Positive Molecular Test Research Articles

High prevalence of asymptomatic SARS-CoV-2 infection in a cohort of liver transplant recipients in central Italy

Asymptomatic subjects account for 25 to 45% of SARS-CoV-2 infections, and in particular, subjects on mild immunosuppressive therapy may have symptoms masked and could spread virus for an extended period of time. To determine the cumulative incidence of symptomatic and asymptomatic SARS-CoV-2 infections and associated risk factors, we conducted a prospective clinical and serological survey in a cohort of 278 liver transplant recipients (LTRs) from Central Italy. Three different serology tests were performed every 4 months in 259 LTRs between April 2020 and April 2021: one based on raw extract of whole SARS-CoV-2 virus and two on specific viral antigens (nucleoprotein and receptor binding domain) to detect specific IgG, IgM and IgA. Hundred fifteen LTRs who reported symptoms or close contact with a SARS-CoV-2-positive subject, or had a positive serological result underwent molecular testing by standard screening procedures (RT-PCR on naso-pharyngeal swab).Thirty-one past or active SARS-CoV-2 infections were identified: 14 had positive molecular test (64% symptomatic), and 17 had positive serology only (18% symptomatic). SARS-CoV-2 infection was not statistically related to gender, age, obesity, diabetes, renal impairment, type of anti-rejection therapy or time from transplant. Asymptomatic SARS-CoV-2 cases (61.3%) were more frequent in males and in those with glomerular filtrate rate >50 ml/min. Overall, the addition of repeated serology to standard diagnostic molecular protocols increased detection of SARS-CoV-2 infection from 5.1% to 10.9%. Anti-SARS-CoV-2 seroprevalence among our LTRs (11.2%) is comparable to the general population of Central Italy, considered a medium-impact area. Only one asymptomatic subject (6%) was found to carry SARS-CoV-2 in respiratory tract at the time of serological diagnosis.

Serosurvey and Molecular Detection of Toxoplasma gondii in Dogs in Rural Areas of Kazeroun District, Fars Province, Southern Iran.

Background. Toxoplasma gondii is an intracellular protozoan parasite responsible for systemic disease in a wide range of warm-blooded animals. The current study is aimed at evaluating the prevalence of Toxoplasma infection in dogs, using serological and molecular methods in rural areas in Kazeroun Township, Fars province, southern Iran. Methods. Blood samples were obtained from 60 clinically healthy dogs with an age range of 1 to 7 years in three rural areas of Fars province, southern Iran. Sera and buffy coats were used to assess the T. gondii infection using both modified agglutination test (MAT) and real-time PCR. Results. Antibodies against T. gondii were detected in 5 out of 60 (8.3%) dogs by the MAT method, and T. gondii DNA was detected in 17 out of 60 (28.3%) studied animals. There was no significant association between sex and seropositivity to Toxoplasma (p > 0.05). Fair agreement (kappa = 0.27) was seen between molecular and serological findings where three dogs with positive serological results had a positive molecular test. Conclusion. Findings of the present study show a relatively high prevalence of T. gondii infection in dogs in rural areas in Fars province, southern Iran. Finding the parasite genotype in dogs deserves further study.

Clinical course and risk factors for severe COVID-19 among Italian patients with cystic fibrosis: a study within the Italian Cystic Fibrosis Society.

PurposeTo describe the clinical course of COVID-19 in patients with cystic fibrosis (CF) and to identify risk factors for severe COVID-19.MethodsWe conducted a prospective study within the Italian CF Society. CF centers collected baseline and follow-up data of patients with virologically confirmed SARS-CoV-2 infection between March 2020 and June 2021. Odds ratios (ORs) for severe SARS-CoV-2 (as defined by hospital admission) were estimated by logistic regression models.ResultsThe study included 236 patients with positive molecular test for SARS-CoV-2. Six patients died, 43 patients were admitted to hospital, 4 admitted to intensive care unit. Pancreatic insufficiency was associated with increased risk of severe COVID-19 (OR 4.04, 95% CI 1.52; 10.8). After adjusting for age and pancreatic insufficiency, forced expiratory volume in one second (FEVp) < 40% (OR 4.54, 95% CI 1.56; 13.2), oxygen therapy (OR 12.3, 95% CI 2.91–51.7), underweight (OR 2.92, 95% CI 1.12; 7.57), organ transplantation (OR 7.31, 95% CI 2.59; 20.7), diabetes (OR 2.67, 95% CI 1.23; 5.80) and liver disease (OR 3.67, 95% CI 1.77; 7.59) were associated with increased risk of severe COVID-19, while use of dornase alfa was associated with a reduced risk (OR 0.34, 95% CI 0.13–0.88). No significant changes were observed in FEVp from baseline to a median follow-up of 2 months (median difference: 0, interquartile range: − 4; 5, P = 0.62).ConclusionClinical features indicative of severe form of CF are associated with increased risk of COVID-19 hospitalization. SARS-CoV-2 infected patients do not experience a deterioration of respiratory function.Supplementary InformationThe online version contains supplementary material available at 10.1007/s15010-021-01737-z.

