Large-Scale, In-House Production of Viral Transport Media To Support SARS-CoV-2 PCR Testing in a Multihospital Health Care Network during the COVID-19 Pandemic

The COVID-19 pandemic has severely disrupted worldwide supplies of viral transport media (VTM) due to widespread demand for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse transcription-PCR (RT-PCR) testing. In response to this ongoing shortage, we began production of VTM in-house in support of diagnostic testing in our hospital network. As our diagnostic laboratory was not equipped for reagent production, we took advantage of space and personnel that became available due to closure of the research division of our medical center. We utilized a formulation of VTM described by the CDC that was simple to produce, did not require filtration for sterilization, and used reagents that were available from commercial suppliers. Performance of VTM was evaluated by several quality assurance measures. Based on cycle threshold (CT ) values of spiking experiments, we found that our VTM supported highly consistent amplification of the SARS-CoV-2 target (coefficient of variation = 2.95%) using the Abbott RealTime SARS-CoV-2 Emergency Use Authorization (EUA) assay on the Abbott m2000 platform. VTM was also found to be compatible with multiple swab types and, based on accelerated stability studies, able to maintain functionality for at least 4 months at room temperature. We further discuss how we met logistical challenges associated with large-scale VTM production in a crisis setting, including use of a staged assembly line for VTM transport tube production.

Sensitivity of Rapid Antigen Testing and RT-PCR Performed on Nasopharyngeal Swabs versus Saliva Samples in COVID-19 Hospitalized Patients: Results of a Prospective Comparative Trial (RESTART)

Saliva sampling could serve as an alternative non-invasive sample for SARS-CoV-2 diagnosis while rapid antigen tests (RATs) might help to mitigate the shortage of reagents sporadically encountered with RT-PCR. Thus, in the RESTART study we compared antigen and RT-PCR testing methods on nasopharyngeal (NP) swabs and salivary samples. We conducted a prospective observational study among COVID-19 hospitalized patients between 10 December 2020 and 1 February 2021. Paired saliva and NP samples were investigated by RT-PCR (Cobas 6800, Roche-Switzerland, Basel, Switzerland) and by two rapid antigen tests: One Step Immunoassay Exdia® COVID-19 Ag (Precision Biosensor, Daejeon, Korea) and Standard Q® COVID-19 Rapid Antigen Test (Roche-Switzerland). A total of 58 paired NP-saliva specimens were collected. A total of 32 of 58 (55%) patients were hospitalized in the intensive care unit, and the median duration of symptoms was 11 days (IQR 5-19). NP and salivary RT-PCR exhibited sensitivity of 98% and 69% respectively, whereas the specificity of these RT-PCRs assays was 100%. The NP RATs exhibited much lower diagnostic performance, with sensitivities of 35% and 41% for the Standard Q® and Exdia® assays, respectively, when a wet-swab approach was used (i.e., when the swab was diluted in the viral transport medium (VTM) before testing). The sensitivity of the dry-swab approach was slightly better (47%). These antigen tests exhibited very low sensitivity (4% and 8%) when applied to salivary swabs. Nasopharyngeal RT-PCR is the most accurate test for COVID-19 diagnosis in hospitalized patients. RT-PCR on salivary samples may be used when nasopharyngeal swabs are contraindicated. RATs are not appropriate for hospitalized patients.

Effect of different storage conditions on COVID-19 RT-PCR results

Reliable and rapid detection of severe acute respiratory syndrome coronavirus 2 in laboratory setting is critical to control the pandemic. We aimed to an evaluated polymerase chain reaction (PCR) efficiency of nasopharyngeal swabs stored in viral transport medium (VTM) in different temperatures. Ninety swabs taken into VTM were analyzed at the first hour, then divided into two groups with similar numbers of positive and negative samples. Positive samples of each group were also subgrouped according to Fam CT values as low CT (<25), medium CT (25-32), and high CT (32-38) groups. One group was stored at 4°C, while the other was stored at room temperature, PCR analyses were repeated every 24 h for 5 days and on Day 12. There was a total of 30 positive samples (12 low CT, 11 medium CT, and 7 high CT). The CT values of both groups remained unchanged in first 3 days while the CT values of the room temperature group increased after the third day. All of the positive samples remained positive in both groups for the first 5 days. On the 12th day, the total number of positives decreased to 8 in the room temperature group and 11 in the 4°C groups. All the low CT samples remained positive in both groups. In conclusion, it is safe to store positive samples in room temperature for up to 5 days. Only samples with high viral loads remain positive for 12 days, regardless of whether stored at room temperature or 4°C. Negative samples don't turn to invalid if stored in VTM.

