Systematic Review and Meta-analysis of Real-time Polymerase Chain Reaction assay for the detection of COVID-19 from clinical samples in low-and middle-income countries: Protocol

Abstract

allow for appropriate management.The main objective of this systematic review is to identify, appraise and summarise the published evidence on the diagnostic performance and effectiveness of SARS-CoV-2 virus in the diagnosis of current or previous COVID-19 using real-time polymerase chain reaction (RT-PCR) assay in low-and middle-income countries (LMICs).
Methods: We will search MEDLINE/PubMed, EMBASE, BIOSIS, LILACS, Cochrane Infectious Diseases Group Specialised Register (CIDG SR), Global Health, and CINAHL for published studies for the diagnosis of COVID-19 using realtime polymerase chain reaction assay in LMICs There will be no restriction regarding the language, date of publication, and publication status.We will include retrospective, cross-sectional and cohort observational studies will be included in the review.
Selection of studies, data extraction and management, assessment of risk of bias, and quality of evidence will be performed by two independent reviewers (EB and BC).A third researcher (GM) will be consulted in case of discrepancies.Depending on the availability and quality of the data, a meta-analysis will be performed.
Otherwise, findings will be qualitatively reported.

Background
Since the first discovery and reported case of a novel coronavirus in Wuhan, China in December 2019, which spread rapidly across the world.The virus was named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the disease that it causes, COVID-19.Since then, several countries have seen a rise of confirmed cases, first coming from cross-border travel and later by subsequent community transmission [1].In the early stage of the pandemic, the World Health Organization (WHO) stated that testing for the virus should be considered for symptomatic patients on the basis of the suspicion and likelihood of COVID-19, as well as in those who are asymptomatic or minimally symptomatic but who have been in contact with confirmed cases [2].SARS-CoV-2 testing is a major bottleneck globally, especially in low-and middle-income countries (LMICs).As the public health sector struggles to meet the increasing need for tests, LMICs are now seeing a rise in COVID-19 cases, particularly in South Asia, South America, and Africa [3] Globally, 70% of decisions with patient care are based on laboratory results [4].

Accurate diagnosis of COVID-19 is a key component in addressing the pandemic.
Diagnostics can play an important role in the containment of COVID-19, enabling the rapid implementation of control measures that limit the spread through case identification, isolation, and contact tracing (i.e., identifying people that may have come in contact with an infected patient).
Diagnosis of COVID-19 in LMICs is confronted with major challenges such as limited resources, inadequate capacity, untrained laboratory personnel, lack of laboratory personnel in testing facilities despite having a pool of unemployed and qualified experts, inadequate funding and lack of policies.Other challenges include the limited number of laboratories with the appropriate biosafety level (BSL) classification and available safety cabinets for processing samples associated with SARS-CoV-2, obtaining governmental approval to conduct SARS-CoV-2 testing remains challenging, the high cost of testing and the high patient-borne costs present a major barrier to testing in LMICs.SARS-CoV-2 has a single-stranded positive sense RNA genome that is ∼30,000 nucleotides in length [5,6].Of 104 strains sequenced between December 2019 and mid-February 2020, 99.9% sequence homology was observed, but, more recently, changes in the viral genome have been catalogued, showing a higher sequence diversity [7,8].Nucleic acid testing is the primary method of diagnosing COVID-19 [9].A number of reverse transcription polymerase chain reaction kits have been designed to detect SARS-CoV-2 genetically.RT-PCR involves the reverse transcription of SARS-CoV-2 RNA into complementary DNA (cDNA) strands, followed by amplification of specific regions of the cDNA [10,11].
Reverse-transcriptase polymerase chain reaction assay detects the presence of SARS-CoV-2 virus usually through the use of methods that recognise and amplify SARS-CoV-2 viral nucleic acid.SARS CoV-2 virus testing is usually done in a specialised laboratory setting using respiratory samples, such as nasopharyngeal swabs.
The purpose of this systematic review is to identify, appraise and summarise the published evidence on the diagnostic performance and effectiveness of SARS-CoV-2 virus in the diagnosis of current or previous COVID-19 using real-time polymerase chain reaction (RT-PCR) platform which is the current gold standard for diagnosis.
The review will also explore the uptakes of this RT-PCR assay in LMICs for the testing/diagnosis across different continents of the globe, and whether testing is laboratory based or done at point of care.

This systematic review protocol has been developed based on the Preferred
Reporting Items for Systematic Reviews and Meta-Analyses Protocols (PRISMA-P) guidelines [18], which is available in Additional file 1.The systematic review protocol was registered with the International Prospective Register of Systematic Reviews (PROSPERO) database (registration ID: CRD42021271894).We will search MEDLINE/PubMed, EMBASE, BIOSIS, LILACS, Cochrane Infectious Diseases Group Specialised Register (CIDG SR), Global Health, and CINAHL using the search strategy and terms used for one of the databases as detailed in Additional file 2. This will be used for published studies that used RT-PCR assays for detecting SARS-CoV-2 in LMICs.The electronic search will be tailored for each database to include its specific keywords and MeSH terms.

Searching other resources
To avoid missing relevant studies to be included, searching other sources by looking through reference lists of relevant reviews and selected studies, searching websites of a relevant organization, performing forward citation searching of relevant articles using the PubMed related articles feature, Google Scholar, Cochrane Library, turning research into practice (TRIP), dissertations, Conference Proceedings Citation Index -Science (CPCI-S), the portal of the WHO International Clinical Trials Registry Platform (www.who.int/trialsearch) to identify ongoing trials, the World Health Organization and Centers for Disease Control and Prevention websites.
We will also contact leading researchers at the Foundation for Innovative New Diagnostics (FIND).There will be no restriction regarding the language, date of cDNA: complementary deoxyribonucleic acid; CPCI-S: Conference Proceedings Citation Index-Science; COVID-19: Corona virus disease or 2019 novel coronavirus or 2019-nCoV; EMBASE: Excerpta Medica database; FIND : Foundation for Innovative New Diagnostics; GRADE: Grades of Recommendation, Assessment, Development and Evaluation; LMICs: low-and middle-income countries; LTBI: Latent tuberculosis infection; MEDLINE: Medical Literature Analysis and Retrieval System Online; MeSH: Medical Subject Headings; PRISMA: Preferred Reporting Items for Systematic Reviews and Meta-Analysis; PRISMA -P: Preferred Reporting Items for Systematic Reviews and Meta-Analysis Protocols; QUADAS-2: Quality assessment of diagnostic accuracy studies-2 tool; RNA: Ribonucleic acid; SARS CoV-2: Severe acute respiratory syndrome coronavirus 2; SROC: summary receiver operating characteristics; TRIP: Turning research into practice; WHO ICTRP: WHO International Clinical Trials Registry Platform.