495. Evaluation of Antigen Testing for Detection of COVID-19 Vaccine Breakthrough Cases in Long-Term Care

BackgroundLong-term care facilities (LTCFs) are at high risk for severe COVID-19 outbreaks due to their congregate nature and vulnerable population. Oregon Health Authority (OHA) deployed point-of-care antigen (Ag) tests to promptly identify COVID-19 cases in LTCFs. However, their performance in identifying vaccine breakthrough cases has not been evaluated.MethodsDuring 2/25/21–5/25/21, OHA supported testing of residents and staff for two outbreaks at a single LTCF. Paired nasal swabs were collected and tested for SARS-CoV-2 by CDC Influenza SARS-CoV-2 Multiplex PCR Assay (molecular test) and Abbott BinaxNOW COVID-19 Ag Card (Ag test) twice weekly during the outbreaks. Participants were considered fully vaccinated if ≥ 14 days had passed since completion of a vaccine series; all others were deemed unvaccinated. A vaccine breakthrough case was defined as a positive Ag or molecular test from a fully vaccinated person’s specimen. Performance characteristics of the Ag test were assessed, with molecular test as the reference standard. Cycle threshold (Ct) values were compared by one-sided independent t-tests.Results94 unvaccinated residents and staff provided 563 paired samples; SARS-CoV-2 was detected in 21 (12 by Ag and molecular test, 6 by molecular test only, 3 by Ag test only), yielding Ag test sensitivity of 66.7% (95% CI: 43.8–83.7%) and specificity of 99.4% (95% CI: 98.4–99.8%). Mean Ct values were higher for specimens positive by PCR but negative by Ag than those positive by both (30.0 vs. 20.7, P < .01). 81 vaccinated persons provided 925 paired samples; SARS-CoV-2 was detected in 5 (1 by Ag and molecular test, 4 by molecular test only), yielding Ag test sensitivity of 20% (95% CI: 3.6–62.5%) and specificity of 100% (95% CI: 99.6–100%). Mean Ct values for specimens from vaccinated cases were higher than those from unvaccinated cases (30.2 vs. 23.8, P < .05). The lone Ag-positive breakthrough case had a Ct of 20; all others had Ct > 29.ConclusionAg test performance and reduced sensitivity on specimens with high Ct values found in this population are consistent with published data. Molecular testing maximizes identification of vaccine breakthrough cases. More studies are needed to estimate the proportion of breakthrough cases missed by Ag testing and their risk of transmitting the virus in LTCFs.Disclosures All Authors: No reported disclosures

Liver transplantation from active COVID-19 donors: A lifesaving opportunity worth grasping?

COVID‐19 pandemic dramatically impacted transplantation landscape. Scientific societies recommend against the use of donors with active SARS‐CoV‐2 infection. Italian Transplant Authority recommended to test recipients/donors for SARS‐CoV‐2‐RNA immediately before liver transplant (LT) and, starting from November 2020, grafts from deceased donors with active SARS‐CoV‐2 infection were allowed to be considered for urgent‐need transplant candidates with active/resolved COVID‐19. We present the results of the first 10 LTs with active COVID‐19 donors within an Italian multicenter series. Only two recipients had a positive molecular test at LT and one of them remained positive up to 21 days post‐LT. None of the other eight recipients was found to be SARS‐CoV‐2 positive during follow‐up. IgG against SARS‐CoV‐2 at LT were positive in 80% (8/10) of recipients, and 71% (5/7) showed neutralizing antibodies, expression of protective immunity related to recent COVID‐19. In addition, testing for SARS‐CoV‐2 RNA on donors’ liver biopsy at transplantation was negative in 100% (9/9), suggesting a very low risk of transmission with LT. Immunosuppression regimen remained unchanged, according to standard protocol. Despite the small number of cases, these data suggest that transplanting livers from donors with active COVID‐19 in informed candidates with SARS‐CoV‐2 immunity, might contribute to safely increase the donor pool.

