Validating the inactivation of viral pathogens with a focus on SARS-CoV-2 to safely transfer samples from high-containment laboratories

Introduction

Pathogen leak from a high-containment laboratory seriously threatens human safety, animal welfare, and environmental security. Transportation of pathogens from a higher (BSL4 or BSL3) to a lower (BSL2) containment laboratory for downstream experimentation requires complete pathogen inactivation. Validation of pathogen inactivation is necessary to ensure safety during transportation. This study established a validation strategy for virus inactivation.

Methods

SARS-CoV-2 wild type, delta, and omicron variants underwent heat treatment at 95°C for 10 minutes using either a hot water bath or a thermocycler. To validate the inactivation process, heat-treated viruses, and untreated control samples were incubated with A549-hACE2 and Vero E6-TMPRSS2-T2A-ACE2 cells. The cells were monitored for up to 72 hours for any cytopathic effects, visually and under a microscope, and for virus genome replication via RT-qPCR. The quality of post-treated samples was assessed for suitability in downstream molecular testing applications.

Results

Heat treatment at 95°C for 10 minutes effectively inactivated SARS-CoV-2 variants. The absence of cytopathic effects, coupled with the inability of virus genome replication, validated the efficacy of the inactivation process. Furthermore, the heat-treated samples proved to be qualified for COVID-19 antigen testing, RT-qPCR, and whole-genome sequencing.

Discussion

By ensuring the safety of sample transportation for downstream experimentation, this validation approach enhances biosecurity measures. Considerations for potential limitations, comparisons with existing inactivation methods, and broader implications of the findings are discussed.

Evaluation of Omnigene-Sputum for Preservation of Sputum Samples for Diagnosis of Mycobacterium tuberculosis

In several low-income countries, the transport of sputa could take up to one week to reach the laboratories, resulting in increased contamination rates and a loss of growth. The aim of this study was to evaluate the effect of the OMNIgene-SPUTUM in preserving Mycobacterium tuberculosis on sputum samples simulating three hypothetical scenarios for conservation and/or decontamination: (1) sputum was mixed with OMN and conserved at room temperature for five days and then processed for culture (OMN); (2) sputum cultures followed the routine standing operating procedure at day 0 (STD); and (3) sputum samples were kept at room temperature for five days and mixed with the standard decontamination reagent (SDT5) and then processed for culture. The positivity rate based on smear microscopy was 36.4%, 29.1%, and 27.3% for STD, STD5, and OMN, respectively. The proportion of positive results by liquid culture (MGIT) was 39.1% (43/110) for STD, 26.4% (29/110) for STD5, and 20.0% for OMN (22/110). The overall concordance of liquid culture results was 51.8% (57/110): 37.3% (41/110) for negative results, 11.8% (13/110) for MTBC growth, and 2.7% (3/110) for contaminated results. The OMN arm showed better performance in solid culture than in liquid culture, with a notable reduction in contaminated results.

Investigation of the effects of pneumatic tube transport system on routine biochemistry, hematology, and coagulation tests in Ankara City Hospital

OBJECTIVES

Academics are far from a consensus regarding the effects of pneumatic tube system (PTS) delivery on sample integrity and laboratory test results. As for the reasons for conflicting opinions, each PTS is uniquely designed, sample tubes and patient characteristics differ among studies. This study aims to validate the PTS utilized in Ankara City Hospital for routine chemistry, coagulation, and hematology tests by comparing samples delivered via PTS and porter.

METHODS

The study comprises 50 healthy volunteers. Blood samples were drawn into three biochemistry, two coagulation, and two hemogram tubes from each participant. Each of the duplicate samples was transferred to the emergency laboratory via Swiss log PTS (aka PTS-immediately) or by a porter. The last of the biochemistry tubes were delivered via the PTS, upon completion of coagulation of the blood (aka PTS-after). The results of the analysis in these groups were compared with multiple statistical analyses.

RESULTS

The study did not reveal any correlation between the PTS and serum hemolysis index. There were statistically significant differences in several biochemistry tests. However, none of them reached the clinical significance threshold. Basophil and large unidentified cell (LUC) tests had poor correlations (r=0.47 and r=0.60; respectively) and reached clinical significance threshold (the average percentages of bias, 10.2%, and 15.4%, respectively). The remainder of the hematology and coagulation parameters did not reach clinical significance level either.

CONCLUSIONS

The modern PTS validated in this study is safe for sample transportation for routine chemistry, coagulation, and hematology tests frequently requested in healthy individuals except for basophil and LUC.

