Molecular Detection of SARS-CoV-2 From Throat Swabs Performed With or Without Specimen Collection From the Tonsils: Protocol for a Multicenter Randomized Controlled Trial.

BACKGROUND: Testing for SARS-CoV-2 is essential to provide early COVID-19 treatment for people at high risk of severe illness and to limit the spread of infection in society. Proper upper respiratory specimen collection is the most critical step in the diagnosis of the SARS-CoV-2 virus in public settings, and throat swabs were the preferred specimens used for mass testing in many countries during the COVID-19 pandemic. However, there is still a discussion about whether throat swabs have a high enough sensitivity for SARS-CoV-2 diagnostic testing, as previous studies have reported a large variability in the sensitivity from 52% to 100%. Many previous studies exploring the diagnostic accuracy of throat swabs lack a detailed description of the sampling technique, which makes it difficult to compare the different diagnostic accuracy results. Some studies perform a throat swab by only collecting specimens from the posterior oropharyngeal wall, while others also include a swab of the palatine tonsils for SARS-CoV-2 testing. However, studies suggest that the palatine tonsils could have a tissue tropism for SARS-CoV-2 that may improve the SARS-CoV-2 detection during sampling. This may explain the variation of sensitivity reported, but no clinical studies have yet explored the differences in sensitivity and patient discomfort whether the palatine tonsils are included during the throat swab or not. OBJECTIVE: The objective of this study is to examine the sensitivity and patient discomfort of a throat swab including the palatine tonsils compared to only swabbing the posterior oropharyngeal wall in molecular testing for SARS-CoV-2. METHODS: We will conduct a randomized controlled study to compare the molecular detection rate of SARS-CoV-2 by a throat swab performed from the posterior oropharyngeal wall and the palatine tonsils (intervention group) or the posterior oropharyngeal wall only (control group). Participants will be randomized in a 1:1 ratio. All participants fill out a baseline questionnaire upon enrollment in the trial, examining their reason for being tested, symptoms, and previous tonsillectomy. A follow-up questionnaire will be sent to participants to explore the development of symptoms after testing. RESULTS: A total of 2315 participants were enrolled in this study between November 10, 2022, and December 22, 2022. The results from the follow-up questionnaire are expected to be completed at the beginning of 2024. CONCLUSIONS: This randomized clinical trial will provide us with information about whether throat swabs including specimens from the palatine tonsils will improve the diagnostic sensitivity for SARS-CoV-2 molecular detection. These results can, therefore, be used to improve future testing recommendations and provide additional information about tissue tropism for SARS-CoV-2. TRIAL REGISTRATION: ClinicalTrials.gov NCT05611203; https://clinicaltrials.gov/study/NCT05611203. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/47446.

Patterns of testing in the extensive Danish national SARS-CoV-2 test set-up.

BACKGROUND: The Danish national SARS-CoV-2 mass test system was among the most ambitious worldwide. We describe its set-up and analyse differences in patterns of testing per demography and time period in relation to the three waves of SARS-CoV-2 transmission in Denmark. METHODS: We included all reported PCR- and rapid antigen-tests performed between 27 February 2020 and 10 March 2022 among all residents aged 2 years or above. Descriptive statistics and Poisson regression models were used to analyse characteristics of individuals tested for SARS-CoV-2 using a national cohort study design. RESULTS: A total of 63.7 million PCR-tests and 60.0 million rapid antigen-tests were performed in the study period, testing 90.9% and 78.8% of the Danish population at least once by PCR or antigen, respectively. Female sex, younger age, Danish heritage and living in the capital area were all factors positively associated with the frequency of PCR-testing. The association between COVID-19 vaccination and PCR-testing changed from negative to positive over time. CONCLUSION: We provide details of the widely available, free-of-charge, national SARS-CoV-2 test system, which served to identify infected individuals, assist isolation of infectious individuals and contact tracing, and thereby mitigating the spread of SARS-CoV-2 in the Danish population. The test system was utilized by nearly the entire population at least once, and widely accepted across different demographic groups. However, demographic differences in the test uptake did exist and should be considered in order not to cause biases in studies related to SARS-CoV-2, e.g., studies of transmission and vaccine effectiveness.

