Recipient: NotApplicable
  • Biotechnology and Biological Sciences Research Council (Award BB/R012504/1)
    • Principle Award Recipient: NotApplicable
© 2022 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000838
2022-07-25
2024-04-24
Loading full text...

Full text loading...

/deliver/fulltext/mgen/8/7/mgen000838.html?itemId=/content/journal/mgen/10.1099/mgen.0.000838&mimeType=html&fmt=ahah

References

  1. Shu Y, McCauley J. GISAID: global initiative on sharing all influenza data - from vision to reality. Euro Surveill 2017; 22:30494 [View Article] [PubMed]
     [Google Scholar]
  2. Huang C, Wang Y, Li X, Ren L, Zhao J et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet 2020; 395:497–506 [View Article] [PubMed]
     [Google Scholar]
  3. Dong E, Du H, Gardner L. An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect Dis 2020; 20:533–534 [View Article] [PubMed]
     [Google Scholar]
  4. Harvey WT, Carabelli AM, Jackson B, Gupta RK, Thomson EC et al. SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol 2021; 19:409–424 [View Article] [PubMed]
     [Google Scholar]
  5. Konings F, Perkins MD, Kuhn JH, Pallen MJ, Alm EJ et al. SARS-CoV-2 variants of interest and concern naming scheme conducive for global discourse. Nat Microbiol 2021; 6:821–823 [View Article] [PubMed]
     [Google Scholar]
  6. Davies NG, Abbott S, Barnard RC, Jarvis CI, Kucharski AJ et al. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science 2021; 372:6538 [View Article] [PubMed]
     [Google Scholar]
  7. Volz E, Mishra S, Chand M, Barrett JC, Johnson R et al. Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature 2021; 593:266–269 [View Article] [PubMed]
     [Google Scholar]
  8. Mlcochova P, Kemp SA, Dhar MS, Papa G, Meng B et al. SARS-CoV-2 B.1.617.2 delta variant replication and immune evasion. Nature 2021; 599:114–119 [View Article] [PubMed]
     [Google Scholar]
  9. Lyngse FP, Mølbak K, Skov RL, Christiansen LE, Mortensen LH et al. Increased transmissibility of SARS-CoV-2 lineage B.1.1.7 by age and viral load. Nat Commun 2021; 12:7251 [View Article] [PubMed]
     [Google Scholar]
  10. Liu Y, Rocklöv J. The reproductive number of the Delta variant of SARS-CoV-2 is far higher compared to the ancestral SARS-CoV-2 virus. J Travel Med 2021; 28:taab124 [View Article] [PubMed]
     [Google Scholar]
  11. Li B, Deng A, Li K, Hu Y, Li Z et al. Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant. Nat Commun 2022; 13:460 [View Article] [PubMed]
     [Google Scholar]
  12. Rigby SE, Lodge TJ, Alotaibi S, Barr AD, Clarke SD et al. Preliminary yield estimation of the 2020 Beirut explosion using video footage from social media. Shock Waves 2020; 30:671–675 [View Article]
     [Google Scholar]
  13. Koweyes J, Salloum T, Haidar S, Merhi G, Tokajian S. COVID-19 pandemic in Lebanon: one year later, what have we learnt?. mSystems 2021; 6:e00351-21 [View Article] [PubMed]
     [Google Scholar]
  14. Page AJ, Mather AE, Le-Viet T, Meader EJ, Alikhan N-F et al. Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management. Microb Genom 2021; 7:000589 [View Article] [PubMed]
     [Google Scholar]
  15. Faria NR, Mellan TA, Whittaker C, Claro IM, Candido D da S et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science 2021; 372:815–821 [View Article] [PubMed]
     [Google Scholar]
  16. Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V et al. Detection of a SARS-CoV-2 variant of concern in South Africa. Nature 2021; 592:438–443 [View Article] [PubMed]
     [Google Scholar]
  17. Mashe T, Takawira FT, Gumbo H, Juru A, Nyagupe C et al. Surveillance of SARS-CoV-2 in Zimbabwe shows dominance of variants of concern. The Lancet Microbe 2021; 2:e177 [View Article] [PubMed]
     [Google Scholar]
  18. Quick J. NCoV-2019 Sequencing Protocol v3 (LoCost); 2020 https://www.protocols.io/view/ncov-2019-sequencing-protocol-v3-locost-bh42j8ye
