The Experience of Testing for Coronavirus Disease (COVID-19) at a Single Diagnostic Center in Paraguay before the Introduction of Vaccination.

Soon after the declaration of the COVID-19 pandemic, the Institute for Health Sciences Research (IICS) of the National University of Asunción, Paraguay became a testing laboratory (COVID-Lab) for SARS-CoV-2. The COVID-Lab testing performance was assessed from 1 April 2020 to 12 May 2021. The effect of the pandemic on the IICS and how the COVID-Lab contributed to the academic and research activities of the institute were also assessed. IICS researchers and staff adjusted their work schedules to support the COVID-Lab. Of the 13,082 nasopharyngeal/oropharyngeal swabs processed, 2704 (20.7%) tested positive for SARS-CoV-2 by RT-PCR. Of the individuals testing positive, 55.4% were female and 48.3% were aged 21-40 years. Challenges faced by the COVID-Lab were unstable reagent access and insufficient staff; shifting obligations regarding research, academic instruction, and grantsmanship; and the continuous demands from the public for information on COVID-19. The IICS provided essential testing and reported on the progress of the pandemic. IICS researchers gained better laboratory equipment and expertise in molecular SARS-CoV-2 testing but struggled to manage their conflicting educational and additional research obligations during the pandemic, which affected their productivity. Therefore, policies protecting the time and resources of the faculty and staff engaged in pandemic-related work or research are necessary components of healthcare emergency preparedness.

Increased suicide rates in Mexico City during the COVID-19 pandemic outbreak: An analysis spanning from 2016 to 2021.

Objective: Coronavirus disease 2019 (COVID-19) has impacted mental health worldwide, and suicide can be a serious outcome of this. Thus, suicide characteristics were examined before and during the COVID-19 pandemic in Mexico City. Methods: This is a retrospective study including all Mexico City residents who had a coroner's record with a cause of death of intentional self-harm (ICD-10) from January 2016 to December 2021. Results: From 2016 to 2021, 3636 people committed suicide, of which 2869 were males (78.9%) and 767 females (21.1%). From 2016 to 2019 the suicide rate remained constant (∼6 per 100000) and dramatically increased in 2020 (10.45 per 100,000), to return to the levels of the previous year in 2021 (6.95 per 100000). The suicide rate in 2020 specifically increased from January to June (COVID-19 outbreak) in all age groups. Moreover, every year young people (15-24 years) have the maximum suicide rate and depression was the main suicide etiology. Conclusion: The COVID-19 pandemic outbreak increased the suicide rate, regardless of age, but suicide prevalence was higher in males and young people, regardless of the COVID-19 pandemic. These findings confirm that suicide is a complex and multifactorial problem and will allow the establishment of new guidelines for prevention and care strategies.

Dyspnea Severity Assessment Based on Vocalization Behavior with Deep Learning on the Telephone.

In this paper, a system to assess dyspnea with the mMRC scale, on the phone, via deep learning, is proposed. The method is based on modeling the spontaneous behavior of subjects while pronouncing controlled phonetization. These vocalizations were designed, or chosen, to deal with the stationary noise suppression of cellular handsets, to provoke different rates of exhaled air, and to stimulate different levels of fluency. Time-independent and time-dependent engineered features were proposed and selected, and a k-fold scheme with double validation was adopted to select the models with the greatest potential for generalization. Moreover, score fusion methods were also investigated to optimize the complementarity of the controlled phonetizations and features that were engineered and selected. The results reported here were obtained from 104 participants, where 34 corresponded to healthy individuals and 70 were patients with respiratory conditions. The subjects' vocalizations were recorded with a telephone call (i.e., with an IVR server). The system provided an accuracy of 59% (i.e., estimating the correct mMRC), a root mean square error equal to 0.98, false positive rate of 6%, false negative rate of 11%, and an area under the ROC curve equal to 0.97. Finally, a prototype was developed and implemented, with an ASR-based automatic segmentation scheme, to estimate dyspnea on line.

Exacerbación de las inequidades educativas en tiempos de Covid-19.

No disponible.

SARS-CoV-2 Variants in Paraguay: Detection and Surveillance with an Economical and Scalable Molecular Protocol.

SARS-CoV-2 variant detection relies on resource-intensive whole-genome sequencing methods. We sought to develop a scalable protocol for variant detection and surveillance in Paraguay, pairing rRT-PCR for spike mutations with Nanopore sequencing. A total of 201 acute-phase nasopharyngeal samples were included. Samples were positive for the SARS-CoV-2 N2 target and tested with the Spike SNP assay to detect mutations associated with the following variants: alpha (501Y), beta/gamma (417variant/484K/501Y), delta (452R/478K), and lambda (452Q/490S). Spike SNP calls were confirmed using amplicon (Sanger) sequencing and whole-genome (Nanopore) sequencing on a subset of samples with confirmed variant lineages. Samples had a mean N2 Ct of 20.8 (SD 5.6); 198/201 samples (98.5%) tested positive in the Spike SNP assay. The most common genotype was 417variant/484K/501Y, detected in 102/198 samples (51.5%), which was consistent with the P.1 lineage (gamma variant) in Paraguay. No mutations (K417 only) were found in 64/198 (32.3%), and K417/484K was identified in 22/198 (11.1%), consistent with P.2 (zeta). Seven samples (3.5%) tested positive for 452R without 478K, and one sample with genotype K417/501Y was confirmed as B.1.1.7 (alpha). The results were confirmed using Sanger sequencing in 181/181 samples, and variant calls were consistent with Nanopore sequencing in 29/29 samples. The Spike SNP assay could improve population-level surveillance for mutations associated with SARS-CoV-2 variants and inform the judicious use of sequencing resources.