Liquid-based cytological and immunohistochemical study of nasopharyngeal swab from persons under investigation for SARS-CoV-2 infection

Introduction

We describe cytologic and immunohistologic findings in virus transport medium on cases under investigation of SARS‐CoV‐2 infection.

Methods

Cytologic findings in cases under investigation of SARS‐CoV‐2 infection from one hundred consecutive nasopharyngeal swab were reviewed. Immunohistochemistry and SARSCoV‐2 RT‐PCR determination were performed to detect virus.

Results

No viral inclusions were noted in squamous cells obtained from virus transport medium. Immunohistochemical study with monoclonal antibody against SARS‐CoV‐2 viral nucleoprotein showed positivity in squamous cells. No positivity was present in others cellular components.

Conclusions

SARS‐CoV‐2 predominantly localizes squamous cells in cytology samples of patients with RT‐PCR positive determination of SARSCoV‐2. The results of the current study support the notion that the nasopharyngeal region is the anatomical station that SARS‐CoV‐2 infects first, and the infection can lead to the migration of the virus into the lower airways.

Practical strategies for SARS-CoV-2 RT-PCR testing in resource-constrained settings

Alternatives to nasopharyngeal sampling are needed to increase capacity for SARS-CoV-2 testing. Among 275 participants, we piloted the collection of nasal mid-turbinate swabs amenable to self-testing, including polyester flocked swabs as well as 3D-printed plastic lattice swabs, placed into viral transport media or an RNA stabilization agent. Flocked nasal swabs identified 104/121 individuals who were PCR-positive for SARS-CoV-2 by nasopharyngeal sampling (sensitivity 87%, 95% CI 79-92%), missing those with low viral load (<10⁶ viral copies/mL). 3D-printed nasal swabs showed similar sensitivity. When nasal swabs were placed directly into RNA preservative, the mean 1.4 log decrease in viral copies/uL compared to nasopharyngeal samples was reduced to <1 log, even when samples were left at room temperature for up to 7 days. We also evaluated pooling strategies that involved pooling specimens in the lab versus pooling swabs at the point of collection, finding both successfully detected samples with >10⁵ viral copies/mL.

Prevalence of Genotype Patterns Associated With High-Risk Human Papillomavirus in Cervical Lesions

Background Cervical lesions, often linked to high-risk human papillomavirus (HR-HPV) infection, pose a significant public health concern globally. Human HPV is considered the principal etiological factor in the development and transformation of pre-malignant lesions of the cervix leading to cervical carcinoma. The global distribution of HPV genotypes exhibits significant variability, liable to be influenced by the intricate interplay of geographical and biological factors among different HPV types and host immunogenetic elements. Owing to limited research addressing the genotypic distribution of HR-HPV in females with cervical lesions in the western zone of India, this study aims to bridge this gap by providing the prevalence of HR-HPV genotypes in women diagnosed with cervical lesions in this zone. Methodology This observational, cross-sectional study was performed in the Laboratory for Genotype Detection in the western zone of India. The study population comprised a total of 215 females in the age range of 18 to 60 years. A thorough examination of clinical specimens was conducted employing molecular techniques for HPV genotyping using TRUPCR® HPV-HR with a 16/18 Genotyping Kit. DNA Extraction was done using 3B Blackbio Biotech India Ltd. as per the standard protocol. The statistical analysis was performed using SPSS version 28 (IBM Corp., Armonk, NY, USA), and continuous variables were compared using Student's t-test. Results The overall prevalence of HR-HPV in women with cervical lesions in the western zone of India was 62.32% (134/215). The most prevalent genotype was HPV16 at 92/134 (68.65%), followed by HPV18 at 33/134 (24.62%) and HPV52 at 9/134 (6.7%). The overall prevalence of single type was 56.71% (76/134). The most prevalent genotype combination after HPV18 + 59 (29.85%) at 40/134 was HPV52 + 39 + 51 (13.43%) at 18/134. HR-HPV infection was found to be significantly (p < 0.05) associated with factors such as having three or more children, having a lower socioeconomic status, residing in rural areas, and being in a pre-menopausal stage. Conclusions This study focused on assessing the prevalence of the genotypes associated with HR-HPV infection, providing valuable insights into the epidemiology of cervical lesions in the western zone of India. The findings revealed high-risk genotype HPV16 to be the most prevalent type, followed by HPV18 and HPV52. The most prevalent genotype combinations were HPV18 + 59 and HPV52 + 39 + 51. The results of the study would potentiate the wealth of epidemiological data related to HPV infection in cervical lesions and could be employed for guiding future interventions and preventive strategies through orientation programs.