Diagnostics and Public Health

Given the massive impact of diagnostics on public health, SPHP&L is pleased to announce a new section, "Diagnostics and Public Health".  Papers and studies focused on improving public health via objective, validated means of diagnosis of medical conditions are solicited. We are especially interesting in papers that apply evaluation science to means of diagnosis specifically aimed at improving accuracy and finding an objective balance between sensitivity, specificity, and cost for combined and integrative approaches to diagnostics. 

Papers are published by invitation only following blinded peer review.  To submit a manuscript for consideration, email title and draft abstract to info@ipak-edu.org.

2022

Editorial

James Lyons-Weiler, PhD

Editor-in-Chief

The Use of Arbitrary and Generalized Ct Values in COVID-19 Non-Quantitative Reverse Transcriptase Polymerase Chain Reaction (nonQ-RT-PCR) Testing Must End

James Lyons-Weiler, PhD

IPAK/IPAK-EDU

FULL TEXT AVAILABLE

An elementary problem with the polymerase chain reaction (PCR) – recognized at its inception – is that non-specific binding of PCR primers to arbitrary targets will cause off-target amplification. This is true whether the target sequence is a gene sequence within a single individual, and it is true when the target is viral, such as the SARS-CoV-2 viral genome in a clinical sample. PCR is used routinely to produce enough copies, or amplicons, of the target nucleotide molecule so the sequence can be determined using either Sanger sequencing or Next-Generation sequencing... (Full Text)

 

2022

Lee, 2022

Peer-reviewed.

Submitted 8/30/2022

Accepted 10/26/2022

Evidence-Based Evaluation of PCR Diagnostics for SARS-CoV-2 and the Omicron Variants by Sanger Sequencing

Sin Hang Lee

Milford Diagnostics, LLC

FULL TEXT AVAILABLE

Abstract

Both SARS-CoV-2 and SARS-CoV-1 initially appeared in China and spread to other parts of the world. SARS-CoV-2 has generated a COVID-19 pandemic causing more than 6 million human deaths worldwide, while the SARS outbreak quickly ended in six months with a global total of 774 reported deaths. One of the factors contributing to this stunning difference in the outcome between these two outbreaks is the inaccuracy of the RT-qPCR tests for SARS-CoV-2, which generated a large number of false-negative and false-positive test results that have misled patient management and public health policymakers. This article presents Sanger sequencing evidence to show that the RT-PCR diagnostic protocol established in 2003 for SARS-CoV-1 can in fact detect SARS-CoV-2 accurately due to the well-known ability of the PCR to amplify similar, homologous sequences. Using nested RT-PCR followed by Sanger sequencing to retest 50 patient samples collected in January 2022 and sold as RT-qPCR positive reference confirmed that 21 (42%) were false-positive. Routine sequencing of the RT-PCR amplicons of the receptor-binding domain (RBD) and N-terminal domain (NTD ) of the Spike protein (S) gene is a tool to avoid false positives and to study the effects of amino acid mutations and multi-allelic single nucleotide polymorphisms (SNPs) in the circulating variants for investigation of their impacts on vaccine efficacies, therapeutics and diagnostics.

Copyright © The Authors — Published Under the Creative Commons License Share/Alike (see https://creative commons.org/licenses/)

Correspondence

Sin Hang Lee; email: shlee01@snet.net Tel. 203 878-1438

Milford Molecular Diagnostics Laboratory

2044 Bridgeport Avenue, Milford, CT 06460, USA

Keywords
SARS-CoV-2; SARS-CoV-1; RT-PCR; Sanger sequencing; RT-qPCR; receptor-binding domain (RBD); N-terminal domain (NTD); Omicron; multi-allelic SNPs; false-positive

Peer Review: Single-Blinded (author was blinded to reviewers)

EDITOR’S NOTE: This article has been updated to change the incorrect reference to “false positive rate” to “false discovery rate”.  This change does not alter the conclusions or interpretation of the study. (11/1/2022)