COVID diagnostics by molecular methods: A systematic review of nucleic acid based testing systems

Parijat Das; Sudipto Mondal; Soumik Pal; Samadrita Roy; Anju Vidyadharan; Rajneesh Dadwal; Sanjay Bhattacharya; Deepak Kumar Mishra; Mammen Chandy

doi:10.1016/j.ijmmb.2021.05.012

COVID diagnostics by molecular methods: A systematic review of nucleic acid based testing systems

Indian J Med Microbiol. 2021 Jul;39(3):271-278. doi: 10.1016/j.ijmmb.2021.05.012. Epub 2021 Jun 10.

Authors

Parijat Das¹, Sudipto Mondal², Soumik Pal², Samadrita Roy², Anju Vidyadharan², Rajneesh Dadwal², Sanjay Bhattacharya², Deepak Kumar Mishra³, Mammen Chandy⁴

Affiliations

¹ Department of Microbiology, Tata Medical Center, 700160, Kolkata, India. Electronic address: parijat.das@tmckolkata.com.
² Department of Microbiology, Tata Medical Center, 700160, Kolkata, India.
³ Department of Laboratory Hematology, Tata Medical Center, 700160, Kolkata, India.
⁴ Department of Clinical Hematology and Director, Tata Medical Center, Kolkata, 700160, India.

Abstract

Background: The selection of appropriate kit and PCR equipment for the detection of SARS CoV-2 is critically important in view of many options available in the diagnostic market. Since last year many molecular products are available for COVID-19 diagnostics., some of these diagnostics have become commercially available for healthcare workers and clinical laboratories. However, the diagnostic technologies have specific limitations and reported several false-positive and false-negative cases, especially during the early stages of kit development and use. The current article addresses these and other relevant questions important to the medical microbiologists running or aspiring to run COVID diagnostic services using PCR and related technologies.

Methods: In this Systematic Review we follow Preferred Reporting Items for a Systematic Review and Meta-analysis of Diagnostic Test Accuracy Studies (PRISMA-DTA). A total of 258 citations retrieved, among those 77 peer reviewed articles was assessed for eligibility, and 181 studies were excluded. Based on inclusion criteria final data extraction was done.

Results: The question of diagnostic dilemma has also been addressed in view of discordant results between assays, inter-test variability, repeat testing requirements in specific settings and inconclusive or indeterminate results. Kit efficiency was satisfactory for all assays and the estimates varied within sample types and technology. Using clinical samples, we observed some variations in detection rate between kits. Importantly, none of the assays showed cross-reactivity with other respiratory (corona) viruses, except as expected for the SARS-CoV-1 E-gene.

Conclusions: We conclude SARS CoV-2 related molecular assays differed considerably in performance. Hence we need to understand importance of molecular diagnostics test interpretation in light of the latest pandemic virus.

Keywords: CBNAAT; COVID; Isothermal amplification; RT-PCR; SARS-CoV-2.

Publication types

Systematic Review

MeSH terms

COVID-19 / metabolism*
Health Personnel
Humans
Reverse Transcriptase Polymerase Chain Reaction
Sensitivity and Specificity