Genomic Epidemiology and Recent Update on Nucleic Acid-Based Diagnostics for COVID-19

Ali A Rabaan¹, Shamsah H Al-Ahmed², Ranjit Sah³, Jaffar A Al-Tawfiq^{4

5

6}, Shafiul Haque⁷, Harapan Harapan^{8

9

10}, Kovy Arteaga-Livias^{11

12}, D Katterine Bonilla Aldana^{13

14}, Pawan Kumar¹⁵, Kuldeep Dhama¹⁶, Alfonso J Rodriguez-Morales^{12

13

14

17}

Affiliations

¹ Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia.
² Specialty Paediatric Medicine, Qatif Central Hospital, Qatif, Saudi Arabia.
³ Department of Microbiology, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal.
⁴ Specialty Internal Medicine, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia.
⁵ Department of Medicine, Indiana University School of Medicine, Indianapolis, IN USA.
⁶ Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA.
⁷ Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia.
⁸ Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia.
⁹ Tropical Disease Centre, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh Indonesia.
¹⁰ Department of Microbiology, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh Indonesia.
¹¹ Facultad de Medicina, Universidad Nacional Hermilio Valdizán, Huánuco, Peru.
¹² Universidad Científica del Sur, Lima, Peru.
¹³ Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnológica de Pereira, Pereira, Risaralda Colombia.
¹⁴ Semillero de Investigación en Zoonosis (SIZOO), Grupo de Investigación BIOECOS, Fundación Universitaria Autónoma de las Américas, Pereira, Risaralda Colombia.
¹⁵ College of Horticulture and Forestry, Rani Lakshmi Bai Central Agricultural University, Jhansi, India.
¹⁶ Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122 India.
¹⁷ Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Américas, Sede Pereira, Pereira, Risaralda Colombia.

PMID: 32989413
PMCID: PMC7513458
DOI: 10.1007/s40475-020-00212-3

Review

Genomic Epidemiology and Recent Update on Nucleic Acid-Based Diagnostics for COVID-19

Ali A Rabaan et al. Curr Trop Med Rep. 2020.

. 2020;7(4):113-119.

doi: 10.1007/s40475-020-00212-3. Epub 2020 Sep 24.

Authors

Affiliations

¹ Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia.
² Specialty Paediatric Medicine, Qatif Central Hospital, Qatif, Saudi Arabia.
³ Department of Microbiology, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal.
⁴ Specialty Internal Medicine, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia.
⁵ Department of Medicine, Indiana University School of Medicine, Indianapolis, IN USA.
⁶ Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA.
⁷ Research and Scientific Studies Unit, College of Nursing & Allied Health Sciences, Jazan University, Jazan, Saudi Arabia.
⁸ Medical Research Unit, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia.
⁹ Tropical Disease Centre, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh Indonesia.
¹⁰ Department of Microbiology, School of Medicine, Universitas Syiah Kuala, Banda Aceh, Aceh Indonesia.
¹¹ Facultad de Medicina, Universidad Nacional Hermilio Valdizán, Huánuco, Peru.
¹² Universidad Científica del Sur, Lima, Peru.
¹³ Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnológica de Pereira, Pereira, Risaralda Colombia.
¹⁴ Semillero de Investigación en Zoonosis (SIZOO), Grupo de Investigación BIOECOS, Fundación Universitaria Autónoma de las Américas, Pereira, Risaralda Colombia.
¹⁵ College of Horticulture and Forestry, Rani Lakshmi Bai Central Agricultural University, Jhansi, India.
¹⁶ Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122 India.
¹⁷ Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Américas, Sede Pereira, Pereira, Risaralda Colombia.

PMID: 32989413
PMCID: PMC7513458
DOI: 10.1007/s40475-020-00212-3

Abstract

Purpose of the review: The SARS-CoV-2 genome has been sequenced and the data is made available in the public domain. Molecular epidemiological investigators have utilized this information to elucidate the origin, mode of transmission, and contact tracing of SARS-CoV-2. The present review aims to highlight the recent advancements in the molecular epidemiological studies along with updating recent advancements in the molecular (nucleic acid based) diagnostics for COVID-19, the disease caused by SARS-CoV-2.

Recent findings: Epidemiological studies with the integration of molecular genetics principles and tools are now mainly focused on the elucidation of molecular pathology of COVID-19. Molecular epidemiological studies have discovered the mutability of SARS-CoV-2 which is of utmost importance for the development of therapeutics and vaccines for COVID-19. The whole world is now participating in the race for development of better and rapid diagnostics and therapeutics for COVID-19. Several molecular diagnostic techniques have been developed for accurate and precise diagnosis of COVID-19.

Summary: Novel genomic techniques have helped in the understanding of the disease pathology, origin, and spread of COVID-19. The whole genome sequence established in the initial days of the outbreak has enabled to identify the virus taxonomy. Several rapid, accurate, and sensitive diagnostic methods have been developed; those are based on the principle of detecting SARS-CoV-2 nucleic acids in clinical samples. Most of these molecular diagnostics are based on RT-PCR principle.

Keywords: Diagnostics; Epidemiology; Molecular epidemiology; RT-PCR.

PubMed Disclaimer

Conflict of interest statement

Conflict of InterestThe authors declare that they have no conflict of interest.