Multisite Clinical Validation of Isothermal Amplification-Based SARS-CoV-2 Detection Assays Using Different Sampling Strategies.

Isothermal amplification-based tests have been introduced as rapid, low-cost, and simple alternatives to real-time reverse transcriptase PCR (RT-PCR) tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. The clinical performance of two isothermal amplification-based tests (Atila Biosystems iAMP coronavirus disease of 2019 [COVID-19] detection test and OptiGene COVID-19 direct plus RT-loop-mediated isothermal amplification [LAMP] test) was compared with that of clinical RT-PCR assays using different sampling strategies. A total of 1,378 participants were tested across 4 study sites. Compared with standard of care RT-PCR testing, the overall sensitivity and specificity of the Atila iAMP test for detection of SARS-CoV-2 were 76.2% and 94.9%, respectively, and increased to 88.8% and 89.5%, respectively, after exclusion of an outlier study site. Sensitivity varied based on the anatomic site from which the sample was collected. Sensitivity for nasopharyngeal sampling was 65.4% (range across study sites, 52.8% to 79.8%), for midturbinate was 88.2%, for saliva was 55.1% (range across study sites, 42.9% to 77.8%), and for anterior nares was 66.7% (range across study sites, 63.6% to 76.5%). The specificity for these anatomic collection sites ranged from 96.7% to 100%. Sensitivity improved in symptomatic patients (overall, 82.7%) and those with a higher viral load (overall, 92.4% for cycle threshold [CT] of ≤25). Sensitivity and specificity of the OptiGene direct plus RT-LAMP test, which was conducted at a single study site, were 25.5% and 100%, respectively. The Atila iAMP COVID test with midturbinate sampling is a rapid, low-cost assay for detecting SARS-CoV-2, especially in symptomatic patients and those with a high viral load, and could be used to reduce the risk of SARS-CoV-2 transmission in clinical settings. Variation of performance between study sites highlights the need for site-specific clinical validation of these assays before clinical adoption. IMPORTANCE Numerous SARS-CoV-2 detection assays have been developed and introduced into the market under emergency use authorizations (EUAs). EUAs are granted primarily based on small studies of analytic sensitivity and specificity with limited clinical validations. A thorough clinical performance evaluation of SARS-CoV-2 assays is important to understand the strengths, limitations, and specific applications of these assays. In this first large-scale multicentric study, we evaluated the clinical performance and operational characteristics of two isothermal amplification-based SARS-CoV-2 tests, namely, (i) iAMP COVID-19 detection test (Atila BioSystems, USA) and (ii) COVID-19 direct plus RT-LAMP test (OptiGene Ltd., UK), compared with those of clinical RT-PCR tests using different sampling strategies (i.e., nasopharyngeal, self-sampled anterior nares, self-sampled midturbinate, and saliva). An important specific use for these isothermal amplification-based, rapid, low-cost, and easy-to-perform SARS-CoV-2 assays is to allow for a safer return to preventive clinical encounters, such as cancer screening, particularly in low- and middle-income countries that have low SARS-CoV-2 vaccination rates.

Patients with schizophrenia have decreased COVID-19 prevalence among hospitalised patients with psychiatric and neurological diseases: A retrospective analysis in Mexican population.

BACKGROUND: Increased coronavirus disease 2019 (COVID-19) incidence and mortality in hospitalised patients with psychiatric and neurologic disorders have been reported. METHODS: The clinical records of 198 patients with psychiatric and neurological disorders hospitalised in the Dr Rafael Serrano Psychiatric Hospital in Puebla during the peak of the first wave of the COVID-19 pandemic in Mexico were analysed for psychiatric or neurologic diagnosis, gender, age, medical diagnosis, and COVID-19 prevalence. For patients with COVID-19, the effects of gender, and medical diagnosis were explored. RESULTS: There was an increased COVID-19 prevalence in the studied population (43.94%), compared with the national Mexican (~0.21% to 0.63%) and worldwide average in the general population (~0.13% to 4.28%). However, the mortality rate (5.75%) was lower than that reported in Mexico (11.28%-13.55%), which was higher than the worldwide average (2.95%-4.98%). We detected increased COVID-19 prevalence in patients with comorbidities (odds ratios [OR] 0.4; 95% CI: 0.2-1, P = .0447). Moreover, patients with schizophrenia spectrum disorders have a decreased predisposition to COVID-19 (OR 0.4, 95% CI: 0.2-0.8; P = .0250), as opposed to patients with intellectual disability that are predisposed to COVID-19 (OR 2.2, 95% CI: 0.2-0.8; P = .0434), in comparison with the rest of the hospital population. CONCLUSION: The prevalence of COVID-19 in hospitalised patients with psychiatric disorders is increased compared with that of the general population; however, a lower mortality rate was detected. Also, an increased risk of COVID-19 was detected in patients with comorbidities. Interestingly, the observed variation in COVID-19 prevalence in patients with schizophrenia and intellectual disability was not associated with age or other specific medical diagnoses.