Challenges and Opportunities for Global Genomic Surveillance Strategies in the COVID-19 Era
Global SARS-CoV-2 genomic surveillance efforts have provided critical data on the ongoing evolution of the virus to inform best practices in clinical care and public health throughout the pandemic. Impactful genomic surveillance strategies generally follow a multi-disciplinary pipeline involving cli...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-11-01
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| Series: | Viruses |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1999-4915/14/11/2532 |
| _version_ | 1827643590821543936 |
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| author | Ted Ling-Hu Estefany Rios-Guzman Ramon Lorenzo-Redondo Egon A. Ozer Judd F. Hultquist |
| author_facet | Ted Ling-Hu Estefany Rios-Guzman Ramon Lorenzo-Redondo Egon A. Ozer Judd F. Hultquist |
| author_sort | Ted Ling-Hu |
| collection | DOAJ |
| description | Global SARS-CoV-2 genomic surveillance efforts have provided critical data on the ongoing evolution of the virus to inform best practices in clinical care and public health throughout the pandemic. Impactful genomic surveillance strategies generally follow a multi-disciplinary pipeline involving clinical sample collection, viral genotyping, metadata linkage, data reporting, and public health responses. Unfortunately, current limitations in each of these steps have compromised the overall effectiveness of these strategies. Biases from convenience-based sampling methods can obfuscate the true distribution of circulating variants. The lack of standardization in genotyping strategies and bioinformatic expertise can create bottlenecks in data processing and complicate interpretation. Limitations and inconsistencies in clinical and demographic data collection and sharing can slow the compilation and limit the utility of comprehensive datasets. This likewise can complicate data reporting, restricting the availability of timely data. Finally, gaps and delays in the implementation of genomic surveillance data in the public health sphere can prevent officials from formulating effective mitigation strategies to prevent outbreaks. In this review, we outline current SARS-CoV-2 global genomic surveillance methods and assess roadblocks at each step of the pipeline to identify potential solutions. Evaluating the current obstacles that impede effective surveillance can improve both global coordination efforts and pandemic preparedness for future outbreaks. |
| first_indexed | 2024-03-09T17:56:23Z |
| format | Article |
| id | doaj.art-99fff91f93974182999817ea556df6e3 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-09T17:56:23Z |
| publishDate | 2022-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-99fff91f93974182999817ea556df6e32023-11-24T10:18:44ZengMDPI AGViruses1999-49152022-11-011411253210.3390/v14112532Challenges and Opportunities for Global Genomic Surveillance Strategies in the COVID-19 EraTed Ling-Hu0Estefany Rios-Guzman1Ramon Lorenzo-Redondo2Egon A. Ozer3Judd F. Hultquist4Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USADivision of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USADivision of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USADivision of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USADivision of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USAGlobal SARS-CoV-2 genomic surveillance efforts have provided critical data on the ongoing evolution of the virus to inform best practices in clinical care and public health throughout the pandemic. Impactful genomic surveillance strategies generally follow a multi-disciplinary pipeline involving clinical sample collection, viral genotyping, metadata linkage, data reporting, and public health responses. Unfortunately, current limitations in each of these steps have compromised the overall effectiveness of these strategies. Biases from convenience-based sampling methods can obfuscate the true distribution of circulating variants. The lack of standardization in genotyping strategies and bioinformatic expertise can create bottlenecks in data processing and complicate interpretation. Limitations and inconsistencies in clinical and demographic data collection and sharing can slow the compilation and limit the utility of comprehensive datasets. This likewise can complicate data reporting, restricting the availability of timely data. Finally, gaps and delays in the implementation of genomic surveillance data in the public health sphere can prevent officials from formulating effective mitigation strategies to prevent outbreaks. In this review, we outline current SARS-CoV-2 global genomic surveillance methods and assess roadblocks at each step of the pipeline to identify potential solutions. Evaluating the current obstacles that impede effective surveillance can improve both global coordination efforts and pandemic preparedness for future outbreaks.https://www.mdpi.com/1999-4915/14/11/2532SARS-CoV-2COVID-19genomic surveillancemolecular surveillancepublic health interventionepidemiology |
| spellingShingle | Ted Ling-Hu Estefany Rios-Guzman Ramon Lorenzo-Redondo Egon A. Ozer Judd F. Hultquist Challenges and Opportunities for Global Genomic Surveillance Strategies in the COVID-19 Era Viruses SARS-CoV-2 COVID-19 genomic surveillance molecular surveillance public health intervention epidemiology |
| title | Challenges and Opportunities for Global Genomic Surveillance Strategies in the COVID-19 Era |
| title_full | Challenges and Opportunities for Global Genomic Surveillance Strategies in the COVID-19 Era |
| title_fullStr | Challenges and Opportunities for Global Genomic Surveillance Strategies in the COVID-19 Era |
| title_full_unstemmed | Challenges and Opportunities for Global Genomic Surveillance Strategies in the COVID-19 Era |
| title_short | Challenges and Opportunities for Global Genomic Surveillance Strategies in the COVID-19 Era |
| title_sort | challenges and opportunities for global genomic surveillance strategies in the covid 19 era |
| topic | SARS-CoV-2 COVID-19 genomic surveillance molecular surveillance public health intervention epidemiology |
| url | https://www.mdpi.com/1999-4915/14/11/2532 |
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