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Background <p>As Nigeria has the sixth-highest population in the world and a significant amount of inbound and outbound travel, the characterization of SARS-CoV-2 genomic diversity across the country is critical for understanding novel pandemic dynamics. We describe the genomic diversity of SARS-CoV-2 in Nigeria throughout the COVID-19 pandemic and examine the coverage of Nigeria's genomic surveillance system.</p> Methods <p>Genome sequences and sample metadata were downloaded from the GISAID repository. A beta regression was used to test for a relationship between fully resolved nucleotide proportion over time, as a proxy for data quality. Sample and sequencing source were compared to assess geographic coverage.</p> Results <p>A total of 7759 COVID-19 sequences collected from February 2020 to March 2023 were included. The majority were collected in 2021 (76.6%) and South West (43%). Eleven states (30%) reported 10 or fewer SARS-CoV-2 genomes across the entire period. The genome sequences submitted to GISAID from Nigeria were of high quality with very few unresolved nucleotides. Waves 4 and 5, predominantly Omicron lineages, show higher diversity around position 23&#xa0;kb than the other waves. Overall, the Nigeria Centre for Disease Control (NCDC) and state-run hospitals were the largest contributors to the sample collection efforts during this study period. However, the collection efforts shifted over time from NCDC in waves 1–3 to regional hospitals and other healthcare facilities in waves 4–5, although this pattern varied by geopolitical zone (GPZ). Sequencing efforts also shifted from research laboratories during the first waves to NCDC during waves 4 and 5.</p> Conclusions <p>The findings suggest the need for a coordinated sequencing strategy and standardized protocols to improve genomic surveillance during future outbreaks of existing and novel pathogens. A network of sequencing laboratories that includes at least one in each GPZ, linked to and coordinated by the national reference laboratory at NCDC might provide more balanced coverage for future pandemics and pathogen surveillance.</p>

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Genomic diversity and surveillance of SARS-CoV-2 in Nigeria

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年10月14日

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  • Thomas J. Y. Kono,
  • Ezenwa J. Onyemata,
  • Natalia Blanco,
  • Chika K. Onwuamah,
  • Nnaemeka Ndodo,
  • Paul Oluniyi,
  • Olanrewaju Lawal,
  • Christina Riley,
  • Sophia Osawe,
  • Cheryl Baxter,
  • Anna Winters,
  • Chenfeng Xiong,
  • Christian T. Happi,
  • Babatunde L. Salako,
  • Ifedayo Adetifa,
  • Alash’le Abimiku,
  • Manhattan Charurat,
  • Kristen A. Stafford,
  • Timothy O’Connor,
  • Meagan Fitzpatrick,
  • Mohammad M. Sajadi,
  • Patrick Dakum,
  • Fati Murtala-Ibrahim,
  • Nifarta Andrew,
  • Aminu Musa,
  • Tolulope Adenekan,
  • Kenneth Ewerem,
  • Victoria Etuk,
  • Mmedorenyin Okon,
  • Weiyu Luo,
  • Xin Wu,
  • Tulio de Oliveira,
  • Eduan Wilkinson,
  • Houriiyah Tegally,
  • Jenicca Poongavanan,
  • Michelle Parker,
  • Danilo Silva,
  • Joicymara S. Xavier,
  • Vivek Naranbhai,
  • Salim A. Karim,
  • Kennedy Otwombe

摘要

Background

As Nigeria has the sixth-highest population in the world and a significant amount of inbound and outbound travel, the characterization of SARS-CoV-2 genomic diversity across the country is critical for understanding novel pandemic dynamics. We describe the genomic diversity of SARS-CoV-2 in Nigeria throughout the COVID-19 pandemic and examine the coverage of Nigeria's genomic surveillance system.

Methods

Genome sequences and sample metadata were downloaded from the GISAID repository. A beta regression was used to test for a relationship between fully resolved nucleotide proportion over time, as a proxy for data quality. Sample and sequencing source were compared to assess geographic coverage.

Results

A total of 7759 COVID-19 sequences collected from February 2020 to March 2023 were included. The majority were collected in 2021 (76.6%) and South West (43%). Eleven states (30%) reported 10 or fewer SARS-CoV-2 genomes across the entire period. The genome sequences submitted to GISAID from Nigeria were of high quality with very few unresolved nucleotides. Waves 4 and 5, predominantly Omicron lineages, show higher diversity around position 23 kb than the other waves. Overall, the Nigeria Centre for Disease Control (NCDC) and state-run hospitals were the largest contributors to the sample collection efforts during this study period. However, the collection efforts shifted over time from NCDC in waves 1–3 to regional hospitals and other healthcare facilities in waves 4–5, although this pattern varied by geopolitical zone (GPZ). Sequencing efforts also shifted from research laboratories during the first waves to NCDC during waves 4 and 5.

Conclusions

The findings suggest the need for a coordinated sequencing strategy and standardized protocols to improve genomic surveillance during future outbreaks of existing and novel pathogens. A network of sequencing laboratories that includes at least one in each GPZ, linked to and coordinated by the national reference laboratory at NCDC might provide more balanced coverage for future pandemics and pathogen surveillance.