Evaluation of four laboratory-based high-throughput SARS-CoV-2 automated antigen tests compared to RT-PCR on nasal and oropharyngeal samples.

BACKGROUND: The demand for RT-PCR testing has been unprecedented during the SARS-CoV-2 pandemic. Fully automated antigen tests (AAT) are less cumbersome than RT-PCR, but data on performance compared to RT-PCR are scarce. METHODS: The study consists of two parts. A retrospective analytical part, comparing the performance of four different AAT on 100 negative and 204 RT-PCR positive deep oropharyngeal samples divided into four groups based on RT-PCR cycle of quantification levels. In the prospective clinical part, 206 individuals positive for and 199 individuals negative for SARS-CoV-2 were sampled from either the anterior nasal cavity (mid-turbinate) or by deep oropharyngeal swabs or both. The performance of AATs was compared to RT-PCR. RESULTS: The overall analytical sensitivity of the AATs differed significantly from 42% (95% CI 35-49) to 60% (95% CI 53-67) with 100% analytical specificity. Clinical sensitivity of the AATs differed significantly from 26% (95% CI 20-32) to 88% (95% CI 84-93) with significant higher sensitivity for mid-turbinate nasal swabs compared to deep oropharyngeal swabs. Clinical specificity varied from 97% to 100%. CONCLUSION: All AATs were highly specific for detection of SARS-CoV-2. Three of the four AATs were significantly more sensitive than the fourth AAT both in terms of analytical and clinical sensitivity. Anatomical test location significantly influenced the clinical sensitivity of AATs.

Combined nasal- and oropharyngeal self-swab provides equivalent performance compared to professionally collected oropharyngeal swabs in detecting SARS-CoV-2 in a real-life setting.

PURPOSE: To investigate the performance of a combined nasal midturbinate- and oropharyngeal (NAOP) self-swab compared to a deep oropharyngeal (OP) swab by health care workers (HCW) in detecting SARS-CoV-2 in a real-life setting. METHODS: Paired swabs from 1119 participants were included. RT-PCR were used to detect SARS-CoV-2 in both swab samples. RESULTS: 330 participants tested positive. The sensitivity of the combined self-swab and OP swab was 96.9 % and 95.4 % respectively, whereas the Ct-values for self-swabs were significantly lower compared to OP swabs. CONCLUSION: The combined NAOP self-swab outperformed the OP swab and thus, the NAOP self-swab may be an alternative sampling method under the given circumstances.

A nationwide analytical and clinical evaluation of 44 rapid antigen tests for SARS-CoV-2 compared to RT-qPCR.

BACKGROUND: The SARS-CoV-2 pandemic has resulted in massive testing by Rapid Antigen Tests (RAT) without solid independent data regarding clinical performance being available. Thus, decision on purchase of a specific RAT may rely on manufacturer-provided data and limited peer-reviewed data. METHODS: This study consists of two parts. In the retrospective analytical part, 33 RAT from 25 manufacturers were compared to RT-PCR on 100 negative and 204 positive deep oropharyngeal cavity samples divided into four groups based on RT-PCR Cq levels. In the prospective clinical part, nearly 200 individuals positive for SARS-CoV-2 and nearly 200 individuals negative for SARS-CoV-2 by routine RT-PCR testing were retested within 72 h for each of 44 included RAT from 26 manufacturers applying RT-PCR as the reference method. RESULTS: The overall analytical sensitivity differed significantly between the 33 included RAT; from 2.5% (95% CI 0.5-4.8) to 42% (95% CI 35-49). All RAT presented analytical specificities of 100%. Likewise, the overall clinical sensitivity varied significantly between the 44 included RAT; from 2.5% (95% CI 0.5-4.8) to 94% (95% CI 91-97). All RAT presented clinical specificities between 98 and 100%. CONCLUSION: The study presents analytical as well as clinical performance data for 44 commercially available RAT compared to the same RT-PCR test. The study enables identification of individual RAT that has significantly higher sensitivity than other included RAT and may aid decision makers in selecting between the included RAT. FUNDING: The study was funded by a participant fee for each test and the Danish Regions.

Increased transmissibility of SARS-CoV-2 lineage B.1.1.7 by age and viral load.

