SARS-CoV-2: Challenges in Reconverting Diagnostic Laboratories to Combat the Pandemic
ABSTRACT Coronavirus disease 2019 (COVID-19) was first detected in Mexico in February 2020. Even though health authorities did not perceive then the value of viral detection tests, we anticipated the demand for them. We set up to develop an expeditious severe acute respiratory syndrome coronavirus 2...
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2022-12-01
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| Series: | Microbiology Spectrum |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.01477-22 |
| _version_ | 1798003871642025984 |
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| author | Hugo Alberto Barrera Saldaña Carolina Rivera Santiago Raúl Rodríguez Palacios |
| author_facet | Hugo Alberto Barrera Saldaña Carolina Rivera Santiago Raúl Rodríguez Palacios |
| author_sort | Hugo Alberto Barrera Saldaña |
| collection | DOAJ |
| description | ABSTRACT Coronavirus disease 2019 (COVID-19) was first detected in Mexico in February 2020. Even though health authorities did not perceive then the value of viral detection tests, we anticipated the demand for them. We set up to develop an expeditious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) molecular diagnostic service through the implementation of standardized protocols for biospecimen sampling, transportation, biobanking, preanalytical validation, and nucleic acids (NA) testing (NAT). Nasopharyngeal and oropharyngeal swabs collected in a special transportation medium were the biospecimens from which NAs were purified either manually or automatically. Viral RNA genome presence was determined using commercial SARS-CoV-2 detection kits (based on reverse transcription coupled with real-time PCR [RT-PCR]). Improvements in laboratory processing speed and reliability resulted from semi-automatizing laboratory processes and adopting a quality control/quality assurance system (QC/QA), respectively. NAs that were purified, either manually or automatically, were validated by preanalytical spectrophotometric characterization. Automated purification was less prone to contamination and reduced the processing time. The following six RT-PCR kits were evaluated for their convenience, specificity, sensitivity, time consumption, and required materials (in order, starting with the kit with the best results): RIDA gene and Viasure (tied), Vircell, LightMix, 1copy, and Logix Smart. Redesigning the laboratories’ working areas, equipment, fluxes of personnel and material, and personnel skills, and overemphasizing biosafety safeguards were major challenges encountered in the middle of the sanitary crisis. Adopting a QC/QA system, utilizing automatization processes, and working closely with health authorities were key factors in our success. IMPORTANCE Rearranging our diagnostic laboratories to improve the fight against a new unexpected, unpredictable, and sudden public health threat demanded that we move quickly to redesign not only the laboratory processes but also the distribution of space, personnel activities, and fluxes of material coming in and out. We also had to work closely with governmental health authorities to gain their trust in our technical competence. Gaining the confidence of the clients, i.e., mainly individuals, the human resource departments of factories and corporations sending employees for testing, and medical institutions, and implementing as much automatization as possible of processes, in which only officially approved reagents (for extraction and analysis of NA) were used to generate opportune trustable testing results, were key factors. Our laboratories have gathered a considerable amount of experience and significant number of solutions, considering our geographic contexts alongside this continuously morphing pandemic, validating many techniques that might help other laboratories find a better and more precise workflow. |
| first_indexed | 2024-04-11T12:14:33Z |
| format | Article |
| id | doaj.art-fede0e2f2d5b4e95a22198ced68d79af |
| institution | Directory Open Access Journal |
| issn | 2165-0497 |
| language | English |
| last_indexed | 2024-04-11T12:14:33Z |
| publishDate | 2022-12-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Microbiology Spectrum |
