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Background <p>The omicron lineage has been declared the fifth variant of concern (VOC) by the World Health Organization (WHO). This study aims to describe the genomic characteristics of omicron sequences from Cameroon and to discuss the potential implications of identified mutations for viral evolution and immune escape, based on existing literature.</p> Methods <p>This study is a retrospective analysis of publicly available SARS-CoV-2 sequences from Cameroon submitted to GISAID (Global Initiative on Sharing Avian Influenza Data). Full-length omicron sequences from across Cameroon were retrieved from the GISAID database. Phylogenetic analyses were conducted using Nextstrain SARS-CoV-2 Workflow version 8.2.0, and mutation analysis was performed using the Nextstrain web tool, with the Wuhan-Hu-1/2019 strain as a reference.</p> Results <p>A total of 1,428 omicron sequences were analyzed, revealing eleven variants: BA.1 lineage (45.0%), B.1.1.529 (0.2%), BA.2 (7.7%), BA.4 (6.5%), BA.5 (16.3%), BE (12.2%), BF (6.3%), BN.2 (0.1%), BQ.1 (3.7%), XBB (0.5%) and JN.1 (1.5%). The sequences exhibited high number of mutations in the spike gene, with the JN.1 lineage showing the highest mutation count. All lineages contained mutations associated with neutralizing antibody evasion, including R346T, K417N, G446S, E484A, or Q493R.</p> Conclusions <p>Ongoing monitoring of omicron lineages is crucial to detect emerging variants and adapt vaccine strategies. The significant mutations, particularly in the JN.1 lineage warrant further investigation to assess their potential impact on transmissibility or immune escape.</p> Clinical trial number <p>Not applicable.</p>

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Genome characterization of the SARS-CoV-2 omicron in Cameroon

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年3月16日

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  • Chavely Gwladys Monamele,
  • Loique Landry Messanga Essengue,
  • Moïse Henri Moumbeket-Yifomnjou,
  • Pauliana Vanessa Ilouga,
  • Aristide Mounchili-Njifon,
  • Ibrahim Pascal Touoyem,
  • Estelle Madaha Longla,
  • Ripa Mohamadou Njankouo,
  • Abdou Fatawou Modiyinji,
  • Ifeanyi F. Omah,
  • Richard Njouom

摘要

Background

The omicron lineage has been declared the fifth variant of concern (VOC) by the World Health Organization (WHO). This study aims to describe the genomic characteristics of omicron sequences from Cameroon and to discuss the potential implications of identified mutations for viral evolution and immune escape, based on existing literature.

Methods

This study is a retrospective analysis of publicly available SARS-CoV-2 sequences from Cameroon submitted to GISAID (Global Initiative on Sharing Avian Influenza Data). Full-length omicron sequences from across Cameroon were retrieved from the GISAID database. Phylogenetic analyses were conducted using Nextstrain SARS-CoV-2 Workflow version 8.2.0, and mutation analysis was performed using the Nextstrain web tool, with the Wuhan-Hu-1/2019 strain as a reference.

Results

A total of 1,428 omicron sequences were analyzed, revealing eleven variants: BA.1 lineage (45.0%), B.1.1.529 (0.2%), BA.2 (7.7%), BA.4 (6.5%), BA.5 (16.3%), BE (12.2%), BF (6.3%), BN.2 (0.1%), BQ.1 (3.7%), XBB (0.5%) and JN.1 (1.5%). The sequences exhibited high number of mutations in the spike gene, with the JN.1 lineage showing the highest mutation count. All lineages contained mutations associated with neutralizing antibody evasion, including R346T, K417N, G446S, E484A, or Q493R.

Conclusions

Ongoing monitoring of omicron lineages is crucial to detect emerging variants and adapt vaccine strategies. The significant mutations, particularly in the JN.1 lineage warrant further investigation to assess their potential impact on transmissibility or immune escape.

Clinical trial number

Not applicable.