Epidemiological evaluation of viruses related to acute respiratory infections in a university campus using the LAMP technique

Authors

DOI:

https://doi.org/10.33448/rsd-v12i14.44662

Keywords:

SARS-CoV-2; Influenza A virus; Influenza B virus.

Abstract

Objective: SARS-CoV-2, Influenza A (IAV) and Influenza B (IBV) epidemiological investigation in the community served by the MonitoraCOVID program of the Federal University of Minas Gerais (UFMG) in 2022 through the standardization and validation of the LAMP technique. Method: Nasopharyngeal swab samples were used in the LAMP reactions, performed simultaneously under the same conditions with visual reading. For epidemiological investigation, 10% of the monthly amount assisted by MonitoraCOVID were tested. Results: LAMP reactions demonstrated sensitivity of 84.0% and 85.2% for SARS-CoV-2 and IAV respectively. The prevalence of IBV was low for analysis of analytical parameters. The specificity obtained was 100% in the three reactions. The annual positivity rate found was: SARS-CoV-2 - 28.7%, IAV - 1.6%, IBV - 0.0%. Indeterminate results were found for SARS-CoV-2 and IAV (0.8% each). Conclusion: The LAMP assay was able to assess the epidemiology of respiratory viruses, and it could be applied in the diagnosis in other populations.

References

Alves, P. A., de Oliveira, E. G., Franco-Luiz, A. P. M., Almeida, L. T., Gonçalves, A. B., Borges, I. A., Richa, F. S., Rocha, R. P., Bezerra, M. F., Miranda, P., Capanema, F. D., Martins, H. R., Weber, G., Teixeira, S. M., Wallau, G. L., & Monte-Neto, R. L. (2021). Optimization and Clinical Validation of Colorimetric Reverse Transcription Loop-Mediated Isothermal Amplification, a Fast, Highly Sensitive and Specific COVID-19 Molecular Diagnostic Tool That Is Robust to Detect SARS-CoV-2 Variants of Concern. Front Microbiol, 12:3172.

Aoki, M. N., de Oliveira Coelho, B., Góes, L. G. B., Minoprio, P., Durigon, E. L., Morello, L. G., Marchini, F. K., Riediger, I. N., Debur, M. C., Nakaya, H. I., & Blandes, L. (2021). Colorimetric RT-LAMP SARS-CoV-2 diagnostic sensitivity relies on color interpretation and viral load. Scientific Reports, 11(1):1–10.

Bukasov, R., Dossym, D., & Filchakova, O. (2021). Detection of RNA viruses from influenza and HIV to Ebola and SARS-CoV-2: a review. Analytical Methods, 13: 34-55.

Carda, S., Invernizzi, M., Bavikatte, G., Bensmaïl, D., Bianchi, F., Deltombe, T., Draulans, N., Esquenazi, A., Francisco, G. E., Gross, R., Jacinto, L. J., Pérez, S. M., W O’dell., M. W., Reebye, R., Verduzco-Gutierreaz, M., Wissel, J., & Molteni, F. (2020). Covid-19 pandemic. What should physical and rehabilitation Medicine specialists do? A clinician’s perspective. Eur J Phys Rehabil Med, 56(4):515–24.

Chow, E. J., Uyeki, T. M., & Chu, H. Y. (2022). The effects of the COVID-19 pandemic on community respiratory virus activity. Nature Reviews Microbiology, 21:3.

Dudley, D. M., Newman, C. M., Weiler, A. M., Ramuta, M. D., Shortreed, C. G., Heffron, A. S., Accola, M. A., Rehrauner, W. M., Friedrich, T., & O’Connor, D. H. (2020). Optimizing direct RT-LAMP to detect transmissible SARS-CoV-2 from primary nasopharyngeal swab samples. PLoS One, 15(12), e0244882.

