Analysis by real‐time PCR of five transport and conservation mediums of nasopharyngeal swab samples to COVID‐19 diagnosis in Santiago of Chile

Barrera-Avalos, Carlos; Luraschi, Roberto; Vallejos‐Vidal, Eva; Figueroa, Maximiliano; Arenillas, Esteban; Barria, Daniela; Hernández, Felipe; Mateluna, Carlos; Mena, Javier; Rioseco, Claudia; Torrent, Claudia; Claudio, Vergara; Gutierrez, Gaby; Quiroz, Javiera; Alarcón, Javiera; Cartagena, Julio; Cayunao, Javiera; Mella-Torres, Andrea; Santibáñez, Álvaro; Tapia, Sebastián M.; Undurraga, Alejandro; Vargas, Deborah; Wong, Valentina; Inostroza-Molina, Ailen; Valdés, Daniel; Imarai, Mónica; Acuña-Castillo, Claudio; Reyes-López, Felipe E.; Sandino, Ana María

doi:10.1002/jmv.27446

Cited by 13 publications

(16 citation statements)

References 32 publications

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“…For instance, Penrod et al, 2021 evaluated five transport media (VTM (containing 29.5g/l tryptose phosphate, 5g/l gelatin, 10,000U/l penicillin, 10,000U/l streptomycin, 25μg/l Fungizone), Copan Universal Transport Medium™, Becton Dickinson Liquid Amies Elution Swab (Eswab) Collection/Transport System, Remel Microtest™ M4RT® Multi-Microbe Media, and sterile 0.9% (w/v) sodium chloride) and reported that they all had equivalent sensitivity/specificity in COVID-19 diagnosis. Similar findings were obtained by several other studies which confirmed that PBS and normal saline not only maintained the stability and integrity of viral RNA (for up to 1 month when stored at -80ºC and 7 days at 4ºC) but also provided results that matched those obtained from other media(3,7,9,10). On the contrary, a different study demonstrated conflicting results of viral samples in 0.9% (w/v) saline not performing as well as commercially available transport media over a 72-hour storage period, although comparisons in this study were of samples during stock outs of VTM with those where VTM was available, rather than for split or standardized samples(11).…”

Section: Introductionsupporting

confidence: 89%

“…On the contrary, a different study demonstrated conflicting results of viral samples in 0.9% (w/v) saline not performing as well as commercially available transport media over a 72-hour storage period, although comparisons in this study were of samples during stock outs of VTM with those where VTM was available, rather than for split or standardized samples(11). Furthermore, a recent report showed that PBS was less sensitive compared to other media such as DNA/RNA shield™, highlighting the need for further research to ascertain the stability of this alternative transport medium(3).…”

Section: Introductionmentioning

confidence: 99%

“…During the initial stages of the Coronavirus Disease-2019 (COVID-19) pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), public health authorities across the globe resorted to mass testing as a strategy to contain the fast-spreading disease (1). A standard COVID-19 test requires a Nasopharyngeal (NP) and/or Oropharyngeal (OP) specimen from the upper airway, from which virus RNA is extracted and detected through quantitative reverse transcription-Polymerase Chain Reaction (qRT-PCR) (2,3). Additionally, the accuracy of a test result is dependent on the integrity of the pre-analytical step, which involves sample collection, storage, transport, and maintenance in cold chain.…”

Section: Introductionmentioning

confidence: 99%

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Validation of saline, PBS and a locally produced VTM at varying storage conditions to detect the SARS-CoV-2 virus by qRT-PCR

Ngetsa

Osoti

Okanda

et al. 2022

Preprint

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Coronavirus Disease-2019 tests require a Nasopharyngeal (NP) and/or Oropharyngeal (OP) specimen from the upper airway, from which virus RNA is extracted and detected through quantitative reverse transcription-Polymerase Chain Reaction (qRT-PCR). The viability of the virus is maintained after collection by storing the NP/OP swabs in Viral Transport Media (VTM). We evaluated the performance of four transport media: locally manufactured (REVITAL) Viral Transport Media (RVTM), Standard Universal Transport Media (SUTM), PBS and 0.9% (w/v) NaCl (normal saline). We used laboratory cultured virus to evaluate: i) viral recovery and maintaining integrity at different time periods and temperatures; ii) stability in yielding detectable RNA consistently for all time points and conditions; and iii) their overall accuracy. Four vials of SARS-CoV-2 cultured virus (2 high and 2 low concentration samples) and 1 negative control sample were prepared for each media type (SUTM, RVTM, PBS and normal saline) and stored at the following temperatures, -80°C, 4°C, room temperature (25°C) and 37°C for 7 days. Viral Ribonucleic acid (RNA) extractions and qRT-PCR were done on the following days after inoculation with the cultured virus, days 1, 2, 3, 4 and 7 to assess virus stability and viral recovery. CT values fell over time at room temperature, but normal saline, PBS, RVTM and SUTM all showed comparable performance in maintaining virus integrity and stability allowing for the detection of SARS-CoV-2 viral RNA. Overall, this study demonstrated that normal saline, PBS and the locally manufactured VTM can be used for COVID-19 sample collection and testing, thus expanding the range of SARS-CoV-2 viral collection media.

