TY - JOUR
T1 - Evaluating Saliva Sampling with Reverse Transcription Loop-mediated Isothermal Amplification to Improve Access to SARS-CoV-2 Diagnosis in Low-Resource Settings
AU - Suwarti, Suwarti
AU - Zanjabila, Sabighoh
AU - Bonifacius,
AU - Da Costa, Yacobus
AU - Bogh, Claus
AU - Subekti, Decy
AU - Jeny, Jeny
AU - Dewi, Ayu Madri
AU - Nuraeni, Nunung
AU - Rahardjani, Mutia
AU - Elyazar, Iqbal
AU - Nelwan, Erni J.
AU - Shankar, Anuraj H.
AU - Baird, J. Kevin
AU - Hamers, Raph L.
N1 - Funding Information:
Financial support: The study is funded by the COVID-19 Research Response Fund of the University of Oxford (0009308). A. H. S., J. K. B. and R. L. H. are supported by the Wellcome Trust Africa Asia Programme Vietnam (106680/Z/14/Z).
Publisher Copyright:
Copyright © 2022 The author(s).
PY - 2022/8
Y1 - 2022/8
N2 - Standard diagnosis of SARS-CoV-2 by nasopharyngeal swab (NPS) and real-time reverse transcriptase-polymerase chain reaction (PCR) requires a sophisticated laboratory, skilled staff, and expensive reagents that are difficult to establish and maintain in isolated, low-resource settings. In the remote setting of tropical Sumba Island, eastern Indonesia, we evaluated alternative sampling with fresh saliva (FS) and testing with colorimetric loop-medicated isothermal amplification (LAMP). Between August 2020 and May 2021, we enrolled 159 patients with suspected SARS-CoV-2 infection, of whom 75 (47%) had a positive PCR on NPS (median cycle threshold [Ct] value: 27.6, interquartile range: 12.5–37.6). PCR on FS had a sensitivity of 72.5% (50/69, 95% confidence interval [CI]: 60.4–82.5) and a specificity of 85.7% (66/77, 95% CI: 75.9–92.6), and positive (PPV) and negative (NPV) predictive values of 82.0% (95% CI: 0.0–90.6) and 77.6% (95% CI: 67.3–86.0), respectively. LAMP on NPS had a sensitivity of 68.0% (51/75, 95% CI: 56.2–78.3) and a specificity of 70.8% (63/84, 95% CI: 58.9–81.0), with PPV 70.8% (95% CI: 58.9-81.0) and NPV 72.4% (95% CI: 61.8–81.5%). LAMP on FS had a sensitivity of 62.3% (43/69, 95% CI: 49.8–73.7%) and a specificity of 72.7% (56/77, 95% CI: 61.4–82.3%), with PPV 67.2% (95% CI: 54.3–78.4) and NPV 68.3% (95% CI: 57.1–78.1%). LAMP sensitivity was higher for NPS and FS specimens with high viral loads (87.1% and 75.0% for Ct value, 26, respectively). Dried saliva on filter paper was stable for 4 days at room temperature. LAMP on either NPS or FS could offer an accessible alternative for SARS-CoV-2 diagnosis in low-resource settings, with potential for optimizing sample collection and processing, and selection of gene targets.
AB - Standard diagnosis of SARS-CoV-2 by nasopharyngeal swab (NPS) and real-time reverse transcriptase-polymerase chain reaction (PCR) requires a sophisticated laboratory, skilled staff, and expensive reagents that are difficult to establish and maintain in isolated, low-resource settings. In the remote setting of tropical Sumba Island, eastern Indonesia, we evaluated alternative sampling with fresh saliva (FS) and testing with colorimetric loop-medicated isothermal amplification (LAMP). Between August 2020 and May 2021, we enrolled 159 patients with suspected SARS-CoV-2 infection, of whom 75 (47%) had a positive PCR on NPS (median cycle threshold [Ct] value: 27.6, interquartile range: 12.5–37.6). PCR on FS had a sensitivity of 72.5% (50/69, 95% confidence interval [CI]: 60.4–82.5) and a specificity of 85.7% (66/77, 95% CI: 75.9–92.6), and positive (PPV) and negative (NPV) predictive values of 82.0% (95% CI: 0.0–90.6) and 77.6% (95% CI: 67.3–86.0), respectively. LAMP on NPS had a sensitivity of 68.0% (51/75, 95% CI: 56.2–78.3) and a specificity of 70.8% (63/84, 95% CI: 58.9–81.0), with PPV 70.8% (95% CI: 58.9-81.0) and NPV 72.4% (95% CI: 61.8–81.5%). LAMP on FS had a sensitivity of 62.3% (43/69, 95% CI: 49.8–73.7%) and a specificity of 72.7% (56/77, 95% CI: 61.4–82.3%), with PPV 67.2% (95% CI: 54.3–78.4) and NPV 68.3% (95% CI: 57.1–78.1%). LAMP sensitivity was higher for NPS and FS specimens with high viral loads (87.1% and 75.0% for Ct value, 26, respectively). Dried saliva on filter paper was stable for 4 days at room temperature. LAMP on either NPS or FS could offer an accessible alternative for SARS-CoV-2 diagnosis in low-resource settings, with potential for optimizing sample collection and processing, and selection of gene targets.
UR - http://www.scopus.com/inward/record.url?scp=85137291350&partnerID=8YFLogxK
U2 - 10.4269/ajtmh.22-0230
DO - 10.4269/ajtmh.22-0230
M3 - Article
AN - SCOPUS:85137291350
SN - 0002-9637
VL - 107
SP - 284
EP - 290
JO - American Journal of Tropical Medicine and Hygiene
JF - American Journal of Tropical Medicine and Hygiene
IS - 2
ER -