Real-world effectiveness of the mRNA-1273 vaccine against COVID-19: Interim results from a prospective observational cohort study

BackgroundPhase 3 trials found mRNA-1273 was highly effective in preventing COVID-19. We conducted a prospective cohort study at Kaiser Permanente Southern California (KPSC) to determine the real-world vaccine effectiveness (VE) of mRNA-1273 in preventing COVID-19 infection and severe disease.MethodsFor this planned interim analysis, individuals aged ≥18 years receiving 2 doses of mRNA-1273 ≥24 days apart (18/12/2020-31/03/2021) were 1:1 matched to randomly selected unvaccinated individuals by age, sex, and race/ethnicity, with follow-up through 30/06/2021. Outcomes were COVID-19 infection (SARS-CoV-2 positive molecular test or COVID-19 diagnosis code) or severe disease (COVID-19 hospitalization and COVID-19 hospital death). Adjusted hazard ratios (aHR) and confidence intervals (CI) for COVID-19 outcomes comparing vaccinated and unvaccinated individuals were estimated by Cox proportional hazards models accounting for multiple comparisons. Adjusted VE was calculated as (1-aHR)x100. Whole genome sequencing was performed on SARS-CoV-2 positive specimens from the KPSC population.FindingsThis analysis included 352,878 recipients of 2 doses of mRNA-1273 matched to 352,878 unvaccinated individuals. VE (99·3% CI) against COVID-19 infection was 87·4% (84·8–89·6%). VE against COVID-19 hospitalization and hospital death was 95·8% (90·7–98·1%) and 97·9% (66·9-99·9%), respectively. VE was higher against symptomatic (88·3% [98·3% CI: 86·1–90·2%]) than asymptomatic COVID-19 (72·7% [53·4–84·0%]), but was generally similar across age, sex, and racial/ethnic subgroups. VE among individuals with history of COVID-19 ranged from 8·2–33·6%. The most prevalent variants were Alpha (41·6%), Epsilon (17·5%), Delta (11·5%), and Gamma (9·1%), with Delta increasing to 54·0% of variants by June 2021.InterpretationThese interim results provide reassuring evidence of the VE of 2 doses of mRNA-1273 across age, sex, and racial/ethnic subgroups, and against asymptomatic and symptomatic COVID-19, and severe COVID-19 outcomes. Among individuals with history of COVID-19, mRNA-1273 vaccination may offer added protection beyond immunity acquired from prior infection. Longer follow-up is needed to fully evaluate VE of mRNA-1273 against emerging SARS-CoV-2 variants.FundingModerna Inc.

Influenza and SARS-CoV-2 Co-infections in California, USA, September 2020-April 2021.

During September 1, 2020–April 30, 2021, the California Department of Public Health, Richmond, California, USA, received 255 positive influenza molecular test results that matched with severe acute respiratory syndrome coronavirus 2 molecular test results; 58 (23%) persons were co-infected. Influenza activity was minimal in California, and co-infections were sporadic.

Feasibility and Effectiveness Assessment of SARS-CoV-2 Antigenic Tests in Mass Screening of a Pediatric Population and Correlation with the Kinetics of Viral Loads.

The gold standard for diagnosis of SARS-CoV-2 infection has been nucleic acid amplification tests (NAAT). However, rapid antigen detection kits (Ag-RDTs), may offer advantages over NAAT in mass screening, generating results in minutes, both as laboratory-based test or point-of-care (POC) use for clinicians, at a lower cost. We assessed two different POC Ag-RDTs in mass screening versus NAAT for SARS-CoV-2 in a cohort of pediatric patients admitted to the Pediatric Emergency Unit of IRCCS—Polyclinic of Sant’Orsola, Bologna (from November 2020 to April 2021). All patients were screened with nasopharyngeal swabs for the detection of SARS-CoV-2-RNA and for antigen tests. Results were obtained from 1146 patients. The COVID-19 Ag FIA kit showed a baseline sensitivity of 53.8% (CI 35.4–71.4%), baseline specificity 99.7% (CI 98.4–100%) and overall accuracy of 80% (95% CI 0.68–0.91); the AFIAS COVID-19 Ag kit, baseline sensitivity of 86.4% (CI 75.0–93.9%), baseline specificity 98.3% (CI 97.1–99.1%) and overall accuracy of 95.3% (95% CI 0.92–0.99). In both tests, some samples showed very low viral load and negative Ag-RDT. This disagreement may reflect the positive inability of Ag-RDTs of detecting antigen in late phase of infection. Among all cases with positive molecular test and negative antigen test, none showed viral loads > 106 copies/mL. Finally, we found one false Ag-RDTs negative result (low cycle thresholds; 9 × 105 copies/mL). Our results suggest that both Ag-RDTs showed good performances in detection of high viral load samples, making it a feasible and effective tool for mass screening in actively infected children.

Pre-Vaccine Positivity of SARS-CoV-2 Antibodies in Alberta, Canada during the First Two Waves of the COVID-19 Pandemic.