Eisen, A. K. A., Gularte, J. S., Demoliner, M., de Abreu Goés Pereira, V. M., Heldt, F. H., Filippi, M., Almeida, P. R., Hansen, A. W., Fleck, J. D., & Spilki, F. R. (2021). Low circulation of Influenza A and coinfection with SARS-CoV-2 among other respiratory viruses during the COVID-19 pandemic in a region of southern Brazil. J Med Virol, 93(7):4392–8.

Hu, X., Deng, Q., Li, J., Chen, J., Wang, Z., Zhang, X., Fang, Z., Li, H., Zhao, Y., Yu, P., Li, W., Wang, X., Li, S., Zhang, L., & Hou, T (2020). Development and Clinical Application of a Rapid and Sensitive Loop-Mediated Isothermal Amplification Test for SARS-CoV-2 Infection. mSphere, 5(4): e00808-20.

Krammer, F., Smith, G. J. D., Fouchier, R. A. M., Peiris, M., Kedzierska, K., Doherty, P. C., Palese, P., Shaw, M., Treanor, J., Wbster, R., & Garcia-Sastre, A. (2018). Influenza [Internet]. Vol. 4, Nature Reviews Disease Primers. Nature Publishing Group, p. 1–21.

Krishna, N. K., & Cunnion, K. M. (2012). Role of molecular diagnostics in the management of infectious disease emergencies. Med Clin North Am, 96(6):1067–78.

Landis, J. R. & Koch, G. G (1977). The Measurement of Observer Agreement for Categorical Data. Biometrics, 33 (1): 159.

Li, J, Lai, S, Gao, G. F., & Shi, W. (2021). The emergence, genomic diversity and global spread of SARS-CoV-2. Nature, 600(7889):408–18.

Li, Y., Fan, P, Zhou, S., & Zhang, L. (2017). Loop-mediated isothermal amplification (LAMP): A novel rapid detection platform for pathogens. Microb Pathog, 107:54-61.

Mahony, J. B., Petrich, A., & Smieja, M. (2011). Molecular diagnosis of respiratory virus infections. Crit Rev Clin Lab Sci, 48:217–49.

Mandu Baba, M., Bitew, M., Fokam, J., Lelo, E. A., Ahidjo, A., Asmamaw, K., Beloumou, G. A., Bulimo, W. D., Buratti, E., Chenwi, C., Dadi, H., D’Agaro, P., Conti, L., Fainguem, N., Gadzama, G., Maiuri, P., Majanaja, J., Meshack, W., Ndjolo, A., Nkenfou, C., Oderinde, B. S., Opanda, S. M., Segat, L., Stuani, C., Symekher, S., Takou, D., Tesfaye, K., Triolo, G., Tuki, K., Zacchigna, S., & Marcello, A (2021). Diagnostic performance of a colorimetric RT -LAMP for the identification of SARS-CoV-2: A multicenter prospective clinical evaluation in sub-Saharan Africa. EClinicalMedicine, 40:101101.

Ministério da Adricultura, Pecuária e Abastacimento (MAPA) (2015). Manual de Verificação de Desempenho de Métodos para Diagnóstico Molecular de Doenças Infecciosas na Rede Nacional de Laboratórios Agropecuários. MAPA/ACS, Brasília. 57p, 2015.

Nakauchi, M., Yoshikawa, T., Nakai, H., Sugata, K., Yoshikawa, A., Asano, Y., Ihira, M., Tashiro, M., & Kageyama, T (2011). Evaluation of reverse transcription loop-mediated isothermal amplification assays for rapid diagnosis of pandemic influenza A/H1N1 2009 virus. J Med Virol, 83(1):10–5.

Nguyen, T., Bang, D. D., & Wolff, A. (2019) Novel coronavirus disease (COVID-19): Paving the road for rapid detection and point-of-care diagnostics. Micromachines (Basel), 11(3):1–7.

Notomi, T., Okayama, H., Masubuchi, H., Yonekawa, T., Watanabe, K., Amino, N., & Hase, T. (2000). Loop-mediated isothermal amplification of DNA. Nucleic Acids Res, 28(12).

