The Effects of “Dry Swab” Incubation on SARS-CoV-2 Molecular Testing

Background Widespread testing of SARS-CoV-2 has resulted in shortages of collection devices and transport media. We evaluated the stability of flocked swabs inoculated with SARS-CoV-2-containing specimen incubated dry (i.e., without transport medium) at room temperature. Methods A pool of SARS-CoV-2 positive specimen was used to inoculate flocked swabs. Five swabs were placed immediately into universal transport media (UTM) following inoculation, and tested immediately (day 0). Fifteen of the swabs were placed into sterile 15-mL conical tubes and incubated at room temperature for 1, 2, or 7 days. Following incubation, swabs were hydrated in separate vials of UTM and tested. This protocol was repeated for viral transport media (VTM) and saline. As a comparison, a series of swabs was prepared and tested in parallel, but stored in the corresponding liquid transport media (UTM, VTM, or saline) and incubated at room temperature. Testing was performed at 1, 2, and 7 days postinoculation in duplicate. All molecular testing was performed using the Roche cobas SARS-CoV-2 assay. Results All dry swabs tested on days 1, 2, and 7 provided results that were within 2 cycle thresholds (CTs) of the average CT values for swabs hydrated in the same media and tested on day 0. There was no statistical difference in CT values between swabs incubated in liquid media versus dry swabs incubated at room temperature prior to hydration in liquid media. Conclusions The utilization of “dry swabs” may simplify specimen collection, negate the need for liquid transport media, and mitigate safety risks while preserving the accuracy of testing.

Automation and validation of a MALDI-TOF MS (Mass-Fix) replacement of immunofixation electrophoresis in the clinical lab

ObjectivesA matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) method (Mass-Fix) as a replacement for gel-based immunofixation (IFE) has been recently described. To utilize Mass-Fix clinically, a validated automated method was required. Our aim was to automate the pre-analytical processing, improve positive specimen identification and ergonomics, reduce paper data storage and increase resource utilization without increasing turnaround time.MethodsSerum samples were batched and loaded onto a liquid handler along with reagents and a barcoded sample plate. The pre-analytical steps included: (1) Plating immunopurification beads. (2) Adding 10 μl of serum. (3) Bead washing. (4) Eluting the immunoglobulins (Igs), and reducing to separate the heavy and light Ig chains. The resulting plate was transferred to a second low-volume liquid handler for MALDI plate spotting. MALDI-TOF mass spectra were collected. Integrated in-house developed software was utilized for sample tracking, driving data acquisition, data analysis, history tracking, and result reporting. A total of 1,029 residual serum samples were run using the automated system and results were compared to prior electrophoretic results.ResultsThe automated Mass-Fix method was capable of meeting the validation requirements of concordance with IFE, limit of detection (LOD), sample stability and reproducibility with a low repeat rate. Automation and integrated software allowed a single user to process 320 samples in an 8 h shift. Software display facilitated identification of monoclonal proteins. Additionally, the process maintains positive specimen identification, reduces manual pipetting, allows for paper free tracking, and does not significantly impact turnaround time (TAT).ConclusionsMass-Fix is ready for implementation in a high-throughput clinical laboratory.

Can the Wondfo® SARS-CoV-2 IgM/IgG antibodies be used as a rapid diagnostic test?

Background: An outbreak of novel coronavirus (SARS-CoV-2) disease (COVID-19) has rapidly spread worldwide. The aim of this study was to evaluate and validate the performance of the Wondfo® lateral-flow immunochromatographic assay that detect SARS-CoV-2- IgG, IgM antibodies (Wondfo® IC), using the results obtained by the fluorescence immunoassay test as reference diagnostic. Material and methods: 97 serum specimens collected and analyzed by four independent laboratories of Sergipe/Brazil was used for validated the Wondfo® SARS-CoV-2 IgM/IgG antibodies test. The COVID-19 positive serum specimens were determined by fluorescence immunoassay technique, used as reference standard. Results: An overall of 97 serum specimens show 39 (39/97) SARS-CoV-2 IgG positive specimens, 33 (33/97) SARS-CoV-2 IgM positive specimen and 25 non-reagent specimens (25/97). However, the Wondfo® IC assay detected only 9 (9/97) IgM/IgG positive specimen and 25 (25/97) no-reagent specimen. A weak correlation was found between the outcomes of the Wondfo® IC assay and fluorescence test. The accuracy between the two tests was 32.08%. The sensitivity, specificity, positive predictive value, and negative predictive value of Wondfo® IC assay were of 11.12%, 100%, 100% and 25.27%, respectively. Moreover, no false positive sample was determinate, whereas 88.89% of false negative results were found. Conclusion: The Wondfo® IC test failed in providing a quick, valid, and reliable results and appears not to be a good alternative for clinical use in detecting pandemic coronavirus. However, if the limitations of the rapid test are known, some correction factors can be used in order to adjust the epidemiological data.