ABSTRACTWe systematically evaluated SARS-CoV-2 IgG positivity in a provincial cohort to understand the local epidemiology of COVID-19 and support evidence-based public health decisions. Residual blood samples were collected for serology testing over 5-day periods monthly from June 2020 to January 2021 from six clinical laboratories across the province of Alberta, Canada. A total of 93,993 individual patient samples were tested with a SARS-CoV-2 nucleocapsid antibody assay with positives confirmed using a spike antibody assay. Population-adjusted SARS-CoV-2 IgG seropositivity was 0.92% (95% confidence interval [CI]: 0.91 to 0.93%) shortly after the first COVID-19 wave in June 2020, increasing to 4.63% (95% CI: 4.61 to 4.65%) amid the second wave in January 2021. There was no significant difference in seropositivity between males and females (1.39% versus 1.27%; P = 0.11). Ages with highest seropositivity were 0 to 9 years (2.71%, 95% CI: 1.64 to 3.78%) followed by 20 to 29 years (1.58%, 95% CI: 1.12 to 2.04%), with the lowest rates seen in those aged 70 to 79 (0.79%, 95% CI: 0.65 to 0.93%) and >80 (0.78%, 95% CI: 0.60 to 0.97%). Compared to the seronegative group, seropositive patients inhabited geographic areas with lower household income ($87,500 versus $97,500; P < 0.001), larger household sizes, and higher proportions of people with education levels of secondary school or lower, as well as immigrants and visible minority groups (all P < 0.05). A total of 53.7% of seropositive individuals were potentially undetected cases with no prior positive COVID-19 nucleic acid test (NAAT). Antibodies were detectable in some patients up to 9 months post positive NAAT result. This seroprevalence study will continue to inform public health decisions by identifying at-risk demographics and geographical areas.IMPORTANCE Using SARS-CoV-2 serology testing, we assessed the proportion of people in Alberta, Canada (population 4.4 million) positive for COVID-19 antibodies, indicating previous infection, during the first two waves of the COVID-19 pandemic (prior to vaccination programs). Linking these results with sociodemographic population data provides valuable information as to which groups of the population are more likely to have been infected with the SARS-CoV-2 virus to help facilitate public health decision-making and interventions. We also compared seropositivity data with previous COVID-19 molecular testing results. Absence of antibody and molecular testing were highly correlated (95% negative concordance). Positive antibody correlation with a previous positive molecular test was low, suggesting the possibility of mild/asymptomatic infection or other reasons leading individuals from seeking medical attention. Our data highlight that the true estimate of population prevalence of COVID-19 is likely best informed by combining data from both serology and molecular testing.

Spectrum of neuro-genetic disorders in the United Arab Emirates national population.

Clinical and molecular characterization of neuro-genetic disorders among UAE national patients seen in the Genetic Clinic at Tawam hospital over a period of 3 years. A retrospective chart review of all Emirati patients assessed by clinical geneticists due to neuro-genetic disorders including global developmental delay, ASD, ID, ADHD, and epilepsy in combination with abnormalities of other organ systems. Each patient had proper assessment including detailed history, three-generation family history, developmental history and detailed physical examination looking for other system involvement. Hearing test and ophthalmological examination were performed when needed. Magnetic resonance imaging (MRI) of the brain, echocardiogram, and renal ultrasound were pursued as indicated. Detailed psychological evaluation and psychometric assessment were done when indicated. The review was done for a period between January 2018 and December 2020. Genetic investigations included chromosome karyotype, FISH study, metabolic/biochemical tests, chromosome microarray, gene sequencing, targeted mutation testing, trio whole exome and trio genome sequencing. A total of 644 patients with developmental delay, ID, learning difficulty, ASD, ADHD, or NNDs, were seen in genetic clinic from January 2018 to December 2020. A total of 506 patients were included in this review, all completed the genetic evaluations during the study period. There were 398 (61.8%) males and 246 (38.2%) females, with a ratio of 1.6:1. Positive family history of NDD was documented in 132 families, while 115 families had negative history and family history was unknown/unclear in the remaining. Fifty seven (11.26% [57/506]) patients had positive microarray results. Hundred ninety seven (38.9% [197/506]) patients had positive molecular testing. Genetic disorders were found in 133 (67.5% [133/197]) and inborn errors of metabolism were found in 42 (21.3% [42/197]). Consanguinity was documented in 139 patients with positive molecular diagnoses (139/197, 70.5%). Sixty nine (35% [69/197]) patients had autosomal dominant disorders, majority were De Novo (84%). Ninety-five (48% [95/197]) patients had autosomal recessive diseases, 40 mutations involved inborn errors of metabolism and 50 mutations involved genetic disorders. Pathogenic variants causing both autosomal dominant and recessive disorders were found in 98 patients (49.7% [98/197]), likely pathogenic variants causing both autosomal dominant and recessive disorders were found in 66 patients (33.5% [66/197]). X-linked related disorders were found in 10 patients (5% [10/197]). Mitochondrial mutation was found in one patient. Novel mutations were found in 76 patients (76/197 i.e., 38.56%). Twenty two patients had variants of unknown significant. The remaining 252 studied patients (252/506 i.e., 49.8%), remained undiagnosed. This study shows that neuro-genetic disorders in the UAE are very heterogeneous at clinical and molecular levels. Using microarray, WES and WGS a diagnosis was reached in 50% of the patients while no diagnosis was reached in other half of the studied patients. It is possible that some mutations were missed by WGS and WES. However, it is also possible that many of disorders in UAE population are novel and the causative mutation is not yet discovered. More researches need to be done in this population to uncover the molecular basis of these disorders.

