Setting-Up a Rapid SARS-CoV-2 Genome Assessment by Next-Generation Sequencing in an Academic Hospital Center (LPCE, Louis Pasteur Hospital, Nice, France)

Introduction: Aside from the reverse transcription-PCR tests for the diagnosis of the COVID-19 in routine clinical care and population-scale screening, there is an urgent need to increase the number and the efficiency for full viral genome sequencing to detect the variants of SARS-CoV-2. SARS-CoV-2 variants assessment should be easily, rapidly, and routinely available in any academic hospital.Materials and Methods: SARS-CoV-2 full genome sequencing was performed retrospectively in a single laboratory (LPCE, Louis Pasteur Hospital, Nice, France) in 103 SARS-CoV-2 positive individuals. An automated workflow used the Ion Ampliseq SARS-CoV-2 panel on the Genexus Sequencer. The analyses were made from nasopharyngeal swab (NSP) (n = 64) and/or saliva (n = 39) samples. All samples were collected in the metropolitan area of the Nice city (France) from September 2020 to March 2021.Results: The mean turnaround time between RNA extraction and result reports was 30 h for each run of 15 samples. A strong correlation was noted for the results obtained between NSP and saliva paired samples, regardless of low viral load and high (>28) Ct values. After repeated sequencing runs, complete failure of obtaining a valid sequencing result was observed in 4% of samples. Besides the European strain (B.1.160), various variants were identified, including one variant of concern (B.1.1.7), and different variants under monitoring.Discussion: Our data highlight the current feasibility of developing the SARS-CoV-2 next-generation sequencing approach in a single hospital center. Moreover, these data showed that using the Ion Ampliseq SARS-CoV-2 Assay, the SARS-CoV-2 genome sequencing is rapid and efficient not only in NSP but also in saliva samples with a low viral load. The advantages and limitations of this setup are discussed.

The Economic Effects on Acute Care Surgery in a New York City Public Hospital During the COVID Pandemic

Background Since the start of the COVID-19 pandemic, less acute care surgical procedures have been performed and consequently hospitals have experienced significant revenue loss. We aim to investigate these procedures performed before and after the start of the COVID-19 pandemic, as well as their effect on the economy. Methods This is a retrospective analysis of patients who underwent cholecystectomies and appendectomies during March–May 2019 compared to the same time period in 2020 using Chi-square and t-tests. Results There were 345 patients who presented with appendicitis or cholecystitis to Elmhurst Hospital Center during the March–May 2019 and 2020 time period. There were three times as many total operations, or about 75%, in 2019 (261) compared to 2020 (84). There was a decrease in the number of admissions from 2019 to 2020 for both acute cholecystitis (149 vs 43, respectively) and acute appendicitis (112 vs 41, respectively). The largest decrease in the number of admissions in 2020 compared to 2019 was observed in April 2020 (98 vs 9, P < .01) followed by May [69 vs 20, P < .01], and March [94 vs 55, P < .01]. Corresponding to the decrease in operative patterns was a noticeable six-time reduction in revenue for the procedures in 2019 ($187,283) compared to 2020 ($30,415). Conclusion We observed almost a triple reduction in the number of cholecystitis and appendicitis procedures performed during the 2020 pandemic surge as compared to the 2019 pre-pandemic data. Elmhurst hospital also experienced four times the loss of revenue during the same time period.

Therapeutic and evolutive aspects of diaphyseal leg fractures at the Joseph Ravoahangy University Hospital Center Andrianavalona Madagascar

La prise en charge d’une fracture de jambe est fonction de la classification de la lésion, du plateau technique et de l’expérience du chirurgien. Le but de notre travail est de déterminer les aspects thérapeutique et évolutif des fractures diaphysaires de la jambe prises en charge au Service de Traumatologie du Centre Hospitalier Universitaire Joseph Ravoahangy Andrianavalona (CHU-JRA) Madagascar. Il s’agissait d’une étude descriptive de 74 patients hospitalisés dans le Service en 2017. Il y a une discrète prédominance des fractures ouvertes (52,7%) dont 41,01% étaient classés type II selon Gustilo Anderson. Les fractures concernaient les deux os dans 79,7%. Le traitement était orthopédique dans 74,7 % par un appareil plâtré cruro-pedieux précédé ou non d’une traction trans-calcanéenne. Parmi ceux qui ont été opérés, 47,4% ont bénéficié d’un enclouage centromédullaire type Kuntcher, 31,58% d’un fixateur externe et 21,02% d’une amputation transtibiale. L’évolution a été favorable dans 87,7%. Les complications étaient dominées par les infections (5,46%), lésions vasculo-nerveuses (4,09%) et les cals vicieux (1,36%). Le séjour hospitalier moyen étaient de 14 jours (1-86 jours). La prise en charge des fractures de jambe reste un challenge pour les chirurgiens dans les pays en voie de développement. L’optimisation de cette prise en charge passe par l’amélioration de l’accès aux soins et l’ajustement de la logistique hospitalière.

Evaluation of sanitary waste generated by the care of COVID patients, in the Jipijapa Basic Hospital

In the current moments in which the world population lives related to the COVID-19 pandemic, a pandemic that has affected all countries worldwide, can only be contained based on the strategies taken by the entire population where hospitals play a fundamental role in mitigation and community transmission. The Jipijapa Basic Hospital is a health institution that has cared for patients infected with this disease. The objective of this research is to find out if the Environmental Risk Management system is complied with in the hospital center, fundamentally-oriented towards compliance with the regulations that regulate the management of sanitary waste in health establishments, in such a way that contamination to personnel is not produced. that works on the site, thereby allowing better environmental conditions to be achieved, mitigating the disease and its transmission mechanisms. For the study, a diagnosis was made on the initial management of sanitary waste, generated in health establishments by the care of COVID-19 patients, in addition to the observation and application of surveys to administrative personnel of the hospital. It was obtained as a result that the workers know and comply with the regulations for the collection of hazardous solid waste within the hospital.

Fast, Reliable, and Simple Point-of-Care-like Adaptation of RT-qPCR for the Detection of SARS-CoV-2 for Use in Hospital Emergency Departments

During COVID-19 pandemics, the availability of testing has often been a limiting factor during patient admissions into the hospital. To circumvent this problem, we adapted an existing diagnostic assay, Seegene Allplex SARS-CoV-2, into a point-of-care-style direct qPCR (POC dqPCR) assay and implemented it in the Emergency Department of Clinical Hospital Center Rijeka, Croatia. In a 4-month analysis, we tested over 10,000 patients and demonstrated that POC-dqPCR is robust and reliable and can be successfully implemented in emergency departments and similar near-patient settings and can be performed by medical personnel with little prior experience in qPCR.

Asthma in Morocco: Retrospective Analysis of Case Characteristics reported by Hospital Units

Asthma is a serious public health problem. This study aimed to identify the characteristics of asthma cases reported by Agadir's Souss-Massa Regional Hospital Center (SMRHC). A retrospective analysis was carried out at the SMRHC's pneumology and paediatrics departments in 2019. As data support, reporting records and a data collection worksheet were used. This year, 141 cases were reported. The highest frequencies were observed in February (21.9%) and April (26.6%). Both males and females were affected (sex ratio Male/Female = 0.98). The asthmatics were, on average 40.7 ± 25.1 years old. The majority of the cases are from areas that are easily accessible for medical consultation at the SMRHC. To obtain more accurate knowledge and contribute to the research, related studies should be undertaken on this topic. Our findings, we hope, will act as a foundation for future research into improving the case registration system (digital support) and upgrading patient data in accordance with WHO and GINA guidelines.