Pooled Saliva Specimens for SARS-CoV-2 Testing

We evaluated saliva (SAL) specimens for SARS-CoV-2 RT-PCR testing by comparison of 459 prospectively paired nasopharyngeal (NP) or mid-turbinate (MT) swabs from 449 individuals with the aim of using saliva for asymptomatic screening. Samples were collected in a drive-through car line for symptomatic individuals (N=380) and in the emergency department (ED) (N=69). The percent positive and negative agreement of saliva compared to nasopharyngeal swab were 81.1% (95% CI: 65.8% – 90.5%) and 99.8% (95% CI: 98.7% – 100%), respectively. The sensitivity increased to 90.0% (95% CI: 74.4% – 96.5%) when considering only samples with moderate to high viral load (Cycle threshold (Ct) for the NP <=34). Pools of five saliva specimens were also evaluated on three platforms: bioMérieux NucliSENS easyMAG with ABI 7500Fast (CDC assay), Hologic Panther Fusion, and Roche COBAS 6800. The median loss of signal upon pooling was 2-4 Ct values across the platforms. The sensitivity of detecting a positive specimen in a pool compared with testing individually was 100%, 93%, and 95% for CDC 2019-nCoV Real-Time RT-PCR, Panther Fusion® SARS-CoV-2 assay, and cobas® SARS-CoV-2 test respectively, with decreased sample detection trending with lower viral load. We conclude that although pooled saliva testing, as collected in this study, is not quite as sensitive as NP/MT testing, saliva testing is adequate to detect individuals with higher viral loads in an asymptomatic screening program, does not require swabs or viral transport media for collection, and may help to improve voluntary screening compliance for those individuals averse to various forms of nasal collections.

Evaluating efficiency of pooling specimens for PCR-based detection of COVID-19

ABSTRACTIn the age of a pandemic, such as the ongoing one caused by SARS-CoV-2, the world faces limited supply of tests, PPE and reagents, and factories are struggling to meet the growing demands. This study aimed to evaluate the efficacy of pooling specimen for testing of SARS-CoV-2 virus, to determine whether costs and resource savings could be achieved without impacting the sensitivity of the testing. Ten specimens were pooled for testing, containing either one or two known positive specimen of varying viral concentrations. Pooling specimens did not affect the sensitivity of detecting SARS-CoV-2, and the PCR cycle threshold (Ct) between testing of pooling specimen and subsequent individual testing was not significantly different using paired t-test. This study also identified cost savings garnered from pooling of specimen for testing at 4 differing prevalence rates, ranging from 0.1-10%. Pooling specimens to test for COVID-19 infection in low prevalence areas or in low risk population can dramatically decrease the resources burden on lab operations by up to 80%. This paves the possibility for large-scale population screening, allowing for assured policy decisions by governmental bodies to ease lockdown restrictions in areas with low incidence of infection, or with lower risk populations.