Continuing Cardiopulmonary Symptoms, Disability, and Financial Toxicity 1 Month After Hospitalization for Third-Wave COVID-19: Early Results From a US Nationwide Cohort.

Patients discharged after COVID-19 report ongoing needs. To measure incident symptoms after COVID-19 hospitalization. Preplanned early look at 1-month follow-up surveys from patients hospitalized August 2020 to January 2021 in NHLBI PETAL Network's Biology and Longitudinal Epidemiology: COVID-19 Observational (BLUE CORAL) study. English- or Spanish-speaking hospitalized adults without substantial pre-COVID-19 disability with a positive molecular test for SARS-CoV-2. Overall, 253 patients were hospitalized for a median of 5 days (interquartile range [IQR], 3-8), and had a median age of 60 years (IQR, 45-68). By race/ethnicity, 136 (53.8%) were non-Hispanic White, 23 (9.1%) were non-Hispanic Black, and 83 (32.8%) were Hispanic. Most (139 [54.9%]) reported a new or worsened cardiopulmonary symptom, and 16% (n = 39) reported new or increased oxygen use; 213 (84.2%) patients reported not feeling fully back to their pre-COVID-19 level of functioning. New limitations in activities of daily living were present in 130 (52.8%) patients. Financial toxicities, including job loss or change (49 [19.8%]), having a loved one take time off (93 [37.8%]), and using up one's savings (58 [23.2%]), were common. Longer lengths of hospital stay were associated with greater odds of 1-month cardiopulmonary symptoms (adjusted odds ratio [aOR], 1.82 per additional week in the hospital; 95% CI, 1.11-2.98) and new disability (aOR, 2.06; 95% CI, 1.21-3.53). There were not uniform demographic patterns of association. We prioritized patients' reports of their own incident problems over objective testing. Patients who survived COVID-19 in the United States during late 2020/early 2021 still faced new burdens 1 month after hospital discharge.

Hubungan Pemeriksaan Basil Tahan Asam pada Penderita Tuberkulosis Sebelum dan Sesudah Pengobatan Rifampicin Selama 6 Bulan di Rumah Sakit Tingkat III 04.06.01 Wijaya Kusuma Purwokerto

Tuberculosis is a lung infection caused by the bacteria Mycobacterium tuberculosis. Early detection is one of the ways to detect tuberculosis. The first detection of tuberculosis is with the Molecular Rapid Test, which is one of the technologies being developed using GeneXpert. Patients with positive Molecular Rapid Test results will be treated with rifampicin for 6 months, then further screening of Acid-Fast Bacilli microscopically will be carried out to determine whether the patient is still positive for pulmonary tuberculosis or not. The purpose of this study was to determine the relationship between acid-fast bacillus examination in tuberculosis patients with positive molecular rapid test results. This study will be conducted experimentally. The results of calculations using the Wilcoxon Test showed that there was a relationship between TCM examination results and BTA follow-up screening in TB patients after and before rifampicin treatment for 6 months.

Myeloid Mixed Chimerism and Relapse in Myelofibrosis after Allogeneic Stem Cell Transplant

