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\begin{document}

\title{Biomarker Development Trial to test the diagnostic accuracy of EUA
approved RT-PCR assay and a Laboratory Developed LAMP SARS-CoV-2 test in
paired nasopharyngeal, saliva, and urine samples}



\author[1]{Ana Purcell-Wiltz}%
\author[2]{Fernando Tadeu Zamuner}%
\author[1]{Karem Caraballo}%
\author[1]{Lorena De Jesus}%
\author[1]{Yaima Miranda}%
\author[1]{Denise Ortiz}%
\author[1]{Amanda García Negrón}%
\author[1]{Andrea Cortés}%
\author[3]{Adriana Baez}%
\author[4]{Josefina Romaguera}%
\author[4]{Ivonne Jiménez-Velázquez}%
\author[4]{Alberto Ortiz}%
\author[4]{Jorge Acevedo Canabal}%
\author[4]{Liliana Viera}%
\author[5]{David Sydranski}%
\author[1]{Rafael Guerrero-Preston}%
\affil[1]{LifeGene BioMarks Inc Puerto Rico}%
\affil[2]{Johns Hopkins Medical Institutions Campus}%
\affil[3]{University of Puerto Rico School of Medicine}%
\affil[4]{University of Puerto Rico Medical Sciences Campus}%
\affil[5]{Johns Hopkins School of Medicine}%


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  \date{May 22, 2024}


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\begin{abstract}
As the SARS-CoV-2 pandemic virus has spread throughout the world,
millions of positive cases of COVID-19 have been registered and, even
though there are millions of people already vaccinated against
SARS-CoV-2, a large part of the global population remains vulnerable to
contracting the virus. Given the difficulty of massive sample collection
in Puerto Rico and the restrictions to perform the molecular test to
detect SARS-CoV-2, this study aims to evaluate the diagnostic accuracy
of the TaqPath RT-PCR COVID-19 kit and a LAMP SARS-CoV-2 Laboratory
Developed Test in paired nasopharyngeal, saliva, and urine samples.
Automated RNA extraction was performed in the KingFisher Flex
instrument, whilst PCR quantification of SARS-CoV-2 on the 7500 Fast Dx
RT-PCR instrument using the TaqPath RT-PCR COVID-19 molecular test. The
PCR data was interpreted by the COVID-19 Interpretive Software from
Applied Biosystems and statistically analyzed with Cohen's kappa
coefficient (k). Cohen's kappa coefficient (k) for paired nasal and
saliva samples was found to be 0.52, showing moderate agreement. Nasal
and saliva samples displayed concordance and it was determined that
saliva samples had a higher viral load. Another objective was to compare
the positive or negative result of the RT-PCR with the positive or
negative result of LifeGene-Biomarks SARS-CoV-2 Rapid Colorimetric LAMP
LDT, which resulted in 90\% concordance. Due to this, the use of saliva
and LifeGene-Biomarks SARS-CoV-2 Rapid Colorimetric LAMP test is
suggested for further evaluation as an alternative to nasal, urine, and
RT-PCR tests for the detection of SARS-CoV-2, since it can be easily
used in clinics, hospitals, the workplace, and at home, optimizing the
surveillance and collection process, which helps mitigate the global
public health and socioeconomic damage caused by airborne pandemics.%
\end{abstract}%



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