The effect of infection of hard ticks Ixodes ricinus (L.) and Ixodes persulcatus Sch. (Acari: Ixodinae) with the causative agent of Lyme borreliosis (Borrelia burgdorferi s.l.) on their host search activity (using attractants)

A series of lab experiments with ticks (collected by flagging in the natural biotopes in North-Western Russia) was carried out in order to study tick reaction to attractants imitating the smell of a potential host. All the ticks that showed either positive or negative reactions to attractants in the experiment were individually PCR-tested for B. burgdorferi s.l DNA.The percent of Borrelia - positive specimen among hungry active adult I. ricinus and I. persulcatus ticks was higher than that among hungry passive ones. The discovered infection of I. persulcatus females by B. burgdorferi s. l. was 56% from which 67% were active and 36% were passive ticks. Total infection of adult ticks was 45% (61% active, 24% passive ticks). Infection of I. ricinus females was 60%, 69% in active individuals and 48% in passive, total infection of adult ticks was 56% (70% in active, 43% in passive). Synthetic kyromonas (attractant) composed of 1-octen-3-ol and a mixture of ethyl myristate-methyl salicylate (1:1), simulated the odour of the host in the experiment, attracted up to 70% of adults of I. ricinus and up to 80% of I. persulcatus. It can be assumed that this percent of adult ticks reflect an overall number of individuals searching for a hosts during the season of activity in natural biotopes.

Laboratory Confirmation Human Specimens Suspected of Anthrax in Kulonprogo District of Yogyakarta Special Region

Anthrax is an acute zoonoses infectious disease caused by Bacillus anthracis bacteria. Bacillus anthracis had ability to form endospores for self-defense. Anthrax infectioncouldbedividedintofourtypesnamelyskinanthrax,gastrointestinalanthrax, anthrax of the respiratory tract (lung) and meningitis anthrax. The examination was performed to confirm the diagnosis of patients suspected of being infected with Bacillus anthracis. The examination methods consisted of culture for whole blood spesimens, konvensional polymerase chain reaction (PCR) on growing colonies and whole blood specimens without growing colony, and enzyme-linked immunosorbent assay (ELISA) for blood serum spesimens. The 6 cultured specimens, there were 2 colony-growing specimens with 1 identical colony with Bacillus anthracis colonies. The colonies confirmed with PCR and only 1 positive as Bacillus anthracis pathogens. The 6 specimens examined there was a positive specimen of Bacillus anthracis pathogen.

Ebola Virus Ribonucleic Acid Detection in Semen More Than Two Years After Resolution of Acute Ebola Virus Infection

Among 149 men who survived Ebola virus disease (EVD) and donated semen 260–1016 days after EVD onset, Ebola virus (EBOV) ribonucleic acid (RNA) was detected in 13 (9%). Of 137 men who donated semen 2 years after EVD onset, 11 (8%) had an EBOV RNA-positive specimen. The mechanism underlying the persistence of EBOV RNA in semen is unclear, and it is unclear whether the detection of viral RNA represents the presence of infectious virus.

Burden of Nursing Home-Onset Clostridium difficile Infection in the United States: Estimates of Incidence and Patient Outcomes

Background. Approximately 4 million Americans receive nursing home (NH) care annually. Nursing home residents commonly have risk factors for Clostridium difficile infection (CDI), including advanced age and antibiotic exposures. We estimated national incidence of NH-onset (NHO) CDI and patient outcomes. Methods. We identified NHO-CDI cases from population-based surveillance of 10 geographic areas in the United States. Cases were defined by C difficile-positive stool collected in an NH (or from NH residents in outpatient settings or ≤3 days after hospital admission) without a positive stool in the prior 8 weeks. Medical records were reviewed on a sample of cases. Incidence was estimated using regression models accounting for age and laboratory testing method; sampling weights were applied to estimate hospitalizations, recurrences, and deaths. Results. A total of 3503 NHO-CDI cases were identified. Among 262 sampled cases, median age was 82 years, 76% received antibiotics in the 12 weeks prior to the C difficile-positive specimen, and 57% were discharged from a hospital in the month before specimen collection. After adjusting for age and testing method, the 2012 national estimate for NHO-CDI incidence was 112 800 cases (95% confidence interval [CI], 93 400–131 800); 31 400 (28%) were hospitalized within 7 days after a positive specimen (95% CI, 25 500–37 300), 20 900 (19%) recurred within 14–60 days (95% CI, 14 600–27 100), and 8700 (8%) died within 30 days (95% CI, 6600–10 700). Conclusions. Nursing home onset CDI is associated with substantial morbidity and mortality. Strategies focused on infection prevention in NHs and appropriate antibiotic use in both NHs and acute care settings may decrease the burden of NHO CDI.