Background:Allogeneic stem cell transplant (SCT) remains the only potential curative treatment for myelofibrosis (MF). However, relapse after transplant is one of the leading causes of death. The role of mixed myeloid chimerism (MMC) in predicting post-transplant molecular and morphologic relapse is not well studied.Methods: Using a large single-center database, all consecutive patients with primary or secondary MF who underwent first allogeneic SCT in the period 2005-2015 were included in the study. Patients were defined to have MMC if they were found to have less than 95% of donor myeloid cells at any point over the duration of their follow up. Peripheral blood chimerism analysis was performed using 8 highly polymorphic microsatellite markers (Integrated DNA Technologies, Coralville, IA) in a multiplex PCR assay. The primary end point was to assess the correlation of MMC with any evidence of morphologic and/or molecular relapse.Results: A total of 85 patients (47 males, 38 females) were identified with a median age at transplant of 57 years (27-74). Among patients with molecular data (n=80), 60% had positive pre-transplant molecular markers. A total of 36 (43%) patients with full chimerism data (n=83) had MMC. All patients with MMC developed morphologic and/or molecular relapse, except for two; the first patient converted to full donor chimerism after immunosuppression reduction and the second patient had progressive myeloid chimerism and graft failure. Among patients with positive molecular testing and available chimerism data (n=46), 22 patients had MMC, of which 95% (n=21) had molecular relapse. Similarly, for patients with available chimerism data and negative pre-transplant molecular testing (n=32), 93% (n=14) of the 15 patients with MMC experienced eventual morphologic relapse. On the other hand, none of the patients with full donor myeloid chimerism (n=47) progressed during the study period, except for one patient with mixed T-Cell chimerism. With a median follow up of 49 months, the 5-year PFS was 7% for those with MMC vs 62% for patients with full donor myeloid chimerism (p<0.0001).Conclusion: Given the high sensitivity of chimera PCR DNA testing and its strong association with molecular and morphologic relapse, we speculate that myeloid chimerism testing, alone or combined with clonal molecular testing, would serve as one of the earliest and best markers to predict MRD and relapse in myelofibrosis post-transplant. DisclosuresOran:Astex: Research Funding; AROG: Research Funding; Celgene: Research Funding. Bose:Incyte Corporation: Honoraria. Pemmaraju:LFB: Consultancy, Honoraria; stemline: Consultancy, Honoraria, Research Funding; novartis: Consultancy, Honoraria, Research Funding; Incyte Corporation: Consultancy, Honoraria; cellectis: Research Funding; roche diagnostics: Consultancy, Honoraria; affymetrix: Research Funding; abbvie: Research Funding. Verstovsek:Galena BioPharma: Research Funding; Blueprint Medicines Corp: Research Funding; CTI BioPharma Corp: Research Funding; Gilead: Research Funding; NS Pharma: Research Funding; Gilead: Research Funding; Astrazeneca: Research Funding; Roche: Research Funding; Bristol Myers Squibb: Research Funding; Roche: Research Funding; NS Pharma: Research Funding; Lilly Oncology: Research Funding; Pfizer: Research Funding; Promedior: Research Funding; Pfizer: Research Funding; Celgene: Research Funding; CTI BioPharma Corp: Research Funding; Genentech: Research Funding; Galena BioPharma: Research Funding; Astrazeneca: Research Funding; Celgene: Research Funding; Bristol Myers Squibb: Research Funding; Blueprint Medicines Corp: Research Funding; Genentech: Research Funding; Promedior: Research Funding; Incyte: Research Funding; Seattle Genetics: Research Funding; Incyte: Research Funding; Seattle Genetics: Research Funding; Lilly Oncology: Research Funding.

Characterization of Xanthomonas campestris pv. campestris in Algeria

Xanthomonas campestris pv. campestris (Xcc) causes the black rot of cruciferous plants. This seed-borne bacterium is considered as the most destructive disease to cruciferous crops. Although sources of contamination are various, seeds are the main source of transmission. Typical symptoms of black rot were first observed in 2011 on cabbage and cauliflower fields in the main production areas of Algeria. Leaf samples displaying typical symptoms were collected during 2011 to 2014, and 170 strains were isolated from 45 commercial fields. Xcc isolates were very homogeneous in morphological, physiological and biochemical characteristics similar to reference strains, and gave positive pathogenicity and molecular test results (multiplex PCR with specific primers). This is the first record of Xcc in Algeria. Genetic diversity within the isolates was assessed in comparison with strains isolated elsewhere. A multilocus sequence analysis based on two housekeeping genes (gyrB and rpoD) was carried out on 77 strains representative isolates. The isolates grouped into 20 haplotypes defined with 68 polymorphic sites. The phylogenetic tree obtained showed that Xcc is in two groups, and all Algerian strains clustered in group 1 in three subgroups. No relationships were detected between haplotypes and the origins of the seed lots, the varieties of host cabbage, the years of isolation and agroclimatic regions.

The utility of ThyroSeq® in the management of indeterminate thyroid nodules by fine-needle aspiration.