New lineages of SARS-CoV-2 are of potential concern due to higher transmissibility, risk of severe outcomes, and/or escape from neutralizing antibodies. Lineage B.1.1.7 (the Alpha variant) became dominant in early 2021, but the association between transmissibility and risk factors, such as age of primary case and viral load remains poorly understood. Here, we used comprehensive administrative data from Denmark, comprising the full population (January 11 to February 7, 2021), to estimate household transmissibility. This study included 5,241 households with primary cases; 808 were infected with lineage B.1.1.7 and 4,433 with other lineages. Here, we report an attack rate of 38% in households with a primary case infected with B.1.1.7 and 27% in households with other lineages. Primary cases infected with B.1.1.7 had an increased transmissibility of 1.5-1.7 times that of primary cases infected with other lineages. The increased transmissibility of B.1.1.7 was multiplicative across age and viral load.

A Biosecurity Survey in Kenya, November 2014 to February 2015.

A biosecurity survey was performed to gather information on the biosecurity level and laboratory capacity in Kenya for the purpose of providing information outlining relevant components for biosecurity legislation, biosecurity implementation, and enforcement of biosecurity measures in Kenya. This survey is, to the authors' knowledge, the first to be published from an African country. A total of 86 facilities with laboratories covering relevant categories, such as training laboratories, human diagnostic laboratories, veterinary diagnostic laboratories, and research laboratories, were selected to participate in the survey. Each facility was visited by a survey team and staff were asked to answer 29 groups of questions from a questionnaire. The survey showed that Kenyan laboratory facilities contain biological agents of biosecurity concern. The restrictions for these agents were found to be limited for several of the facilities, in that many laboratory facilities and storage units were open for access by either students or staff who had no need of access to the laboratory. The survey showed a great deal of confusion in the terms biosecurity and biosafety and a generally limited biosecurity awareness among laboratory personnel. The survey showed that the security of biological agents of biosecurity concern in many facilities does not meet the international requirements. The authors recommend developing a legal framework in Kenya for effective controls, including national biosecurity regulations, guidelines, and procedures, thereby reducing the risk that a Kenyan laboratory would be the source of a future biological attack.

Modernizing stockpiles of medical countermeasures against smallpox: Benefits, risks, and knowledge gaps.

OBJECTIVE: New smallpox medical countermeasures are entering the marketplace, offering the opportunity to modernize existing stockpiles. However, new smallpox countermeasures are developed under the animal rule, meaning that human efficacy data are lacking, and human safety data may be limited. Also, stockpile modernization would require prioritization of increasingly limited public funds. Approaches to address these issues are needed. METHODS: Smallpox vaccine data were gathered by literature search. The financial value of vaccination in the face of an outbreak was evaluated using a threatbased cost/benefit analysis model, involving i) estimation of the efficacy of new smallpox vaccines based on available clinical data on virus-neutralizing seroconversion in vaccinees, ii) estimation of the likelihood for a smallpox outbreak in Denmark, and iii) estimation of the expected life-saving effects of postevent vaccination. RESULTS: The authors estimated that i) the likelihood of a smallpox outbreak in Denmark is very low (one event in 200,000 years), ii) the expected efficacy of currently available and new vaccines is 95 and 75 percent, respectively, iii) the expected frequency of serious side effects from vaccination is between 100 and 10,000 fold lower for new than for existing vaccines, depending on modes of action. CONCLUSIONS: Despite the very low likelihood for a smallpox outbreak, the potentially large consequences combined with the protective effect of vaccination make maintenance of the smallpox vaccine stockpile justified and valuable. For vaccination in the face of a smallpox outbreak, a high efficacy rather than a lowered rate of adverse effects would maximize the number of lives saved.

Development of an ELISA for evaluation of swab recovery efficiencies of bovine serum albumin.

After a potential biological incident the sampling strategy and sample analysis are crucial for the outcome of the investigation and identification. In this study, we have developed a simple sandwich ELISA based on commercial components to quantify BSA (used as a surrogate for ricin) with a detection range of 1.32-80 ng/mL. We used the ELISA to evaluate different protein swabbing procedures (swabbing techniques and after-swabbing treatments) for two swab types: a cotton gauze swab and a flocked nylon swab. The optimal swabbing procedure for each swab type was used to obtain recovery efficiencies from different surface materials. The surface recoveries using the optimal swabbing procedure ranged from 0-60% and were significantly higher from nonporous surfaces compared to porous surfaces. In conclusion, this study presents a swabbing procedure evaluation and a simple BSA ELISA based on commercial components, which are easy to perform in a laboratory with basic facilities. The data indicate that different swabbing procedures were optimal for each of the tested swab types, and the particular swab preference depends on the surface material to be swabbed.