Organização Mundial da Saúde (OMS) (2022). Painel de controle Coronavirus (COVID-19). OMS, 29 jun. 2022. Disponível em: https://covid19.who.int/. Acesso em: 09 mar. 2023.

Pawlowski, C., Silvert, E., O’Horo, J. C., Lenehan, P. J., Challener, D., Gnass, E., Murugadoss, K., Ross, J., Speicher, L., Geyer, H., Venkatakrishnan, A. J., Badley, A. D., & Soundararajan, V. (2022). SARS-CoV-2 and influenza coinfection throughout the COVID-19 pandemic: an assessment of coinfection rates, cohort characteristics, and clinical outcomes. PNAS, 1(3): pgac071.

Pereira, A. S., Shitsuka, D. M., Parreira, F. J., & Shitsuka, R. (2018). Metodologia da pesquisa científica. [free e-book]. Santa Maria/RS. Ed. UAB/NTE/UFSM.

Peteranderl, C., Herold, S., & Schmoldt, C. (2016). Human Influenza Virus Infections. Semin Respir Crit Care Med, 37(4):487-500.

Rhoads, D., Peaper, D. R., She, R. C., Nolte, F. S., Wojewoda, C. M., Anderson, N. W., & Pritt, B. (2021). College of American Pathologists (CAP) Microbiology Committee Perspective: Caution Must Be Used in Interpreting the Cycle Threshold (Ct) Value. Clinical Infectious Diseases, 72(10):e685–6.

Silva, S. J. R., & Pena, L. (2021). Collapse of the public health system and the emergence of new variants during the second wave of the COVID-19 pandemic in Brazil. One Health, 13:100287.

Su, S., Wong, G., Shi, W., Liu, J., Lai, A. C. K., Zhou, J., Liu, W., Bi, Y., & Gao, G. (2016). Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses. Trends Microbiol, 24(6):490-502.

Takayama, I., Nakauchi, M., Takahashi, H., Oba, K., Semba, S., Kaida, A., Kubo, H., Saito, S., Nagata, S., Odagiri, T., & Kageyama, T. (2019) Development of real-time fluorescent reverse transcription loop-mediated isothermal amplification assay with quenching primer for influenza virus and respiratory syncytial virus. J Virol Methods, 267:53-58.

Wikramaratna, O. S., & Gupta, S (2009). Influenza outbreaks. Cell Microbiol, 11(7):1016–24.

Wilson-Davies, E. S. W., Mahanama, A. I. K., Samaraweera, B., Ahmed, N., Friar, S., & Pelosi, E. (2021). Concerns regarding the sensitivity of the OptiGene direct SARS-CoV-2 LAMP assay and its suitability for use in at-risk groups and hospital staff. Journal of Infection, 82(2):282–327.

Zhang, Y., & Tanner, N. A. (2020). Development of Multiplexed RT-LAMP for Detection of SARS-CoV-2 and Influenza Viral RNA doi: medRxiv preprint. medRxiv, 2020.10.26.20219972.

Zhuang, J., Yin, J., Lv, S., Wang, B., & Mu, Y. (2020). Advanced “lab-on-a-chip” to detect viruses – Current challenges and future perspectives. Biosens Bioelectron. 1:163:112291.

Published

27/12/2023

How to Cite

BRETZ , G. P. M. .; CAROBIM , N. V. .; FERNANDES , A. B. .; SABINO , A. de P. .; SOARDI , F. C. .; GOMES, K. B. . Epidemiological evaluation of viruses related to acute respiratory infections in a university campus using the LAMP technique. Research, Society and Development, [S. l.], v. 12, n. 14, p. e111121444662, 2023. DOI: 10.33448/rsd-v12i14.44662. Disponível em: https://rsdjournal.org/index.php/rsd/article/view/44662. Acesso em: 25 dec. 2024.

Issue

Section

Health Sciences