| spelling | doaj.art-fede0e2f2d5b4e95a22198ced68d79af2022-12-22T04:24:25ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972022-12-0110610.1128/spectrum.01477-22SARS-CoV-2: Challenges in Reconverting Diagnostic Laboratories to Combat the PandemicHugo Alberto Barrera Saldaña0Carolina Rivera Santiago1Raúl Rodríguez Palacios2Columbia Comercial, SA de CV, División Columbia Biotec, Tlalpan, Mexico City, MéxicoColumbia Comercial, SA de CV, División Columbia Biotec, Tlalpan, Mexico City, MéxicoVitagénesis, SA de CV, and Innbiogem SC at LANSEIDI-CONACyT, Monterrey, Nuevo León, MéxicoABSTRACT Coronavirus disease 2019 (COVID-19) was first detected in Mexico in February 2020. Even though health authorities did not perceive then the value of viral detection tests, we anticipated the demand for them. We set up to develop an expeditious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) molecular diagnostic service through the implementation of standardized protocols for biospecimen sampling, transportation, biobanking, preanalytical validation, and nucleic acids (NA) testing (NAT). Nasopharyngeal and oropharyngeal swabs collected in a special transportation medium were the biospecimens from which NAs were purified either manually or automatically. Viral RNA genome presence was determined using commercial SARS-CoV-2 detection kits (based on reverse transcription coupled with real-time PCR [RT-PCR]). Improvements in laboratory processing speed and reliability resulted from semi-automatizing laboratory processes and adopting a quality control/quality assurance system (QC/QA), respectively. NAs that were purified, either manually or automatically, were validated by preanalytical spectrophotometric characterization. Automated purification was less prone to contamination and reduced the processing time. The following six RT-PCR kits were evaluated for their convenience, specificity, sensitivity, time consumption, and required materials (in order, starting with the kit with the best results): RIDA gene and Viasure (tied), Vircell, LightMix, 1copy, and Logix Smart. Redesigning the laboratories’ working areas, equipment, fluxes of personnel and material, and personnel skills, and overemphasizing biosafety safeguards were major challenges encountered in the middle of the sanitary crisis. Adopting a QC/QA system, utilizing automatization processes, and working closely with health authorities were key factors in our success. IMPORTANCE Rearranging our diagnostic laboratories to improve the fight against a new unexpected, unpredictable, and sudden public health threat demanded that we move quickly to redesign not only the laboratory processes but also the distribution of space, personnel activities, and fluxes of material coming in and out. We also had to work closely with governmental health authorities to gain their trust in our technical competence. Gaining the confidence of the clients, i.e., mainly individuals, the human resource departments of factories and corporations sending employees for testing, and medical institutions, and implementing as much automatization as possible of processes, in which only officially approved reagents (for extraction and analysis of NA) were used to generate opportune trustable testing results, were key factors. Our laboratories have gathered a considerable amount of experience and significant number of solutions, considering our geographic contexts alongside this continuously morphing pandemic, validating many techniques that might help other laboratories find a better and more precise workflow.https://journals.asm.org/doi/10.1128/spectrum.01477-22SARS-CoV-2 diagnosislaboratory techniquescommercial RT-PCR kitsRT-PCR |
| spellingShingle | Hugo Alberto Barrera Saldaña Carolina Rivera Santiago Raúl Rodríguez Palacios SARS-CoV-2: Challenges in Reconverting Diagnostic Laboratories to Combat the Pandemic Microbiology Spectrum SARS-CoV-2 diagnosis laboratory techniques commercial RT-PCR kits RT-PCR |
| title | SARS-CoV-2: Challenges in Reconverting Diagnostic Laboratories to Combat the Pandemic |
| title_full | SARS-CoV-2: Challenges in Reconverting Diagnostic Laboratories to Combat the Pandemic |
| title_fullStr | SARS-CoV-2: Challenges in Reconverting Diagnostic Laboratories to Combat the Pandemic |
| title_full_unstemmed | SARS-CoV-2: Challenges in Reconverting Diagnostic Laboratories to Combat the Pandemic |
| title_short | SARS-CoV-2: Challenges in Reconverting Diagnostic Laboratories to Combat the Pandemic |
| title_sort | sars cov 2 challenges in reconverting diagnostic laboratories to combat the pandemic |
| topic | SARS-CoV-2 diagnosis laboratory techniques commercial RT-PCR kits RT-PCR |
| url | https://journals.asm.org/doi/10.1128/spectrum.01477-22 |
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