  19. Baker DJ, Aydin A, Le-Viet T, Kay GL, Rudder S et al. CoronaHiT: high-throughput sequencing of SARS-CoV-2 Genomes. Genome Med 2021; 13: [View Article]
     [Google Scholar]
  20. Ncov2019-Artic-Nf n.d https://github.com/connor-lab/ncov2019-artic-nf
  21. Krueger F. FelixKrueger/TrimGalore. Perl 2016 https://github.com/FelixKrueger/TrimGalore
     [Google Scholar]
  22. Li H. Aligning Sequence Reads, Clone Sequences and Assembly Contigs with 175 BWA-MEM; 2013 http://arxiv.org/abs/1303.3997
  23. Grubaugh ND, Gangavarapu K, Quick J, Matteson NL, Jesus JGD et al. An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and IVar. Genome Biol 2019; 20:
     [Google Scholar]
  24. Rambaut A, Holmes EC, O’Toole Á, Hill V, McCrone JT et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020; 5:1403–1407 [View Article]
     [Google Scholar]
  25. Turakhia Y, Maio ND, Thornlow B, Gozashti L, Lanfear R et al. Stability of SARS-CoV-2 Phylogenies. PLOS Genet 2020; 16:e1009175
     [Google Scholar]
  26. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Edited by Emma Teeling. Mol Biol Evol 2020; 37:1530–1534
     [Google Scholar]
  27. Hasegawa M, Kishino H, Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 1985; 22:160–174
     [Google Scholar]
  28. Yang Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol 1994; 39:306–314
     [Google Scholar]
  29. Ghafari M, du Plessis L, Raghwani J, Bhatt S, Xu B et al. Purifying selection determines the short-term time dependency of evolutionary rates inurifying selection determines the short-term time dependency of evolutionary rates in SARS-cov-2 and PH1N1 iinfluenza. Mol Biol Evol 2022; 39: msac009 [View Article]
     [Google Scholar]
  30. Hill V, Plessis LD, Peacock TP, Aggarwal D, Colquhoun R et al. The origins and molecular evolution of SARS-CoV-2 Lineage B.1.1.7 in the UK. bioRxiv 2022
     [Google Scholar]
  31. Louca S, Doebeli M. Efficient comparative phylogenetics on large trees. Edited by Alfonso Valencia. Bioinformatics 2018; 34:1053–1055
     [Google Scholar]
  32. Cochrane G, Karsch-Mizrachi I, Toshihisa T. The International Nucleotide Sequence Database Collaboration The international nucleotide sequence database collaboration. Nucleic Acids Res 2016; 44:D48–D50 [View Article]
     [Google Scholar]
  33. Aggarwal D, Page AJ, Schaefer U, Savva GM, Myers R et al. Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission. Nat Commun 2022; 13:1012 [View Article] [PubMed]
     [Google Scholar]
  34. Hill V, Du Plessis L, Peacock TP, Aggarwal D, Colquhoun R et al. The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK. bioRxiv 2022 [View Article]
     [Google Scholar]
  35. Ghafari M, du Plessis L, Raghwani J, Bhatt S, Xu B et al. Purifying selection determines the short-term time dependency of evolutionary rates in SARS-CoV-2 and PH1N1 influenza. Mol Biol Evol 2022; 39:msac009 [View Article] [PubMed]
     [Google Scholar]
  36. Feghali R, Merhi G, Kwasiborski A, Hourdel V, Ghosn N et al. Genomic characterization and phylogenetic analysis of the first SARS-CoV-2 variants introduced in Lebanon. PeerJ 2021; 9:e11015 [View Article] [PubMed]
     [Google Scholar]
  37. Hodcroft EB, Zuber M, Nadeau S, Vaughan TG, Crawford KHD et al. Spread of a SARS-CoV-2 variant through Europe in the summer of 2020. Nature 2021; 595:707–712 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000838
Loading
Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021
M Gen 8, 000838 (2022); https://doi.org/10.1099/mgen.0.000838
/content/journal/mgen/10.1099/mgen.0.000838
/content/journal/mgen/10.1099/mgen.0.000838
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

EXCEL

Supplementary material 3

EXCEL

Supplementary material 4

EXCEL

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error