Effects of Refrigeration at 5°C for Long Periods of Time on Bovine Ear Skin as a Strategy to Transport Biological Material and Isolate Fibroblasts to Use in the Nuclear Transfer

Animal cloning is an important technique used to produce clones from valuable farm animals, to rescue animals in risk of extinction, and for producing transgenic animals. The objective of this work was to evaluate the effects of refrigeration on bovine ear skin as a strategy to transport biological material for long periods of time to isolate viable fibroblasts. Ears from eight cows were collected after death and stored for 30 days at 5°C. On days 0, 2, 4, 7, 14, 21, and 30, skin biopsies were cultured in vitro for fibroblast isolation. The time for first fibroblast outgrowth, time to reach 100% confluence. and cell concentration before freezing were observed for each period. In addition, plasma membrane integrity, cell apoptosis, and necrosis in cells were evaluated through fluorescent colorant combination in a flow cytometer from all periods after thawing. Fibroblasts obtained after 30 days of storage, considered a critical period, were tested for embryo production using nuclear transfer (NT) with micromanipulators. All time points allowed for cell culture. The time of cell growth onset was longer in samples refrigerated for 14, 21, and 30 days. The time to reach confluence also increased with longer refrigeration periods. Cells from day 0 reached confluence in 24 ± 2 days, while day 30 cells took 31 ± 0 days. Cell concentration and viability dropped with increased storage time and freezing/thawing, respectively. It was found that a long period of sample storage results in cell damage, making cultivation more difficult and decreasing cell viability post-thawing and cell concentration. However, when cells from day 30 were used as nuclei donors in NT, a 26.05% blastocyst rate after 7 days in culture was obtained. In conclusion, refrigeration at 5°C was shown to be efficient in maintaining viable tissue for up to 30 days, and fibroblasts isolated can be used for cloned embryo production.

An Unstructured Supplementary Service Data System for Daily Tracking of Patient Samples and Diagnostic Results in a Diagnostic Network in Malawi: System Development and Field Trial

Background

Diagnostics in many low- and middle-income countries are conducted through centralized laboratory networks. Samples are collected from patients at remote point-of-care health facilities, and diagnostic tests are performed at centralized laboratories. Sample transportation systems that deliver diagnostic samples and test results are crucial for timely diagnosis and treatment in such diagnostic networks. However, they often lack the timely and accurate data (eg, the quantity and location of samples prepared for collection) required for efficient operation.

Objective

This study aims to demonstrate the feasibility, adoption, and accuracy of a distributed data collection system that leverages basic mobile phone technology to gather reports on the quantity and location of patient samples and test results prepared for delivery in the diagnostic network of Malawi.

Methods

We designed a system that leverages unstructured supplementary service data (USSD) technology to enable health workers to submit daily reports describing the quantity of transportation-ready diagnostic samples and test results at specific health care facilities, free of charge with any mobile phone, and aggregate these data for sample transportation administrators. We then conducted a year-long field trial of this system in 51 health facilities serving 3 districts in Malawi. Between July 2019 and July 2020, the participants submitted daily reports containing the number of patient samples or test results designated for viral load, early infant diagnosis, and tuberculosis testing at each facility. We monitored daily participation and compared the submitted USSD reports with program data to assess system feasibility, adoption, and accuracy.

Results

The participating facilities submitted 37,771 reports over the duration of the field trial. Daily facility participation increased from an average of 50% (26/51) in the first 2 weeks of the trial to approximately 80% (41/51) by the midpoint of the trial and remained at or above 80% (41/51) until the conclusion of the trial. On average, more than 80% of the reports submitted by a facility for a specific type of sample matched the actual number of patient samples collected from that facility by a courier.

Conclusions

Our findings suggest that a USSD-based system is a feasible, adoptable, and accurate solution to the challenges of untimely, inaccurate, or incomplete data in diagnostic networks. Certain design characteristics of our system, such as the use of USSD, and implementation characteristics, such as the supportive role of the field team, were necessary to ensure high participation and accuracy rates without any explicit financial incentives.

Investigation of particle transfer to sampler covers during the transportation of samples

This study investigated the effects of particle transfer to the covers of aerosol samplers during transportation of wood dust and welding fume samples. Wood dust samples were collected in a sanding chamber using four sampler types: closed-face cassettes (CFC), CFC with Accu-CAP inserts, disposable inhalable samplers (DIS), and Institute of Occupational Medicine (IOM). Welding fumes were collected in a walk-in chamber using the same samplers, with Solu-Sert replacing Accu-CAP. The samples were divided into two groups, with one group transported by air and the other by land. They were returned in the same manner and analyzed gravimetrically for wood dust and chemically for welding fumes. For wood dust, IOM showed a significantly higher percentage of particles transferred to the covers compared with the other samplers regardless of the transportation mode (p < 0.0001; 64% by air and 15% by land), while other samplers showed less than or close to 10% (3.5-12%). When the percentages of particle transfer to the covers were compared between the air and land transportation, both IOM and CFC samples showed differences between modes of transportation, while others did not. For welding fumes, most samples (61% of samples for copper [Cu] and 76% of samples for manganese [Mn]) showed nondetectable amounts of the analyte on the covers. For all samplers, the particle transfer to the covers for both transportation modes ranged from 0.2-33% for Cu and less than 4.5% for Mn. Overall, this study confirms that particle transfer to sampler covers during transport highly depends upon the transportation mode and sampler type for wood dust, whereas particle transfer seems minimal for welding fumes. The findings of this study are based on two materials and limited sample sizes. Further investigation considering different industry types and tasks, particle size ranges, and materials might be necessary. Nevertheless, occupational professionals should account for this transfer when handling and analyzing samples in practice.