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Section: Introductionsupporting

confidence: 89%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Validation of saline, PBS and a locally produced VTM at varying storage conditions to detect the SARS-CoV-2 virus by qRT-PCR

Ngetsa

Osoti

Okanda

et al. 2022

Preprint

View full text Add to dashboard Cite

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“…A47532 and E, N, and RdRp gene for Allplex™ 2019-nCoV Assay, Seegene, Seúl, South Korea. Cat, No RP10244Y) as previously reported by our group ( 13 ) and other authors ( 14 , 15 ). The detection of virus-specific mutations by Real-Time RT-PCR kit (Bioneer, Daejeon, South Korea.…”

Section: Diagnostic Assessmentsupporting

confidence: 66%

Description of Symptoms Caused by the Infection of the SARS-CoV-2 B.1.621 (Mu) Variant in Patients With Complete CoronaVac Vaccination Scheme: First Case Report From Santiago of Chile

Barrera-Avalos

Luraschi

Acuña-Castillo

et al. 2022

Front. Public Health

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Vaccine administration is one of the most efficient ways to control the current coronavirus disease 2019 (COVID-19) pandemic. However, the appearance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants can avoid the immunity generated by vaccines. Thus, in patients with a complete vaccine schedule, the infection by SARS-CoV-2 may cause severe, mild, and asymptomatic manifestations of the disease. In this case report, we describe for the first time the clinical symptoms of four patients (three symptomatic; one asymptomatic) from Santiago of Chile, with a complete vaccination schedule with two doses of CoronaVac (Sinovac Life Science) infected with the variant of interest (VOI) B.1.621 (Mu). They were compared with four unvaccinated patients, who had a higher prevalence of symptoms after infection compared to vaccinated patients. In the CoronaVac-vaccinated group, an 80-year-old patient who registered various comorbidities required Invasive mechanical ventilation for 28 days with current home medical recovery discharge. By contrast, in the unvaccinated group, a 71-year-old presented more symptoms with more than 45 days of Invasive mechanical ventilation, which continues to date, presenting greater lung damage than the vaccinated hospitalized patient. This first report evidence differences in the clinical symptomatology of patients vaccinated and non-vaccinated infected with the VOI B.1.621 (Mu) and suggest the protective effects of CoronaVac against this variant.

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“…Samples were transported to the Universidad de Santiago Laboratory in a viral transport medium (GenoSur, Chile). Total RNA was extracted as previously described [ 8 ]. The detection of SARS-CoV-2 was carried out using the ORF1ab gene probe (TaqMan™ 2019nCoV Assay Kit v1 (Thermo Fisher Scientific, Reference code: A47532) using a one-step strategy as previously reported by our group [ 8 ].…”

Section: Methodsmentioning

confidence: 99%

First Identification of Reinfection by a Genetically Different Variant of SARS‐CoV‐2 in a Homeless Person from the Metropolitan Area of Santiago, Chile

Acuña-Castillo

Vidal

Inostroza-Molina

et al. 2022

Journal of Environmental and Public Health

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The identification and tracking of SARS-CoV-2 infected patients in the general population are essential components of the global strategy to limit the COVID-19 viral spread, specifically for maintaining traceability and suppressing the resurgence of local outbreaks. Public health programs that include continuous RT-qPCR testing for COVID-19 in the general population, viral sequencing, and genomic surveillance for highly contagious forms of the virus have allowed for the identification of SARS-CoV-2 infections and reinfections. This work identified SARS-CoV-2 reinfection in a homeless person, which occurred 58 days after the first COVID-19 diagnosis. Genomic sequencing identified a different Nextstrain classification clade (20A and 20B) and PANGO lineage, with a divergence of 4 single nucleotide variants (SNVs) in S and ORF1ab genes, suggesting reinfection by different viral variants. This study is the first from the great metropolitan area of Santiago, Chile, one of the top ten countries in the world to live during the COVID-19 pandemic. We support the importance of performing intensive genomic surveillance programs in the whole population and high-risk groups, such as homeless people, nearly 20 thousand people in Chile, and have limited access to health care services and poor viral traceability.

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Analysis by real‐time PCR of five transport and conservation mediums of nasopharyngeal swab samples to COVID‐19 diagnosis in Santiago of Chile

Cited by 13 publications

References 32 publications

Validation of saline, PBS and a locally produced VTM at varying storage conditions to detect the SARS-CoV-2 virus by qRT-PCR

Validation of saline, PBS and a locally produced VTM at varying storage conditions to detect the SARS-CoV-2 virus by qRT-PCR

Description of Symptoms Caused by the Infection of the SARS-CoV-2 B.1.621 (Mu) Variant in Patients With Complete CoronaVac Vaccination Scheme: First Case Report From Santiago of Chile

First Identification of Reinfection by a Genetically Different Variant of SARS‐CoV‐2 in a Homeless Person from the Metropolitan Area of Santiago, Chile

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