Evaluating 6 ricin field detection assays.

This study presents data showing the performance of 6 commercial detection assays against ricin around concentrations specified as detection limits by the producers. A 2-fold dilution series of 20 ng/ml ricin was prepared and used for testing the lateral-flow kits: BADD, Pro Strips™, ENVI, RAID DX, Ricin BioThreat Alert, and IMASS™ device. Three of the 6 tested field assays (IMASS™ device, ENVI assay, and the BioThreat Alert assay) were able to detect ricin, although differences in the measured detection limits compared to the official detection limits and false-negative results were observed. We were not able to get the BADD, Pro Strips™, and RAID assays to function in our laboratory. We conclude that when purchasing a field responder assay, there is large variation in the specificity of the assays, and a number of in-house tests must be performed to ensure functionality.

Botulinum toxin field assays evaluated using cosmetic botox preparations.

Several quick tests for identifying botulinum toxins (BoNTs) are commercially available, but generally these tests have not been evaluated by independent laboratories. This study presents data on the evaluation of a number of commercial tests and demonstrates the use of cosmetic preparations of BoNT A and B as positive controls. For reference we used an in-house ELISA procedure. The cosmetic toxins, Botox(®) and Neurobloc(®), were found to be useful-that is, they had a sufficiently high toxin content to be used in test evaluation studies. Some commercial kits based on columns (ABICAP(®)) or lateral flow technology were tested for their detection limits. The ABICAP column system was found to be a useful alternative to an in-house ELISA method. In general, the lateral flow-based test systems evaluated here were not able to detect BoNT, and a large proportion of the tests showed construction failures. In conclusion, this study showed that cosmetic BoNT products have enough toxin content to be used as convenient and accessible means of testing commercially available quick tests. The lateral flow tests used in this study were not satisfactory, while the ABICAP system was found to be a good alternative to an ELISA.

Ascaris suum infection negatively affects the response to a Mycoplasma hyopneumoniae vaccination and subsequent challenge infection in pigs.

Since their first introduction more than a century ago, vaccines have become one of the most cost-effective tools to prevent and manage infectious diseases in human and animal populations. It is vital to understand the possible mechanisms that may impair optimal vaccine efficacy. The hypothesis posed in this study was that a concurrent Ascaris suum infection of pigs vaccinated with a Mycoplasma hyopneumoniae (Mh) vaccine would modulate the protective immune response to a subsequent challenge infection. Four groups of pigs were either (1) untreated (group C), (2) vaccinated against Mh 3 weeks after the start of the study (group V), (3) given a trickle infection with A. suum throughout the study (group A), or (4) given a trickle infection with A. suum and vaccinated against Mh (group AV). All pigs were subsequently inoculated with live Mh bacteria 4 weeks after the Mh vaccination and necropsied after another 4 weeks. All pigs in group V sero-converted 3 weeks after vaccination (100%), as opposed to only 33% of group AV pigs that were Mh-vaccinated and given A. suum. At the end of the study, only 78% of pigs in group AV had sero-converted. Pigs in group AV had a higher mean percentage of lung pathology and the variation was significantly higher in these pigs compared to pigs in group V. The pattern of gene expression in the lungs and draining lymph nodes indicated a local Th2-skewed response induced by A. suum. Our study indicated that A. suum significantly compromised the effect of Mh vaccination. The impact of reduced vaccine efficacy caused by a common gastrointestinal helminth emphasises the importance of parasite control. More focus should be put into this area of research to outline the practical consequences of this interaction, and to be able to predict, prevent and correct negative interactions.

Concurrent infections and socioeconomic determinants of geohelminth infection: a community study of schoolchildren in periurban Guinea-Bissau.