Comparison of pneumatic tube system with manual transport for routine chemistry, hematology, coagulation and blood gas tests

BACKGROUND

The pneumatic tube system (PTS) is commonly used in modern clinical laboratories to provide quick specimen delivery. However, its impact on sample integrity and laboratory testing results are still debatable. In addition, each PTS installation and configuration is unique to its institution. We sought to validate our Swisslog PTS by comparing routine chemistry, hematology, coagulation and blood gas test results and sample integrity indices between duplicate samples transported either manually or by PTS.

METHODS

Duplicate samples were delivered to the core laboratory manually by human courier or via the Swisslog PTS. Head-to-head comparisons of 48 routine chemistry, hematology, coagulation and blood gas laboratory tests, and three sample integrity indices were conducted on 41 healthy volunteers and 61 adult patients.

RESULTS

The PTS showed no impact on sample hemolysis, lipemia, or icterus indices (all p<0.05). Although alkaline phosphatase, total bilirubin and hemoglobin reached statistical significance (p=0.009, 0.027 and 0.012, respectively), all had very low average bias which ranged from 0.01% to 2%. Potassium, total hemoglobin and percent deoxyhemoglobin were statistically significant for the neonatal capillary tube study (p=0.011, 0.033 and 0.041, respectively) but no biases greater than ±4% were identified for these parameters. All observed differences of these 48 laboratory tests were not clinically significant.

CONCLUSIONS

The modern PTS investigated in this study is acceptable for reliable sample delivery for routine chemistry, hematology, coagulation and blood gas (in syringe and capillary tube) laboratory tests.

Stability of 35 biochemical and immunological routine tests after 10 hours storage and transport of human whole blood at 21°C

Background

Suitable procedures for transport of blood samples from general practitioners to hospital laboratories are requested. Here we explore routine testing on samples stored and transported as whole blood in lithium-heparin or serum tubes.

Methods

Blood samples were collected from 106 hospitalized patients, and analyzed on Architect c8000 or Advia Centaur XP for 35 analytes at base line, and after storage and transport of whole blood in lithium-heparin or serum tubes at 21 ± 1°C for 10 h. Bias and imprecision (representing variation from analysis and storage) were calculated from values at baseline and after storage, and differences tested by paired t-tests. Results were compared to goals set by the laboratory.

Results

We observed no statistically significant bias and results within the goal for imprecision between baseline samples and 10-h samples for albumin, alkaline phosphatase, antitrypsin, bilirubin, creatinine, free triiodothyronine, γ-glutamyl transferase, haptoglobin, immunoglobulin G, lactate dehydrogenase, prostate specific antigen, total carbon dioxide, and urea. Alanine aminotransferase, amylase, C-reactive protein, calcium, cholesterol, creatine kinase, ferritin, free thyroxine, immunoglobulin A, immunoglobulin M, orosomucoid, sodium, transferrin, and triglycerides met goals for imprecision, though they showed a minor, but statistically significant bias in results after storage. Cobalamin, folate, HDL-cholesterol, iron, phosphate, potassium, thyroid stimulating hormone and urate warranted concern, but only folate and phosphate showed deviations of clinical importance.

Conclusions

We conclude that whole blood in lithium-heparin or serum tubes stored for 10 h at 21 ± 1°C, may be used for routine analysis without restrictions for all investigated analytes but folate and phosphate.

[Preanalytical phase and accreditation: acceptance criteria for samples of multisite laboratory]

Performing high quality analyses in order to help physicians in their diagnoses and to ensure better patient care: this represents our routine mission for clinical lab. To achieve this goal, all steps from sampling to the final data transfer must be controlled. The preanalytical phase is one of the most crucial, but also one of the most complicated, especially in the context of a consolidated laboratory network. Transport conditions, delays, temperature, regulatory constraints are all criteria that we need to take into consideration in order to comply to ISO 15189, section 5.4. In this context, our laboratory would like to address the following issues: to control the transport conditions in order to guarantee optimal preservation of the samples, and to define an internal process and identify non-conforming situations linked to delay in sample delivery. An original study dealing with the stability in whole blood of common clinical chemistry and immunochemistry tests in defined transport conditions (delays, temperature, tube position) was performed on a panel of 100 patients' samples. This panel is intended to be a good reflection of the patients usually seen in multi-site laboratory. We observed that most of the analytes (35 of 41) were stable in whole blood; however, some of them demonstrated instability over time. All these results were integrated into our collection manual.