We aim to evaluate the impact of ThyroSeq® in the management of indeterminate thyroid nodules (ITN), including Bethesda III and IV nodules. ITNs that underwent ThyroSeq testing between 2016 and 2019 were retrospectively reviewed. A control cohort included ITNs without molecular testing. Cytological, molecular, and histological data were collected. We identified 202 ITNs that underwent molecular testing (128 in Bethesda III and 74 in Bethesda IV). Mutations were found in 58 nodules with mutation rates of 21.9% in Bethesda III and 40.5% in Bethesda IV. In this cohort, 49 cases had surgical resection with a resection rate of 24.3% (49/202, 15.6% in Bethesda III and 39.2% in Bethesda IV). Among the resected cases, 42 cases had positive molecular results. Thyroid cancer was diagnosed in 21 nodules with a malignancy detection rate of 10.4%. In the other cohort, we identified 236 ITNs (158 in Bethesda III and 78 in Bethesda IV). Surgical resection was performed in 127 cases, with a resection rate of 53.8% (127/236, 46.2% in Bethesda III and 69.2% in Bethesda IV). Thyroid cancer was diagnosed in 21 nodules, with a malignancy detection rate of 8.9%. The risk of malignancy (ROM) recalculated based on positive ThyroSeq results was significantly higher (21.4%-35.5% in Bethesda III and 50%-60% in Bethesda IV) than that without molecular testing (4.4%-9.6% in Bethesda III and 17.9%-25.9% in Bethesda IV). We concluded that ThyroSeq significantly decreased the surgical resection rate (from 53.8% to 24.3%) without significantly affecting the malignancy detection rate in ITNs. Furthermore, positive molecular testing significantly increased ROM in ITNs. We believe that the recalculated ROM should be incorporated into the management of ITNs.

A controlled human infection model of Streptococcus pyogenes pharyngitis (CHIVAS-M75): an observational, dose-finding study

Streptococcus pyogenes is a leading cause of infection-related morbidity and mortality. A reinvigorated vaccine development effort calls for new clinically relevant human S pyogenes experimental infection models to support proof of concept evaluation of candidate vaccines. We describe the initial Controlled Human Infection for Vaccination Against S pyogenes (CHIVAS-M75) study, in which we aimed to identify a dose of emm75 S pyogenes that causes acute pharyngitis in at least 60% of volunteers when applied to the pharynx by swab. This observational, dose-finding study was done in a clinical trials facility in Melbourne (VIC, Australia). Groups of healthy volunteers aged 18-40 years, at low risk of complicated S pyogenes disease, and without high type-specific anti-emm75 IgG antibodies against the challenge strain were challenged and closely monitored as inpatients for up to 6 days, and then as outpatients for 6 months. Antibiotics were started upon diagnosis (clinical signs and symptoms of pharyngitis and a positive rapid molecular test) or after 5 days in those without pharyngitis. Rapid test results were confirmed by standard bacterial culture. After a sentinel participant, cohorts of five and then ten participants were challenged, with protocol-directed dose-escalation or de-escalation for subsequent cohorts. The primary outcome was the proportion of participants at each dose level with pharyngitis by day 5 after challenge. The study is registered with ClinicalTrials.gov, NCT03361163. Between July 10, 2018, and Sept 23, 2019, 25 healthy adults were challenged with emm75 S pyogenes and included in analyses. Pharyngitis was diagnosed in 17 (85%; 95% CI 62-97) of 20 participants at the starting dose level (1-3 × 105 colony-forming units [CFU]/mL). This high proportion prompted dose de-escalation. At the lower dose level (1-3 × 104 CFU/mL), pharyngitis was diagnosed in one of five participants. Immunological, biochemical, and microbiological results supported the clinical picture, with acute symptomatic pharyngitis characterised by pharyngeal colonisation by S pyogenes accompanied by significantly elevated C-reactive protein and inflammatory cytokines (eg, interferon-γ and interleukin-6), and modest serological responses to streptolysin O and deoxyribonuclease B. There were no severe (grade 3) or serious adverse events related to challenge. We have established a reliable pharyngitis human infection model with reassuring early safety findings to accelerate development of vaccines and other interventions to control disease due to S pyogenes. Australian National Health and Medical Research Council.

Use of Predictive Modeling to Tailor Molecular Testing Utilization for Thyroid Nodules.

Various risk stratification systems for cytologically indeterminate thyroid nodules are available. However, malignancy risk assessment data, such as ultrasound features, are not always used when the decision is to order molecular testing or not. Our aim was to investigate the utility of molecular testing after incorporating an algorithm with ultrasound-based risk of malignancy (ROM) estimation. Diagnostic/prognostic study. Single-institution urban tertiary care center. We performed a single-institution retrospective chart review of all thyroid nodules that had undergone molecular testing. A web-based Malignancy Risk Estimation System for Thyroid Nodules was utilized with ultrasound findings to stratify malignancy risk according to the Korean Thyroid Imaging Reporting and Data System (TI-RADS), French TI-RADS, American Association of Clinical Endocrinology guideline, and American Thyroid Association guideline. A novel algorithm for utilizing molecular testing at our institution was developed with the Korean TI-RADS and with recommendations from the American Thyroid Association and National Comprehensive Cancer Network. The Korean TI-RADS performed best in our population (area under the curve = 0.83). A positive molecular test result had a positive association with a higher ROM according to all 4 models (P < .05). Use of our algorithm prior to molecular testing would have prevented 38% of benign/low-ROM negative nodules (n = 28) from being tested. In patients with indeterminate thyroid nodules, an algorithm built on pre- and posttest probability to guide molecular testing might reduce unnecessary testing of benign and low-risk nodules.