We explored the association between subclinical intestinal helminth infections and other gastrointestinal pathogens in 706 schoolchildren from a poor semirural area while adjusting for socioeconomic risk factors. The study was carried out in two neighbouring areas in the capital of Guinea-Bissau in West Africa. Children aged 4-12 years were visited and one child per mother was invited to participate in the study. Among the 706 children included in the study, helminths were detected in 44.2%, enteropathogenic bacteria in 13.7%, protozoans in 51.1% and rotavirus in 5.9%. A total of 76.1% had an infection of some sort and 41.8% were concomitantly infected with more than one and up to five gastrointestinal pathogens. After adjustment for possible confounding factors, infection with helminths and Entamoeba histolytica/E. dispar remained associated. Other risk factors for helminths included increasing age, male gender, small mid-upper arm circumference and chicken husbandry. Maternal school attendance and belonging to a Muslim family were associated with a lower prevalence of helminths. Investigations of concomitant infections are valuable as they may have implications for control and treatment strategies.

Infection with parasitic nematodes confounds vaccination efficacy.

T helper (Th) cells produce signature cytokine patterns, induced largely by intracellular versus extracellular pathogens that provide the cellular and molecular basis for counter regulatory expression of protective immunity during concurrent infections. The production of IL-12 and IFN-gamma, for example, resulting from exposure to many bacterial, viral, and protozoan pathogens is responsible for Th1-derived protective responses that also can inhibit development of Th2-cells expressing IL-4-dependent immunity to extracellular helminth parasites and vice versa. In a similar manner, concurrent helminth infection alters optimal vaccine-induced responses in humans and livestock; however, the consequences of this condition have not been adequately studied especially in the context of a challenge infection following vaccination. Demands for new and effective vaccines to control chronic and emerging diseases, and the need for rapid deployment of vaccines for bio security concerns requires a systematic evaluation of confounding factors that limit vaccine efficacy. One common albeit overlooked confounder is the presence of gastrointestinal nematode parasites in populations of humans and livestock targeted for vaccination. This is particularly important in areas of the world were helminth infections are prevalent, but the interplay between parasites and emerging diseases that can be transmitted worldwide make this a global issue. In addition, it is not clear if the epidemic in allergic disease in industrialized countries substitutes for geohelminth infection to interfere with effective vaccination regimens. This presentation will focus on recent vaccination studies in mice experimentally infected with Heligmosomoides polygyrus to model the condition of gastrointestinal parasite infestation in mammalian populations targeted for vaccination. In addition, a large animal vaccination and challenge model against Mycoplasma hyopneumonia in swine exposed to Ascaris suum will provide a specific example of the need for further work in this area, and for controlled field studies to assess the impact of other similar scenarios.

Excretion in feces and mucosal persistence of Salmonella ser. Typhimurium in pigs subclinically infected with Oesophagostomum spp.

OBJECTIVE: To determine interactions between Oesophagostomum spp and Salmonella ser. Typhimurium in pigs. ANIMALS: 30 healthy 5- to 6-week-old pigs. PROCEDURE: Pigs were allotted to 3 groups (n = 10 pigs/group) and treated as follows: group A was given Oesophagostomum dentatum and O quadrispinulatum; group B was given O dentatum, O quadrispinulatum, and S Typhimurium; and group C was given S Typhimurium only. Pigs in groups A and B were trickle infected with Oesophagostomum spp 3 times weekly throughout the study. After 19 days, groups B and C were inoculated once with S Typhimurium. One pig from each group was euthanatized on the day of Salmonella exposure and 2 and 4 days after Salmonella exposure. The remaining pigs were euthanatized on days 16 and 17 after Salmonella exposure. RESULTS: Pigs with dual infections of nematodes and bacteria (group B) excreted significantly higher amounts of S Typhimurium in feces, compared with nematode-free pigs (group C). In addition, group-B pigs excreted S Typhimurium on more days than pigs in group C. Salmonella Typhimurium was detected in the cecum and colon in the majority of pigs in group B, whereas S Typhimurium was only detected in the colon in pigs in group C. Immunohistochemical examination detected S Typhimurium in 7 of 9 pigs in group B but only 2 of 9 pigs in group C. CONCLUSIONS AND CLINICAL RELEVANCE: Interactions between intestinal nematodes and bacteria may play an important role in the dynamics of S Typhimurium infections.