Cited by

SARS-CoV-2 Outbreak Investigation Using Contact Tracing and Whole-Genome Sequencing in an Ontario Tertiary Care Hospital.
Tsang KK, Ahmad S, Aljarbou A, Al Salem M, Baker SJC, Panousis EM, Derakhshani H, Rossi L, Nasir JA, Bulir DC, Surette MG, Lee RS, Smaill F, Mertz D, McArthur AG, Khan S. Tsang KK, et al. Microbiol Spectr. 2023 Jun 15;11(3):e0190022. doi: 10.1128/spectrum.01900-22. Epub 2023 Apr 24. Microbiol Spectr. 2023. PMID: 37093060 Free PMC article.
[Performance of the Procleix SARS-CoV-2 transcriptase-mediated amplification (TMA) assay for the diagnosis of COVID-19 in nasopharyngeal sample pools. Small pilot study].
Pérez-Abeledo M, Ramos B, Candel FJ, Sanz JC. Pérez-Abeledo M, et al. Rev Esp Quimioter. 2022 Feb;35(1):103-104. doi: 10.37201/req/101.2021. Epub 2021 Dec 26. Rev Esp Quimioter. 2022. PMID: 34953472 Free PMC article. Spanish. No abstract available.
COVID-19 vaccination campaign in Nepal, emerging UK variant and futuristic vaccination strategies to combat the ongoing pandemic.
Sah R, Khatiwada AP, Shrestha S, Bhuvan KC, Tiwari R, Mohapatra RK, Dhama K, Rodriguez-Morales AJ. Sah R, et al. Travel Med Infect Dis. 2021 May-Jun;41:102037. doi: 10.1016/j.tmaid.2021.102037. Epub 2021 Mar 27. Travel Med Infect Dis. 2021. PMID: 33781945 Free PMC article.
The Constant Threat of Zoonotic and Vector-Borne Emerging Tropical Diseases: Living on the Edge.
Rodriguez-Morales AJ, Paniz-Mondolfi AE, Faccini-Martínez ÁA, Henao-Martínez AF, Ruiz-Saenz J, Martinez-Gutierrez M, Alvarado-Arnez LE, Gomez-Marin JE, Bueno-Marí R, Carrero Y, Villamil-Gomez WE, Bonilla-Aldana DK, Haque U, Ramirez JD, Navarro JC, Lloveras S, Arteaga-Livias K, Casalone C, Maguiña JL, Escobedo AA, Hidalgo M, Bandeira AC, Mattar S, Cardona-Ospina JA, Suárez JA. Rodriguez-Morales AJ, et al. Front Trop Dis. 2021 May 4;2:676905. doi: 10.3389/fitd.2021.676905. eCollection 2021. Front Trop Dis. 2021. PMID: 34010366 Free PMC article. No abstract available.
Challenges in Emerging and Reemerging Arboviral Diseases: The Examples of Oropouche and Yellow Fever.
Rodriguez-Morales AJ, Sah R, Silva-Ramos CR, Pava-Garzón DM. Rodriguez-Morales AJ, et al. Pathogens. 2025 Jun 23;14(7):621. doi: 10.3390/pathogens14070621. Pathogens. 2025. PMID: 40732669 Free PMC article.

See all "Cited by" articles

References

1. Rodriguez-Morales AJ, Cardona-Ospina JA, Gutiérrez-Ocampo E, Villamizar-Peña R, Holguin-Rivera Y, Escalera-Antezanaet JP, et al. Clinical, laboratory and imaging features of COVID-19: a systematic review and meta-analysis. Travel Med Infect Dis. 2020;34:101623. - PMC - PubMed
1. Rodriguez-Morales AJ, Bonilla-Aldana DK, Balbin-Ramon GJ, Rabaan AA, Ranjit Sah R, Paniz-Mondolfi A, et al. History is repeating itself, a probable zoonotic spillover as a cause of an epidemic: the case of 2019 novel coronavirus. Infez Med. 2020;28(1):3–5. - PubMed
1. Bracken MB. Genomic epidemiology of complex disease: the need for an electronic evidence-based approach to research synthesis. Am J Epidemiol. 2005;162(4):297–301. doi: 10.1093/aje/kwi200. - DOI - PubMed
1. Porta M. Molecular epidemiology. In: Porta M, editor. A dictionary of epidemiology. Oxford: Oxford University Press; 2014.
1. Tang P, Croxen MA, Hasan MR, Hsiao WW, Hoang LM. Infection control in the new age of genomic epidemiology. Am J Infect Control. 2017;45(2):170–179. doi: 10.1016/j.ajic.2016.05.015. - DOI - PubMed

Publication types

Actions

LinkOut - more resources

Full Text Sources
- Europe PubMed Central
- PubMed Central
Research Materials
- NCI CPTC Antibody Characterization Program
Miscellaneous
- NCI CPTAC Assay Portal

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Genomic Epidemiology and Recent Update on Nucleic Acid-Based Diagnostics for COVID-19

Affiliations

Genomic Epidemiology and Recent Update on Nucleic Acid-Based Diagnostics for COVID-19

Authors

Affiliations

Abstract

Conflict of interest statement

Similar articles

Cited by

References

Publication types

LinkOut - more resources

Full Text Sources

Research Materials

Miscellaneous