Maternal-perinatal outcomes in pregnant women with covid-19 in a level III hospital in Peru.

The present study aimed to describe the perinatal outcomes of newborns of mothers with 2019 coronavirus infection identified before delivery in a level III hospital in Peru. Sociodemographic variables, obstetric complications, and neonatal morbidities were evaluated in the births that occurred between April 1 and June 30, 2020, at the National Maternal Perinatal Institute of Peru. 43 newborns were registered: 93% came from asymptomatic mothers, the most frequent obstetric complications were premature rupture of membranes (18.6%) and pre-eclampsia (11.6%), 65.1% of the births were vaginally, only one of the newborns had a positive result to RT-PCR for COVID-19, the comorbidities of the newborns were prematurity (11.3%) and low birth weight (9.3%); four were admitted to intermediate care and two to intensive care. It is concluded that 2.4% of newborns born to mothers with COVID-19 presented positive molecular test of RT-PCR, 14% of newborns presented morbidity as prematurity, low birth weight, sepsis and pneumonia that required ventilation. Neonatal morbidity was found in newborns whose RT-PCR test was negative for COVID-19.

Clinical prediction rule for SARS-CoV-2 infection from 116 U.S. emergency departments 2-22-2021.

Accurate and reliable criteria to rapidly estimate the probability of infection with the novel coronavirus-2 that causes the severe acute respiratory syndrome (SARS-CoV-2) and associated disease (COVID-19) remain an urgent unmet need, especially in emergency care. The objective was to derive and validate a clinical prediction score for SARS-CoV-2 infection that uses simple criteria widely available at the point of care. Data came from the registry data from the national REgistry of suspected COVID-19 in EmeRgency care (RECOVER network) comprising 116 hospitals from 25 states in the US. Clinical variables and 30-day outcomes were abstracted from medical records of 19,850 emergency department (ED) patients tested for SARS-CoV-2. The criterion standard for diagnosis of SARS-CoV-2 required a positive molecular test from a swabbed sample or positive antibody testing within 30 days. The prediction score was derived from a 50% random sample (n = 9,925) using unadjusted analysis of 107 candidate variables as a screening step, followed by stepwise forward logistic regression on 72 variables. Multivariable regression yielded a 13-variable score, which was simplified to a 13-point score: +1 point each for age>50 years, measured temperature>37.5°C, oxygen saturation<95%, Black race, Hispanic or Latino ethnicity, household contact with known or suspected COVID-19, patient reported history of dry cough, anosmia/dysgeusia, myalgias or fever; and -1 point each for White race, no direct contact with infected person, or smoking. In the validation sample (n = 9,975), the probability from logistic regression score produced an area under the receiver operating characteristic curve of 0.80 (95% CI: 0.79-0.81), and this level of accuracy was retained across patients enrolled from the early spring to summer of 2020. In the simplified score, a score of zero produced a sensitivity of 95.6% (94.8-96.3%), specificity of 20.0% (19.0-21.0%), negative likelihood ratio of 0.22 (0.19-0.26). Increasing points on the simplified score predicted higher probability of infection (e.g., >75% probability with +5 or more points). Criteria that are available at the point of care can accurately predict the probability of SARS-CoV-2 infection. These criteria could assist with decisions about isolation and testing at high throughput checkpoints.

COVID-19 Microbiological and Radiological Diagnostics

The purpose of this paper is to present SARS-CoV-2 diagnostic methods and their optimal implementation. The main routine microbiological diagnostic tools are molecular and serological methods. Sensitivity and utilisation of molecular methods is the best at the disease onset, while serological methods are the best if used at least 5-7 days after disease onset. Positive molecular test result (real-time polymerase chain reaction; RT-PCR) must be interpreted in the clinical presentation context. A sampling site for molecular analysis is based on disease severity; upper and lower respiratory tract samples are used for mild and severe presentations, respectively. Virus cultivation is the only method of proving the existence of a viable virus in a tissue sample, but due to the method complexity, it is not a part of a routine process. Ground glass opacities with or without reticular pattern and/or consolidation are typical findings for COVID-19 pneumonia. Multi-slice computerized tomography (MSCT) is a superior radiological method for performing X-ray of the chests.