Genomic epidemiology of SARS-CoV-2 in Sudan: A retrospective analysis 2020-2022 (preprint)

SARS-CoV-2 was first detected in Sudan on 13th March 2020. Here, we describe the genomic epidemiology of SARS-CoV-2 in Sudan between May 2020 and April 2022 to understand the introduction and transmission of SARS-CoV-2 variants in the country. A total of 667 SARS-CoV-2 positive samples were successfully sequenced using the nCoV-19 Artic protocol on the Oxford Nanopore Technology ([≥]70% genome completeness). The genomes were compared with a select contemporaneous global dataset to determine genetic relatedness and estimate import/export events. The genomes were classified into 37 Pango lineages within the ancestral strain (107 isolates across 13 Pango lineages), Eta variant of interest (VOI) (78 isolates in 1 lineage), Alpha variant of concern (VOC) (10 isolates in 2 lineages), Beta VOC (26 isolates in 1 lineage), Delta VOC (171 isolates across 8 lineages) and Omicron VOC (242 isolates across 12 lineages). We estimated a total of 144 introductions of the observed variants from different countries across the globe. Multiple introductions of the Eta VOI, Beta VOC and Omicron VOC were observed in Sudan mainly from Europe and Africa. These findings suggest a need for continuous genomic surveillance of SARS-CoV-2 to monitor their introduction and spread consequently inform public health measures to combat SARS-CoV-2 transmission.

A multi-country phase 2 study to evaluate the suitcase lab for rapid detection of SARS-CoV-2 in seven Sub-Saharan African countries: Lessons from the field

Background : The COVID-19 pandemic led to severe health systems collapse, as well as logistics and supply delivery shortages across sectors. Delivery of PCR related healthcare supplies continue to be hindered. There is the need for a rapid and accessible SARS-CoV-2 molecular detection method in low resource settings. Objectives : To validate a novel isothermal amplification method for rapid detection of SARS-CoV-2 across seven sub-Sharan African countries. Study design : In this multi-country phase 2 diagnostic study, 3,231 clinical samples in seven African sites were tested with two reverse transcription Recombinase-Aided Amplification (RT-RAA) assays (based on SARS-CoV-2 Nucleocapsid (N) gene and RNA-dependent RNA polymerase (RdRP) gene). The test was performed in a mobile suitcase laboratory within 15 minutes. All results were compared to a real-time RT-PCR assay. Extraction kits based on silica gel or magnetic beads were applied. Results : Four sites demonstrated good to excellent agreement, while three sites showed fair to moderate results. The RdRP gene assay exhibited an overall PPV of 0.92 and a NPV of 0.88. The N gene assay exhibited an overall PPV of 0.93 and a NPV 0.88. The sensitivity of both RT-RAA assays varied depending on the sample Ct values. When comparing sensitivity between sites, values differed considerably. For high viral load samples, the RT-RAA assay sensitivity ranges were between 60.5 and 100% (RdRP assay) and 25 and 98.6 (N assay). Conclusion : Overall, the RdRP based RT-RAA test showed the best assay accuracy. This study highlights the challenges of implementing rapid molecular assays in field conditions. Factors that are important for successful deployment across countries include the implementation of standardized operation procedures, in-person continuous training for staff, and enhanced quality control measures.

Emerging Hybrid Online Learning in Post-pandemic Situation: Idealism and Reality

The Covid-19 pandemic has significantly changed the way of learning models, one of which is the implementation of hybrid online learning (HOL). Although some instructors have applied this model to their learning activities, the process and results are still not optimal due to various constraints. Therefore, this paper explores HOL implementation regarding its idealism and reality in post-pandemic situations where face-to-face (F2F) learning is allowed in limited circumstances. For this reason, a descriptive-analytical systematic review of the relevant papers discusses the implementation of learning with the HOL model and is relied upon in this study to draw the reality of its implementation and offer solutions to potential problems. The investigation shows that many instructors have tried to apply this learning model because it is considered very suitable in post-pandemic situations to facilitate students who can attend face-to-face (F2F) in classrooms and for those who choose to be in a different room but still need to keep interacting synchronously with the other participants in the classroom. However, this learning model is considered not optimal in the real situation, both regarding the learning process and achievement of expected learning outcomes, due to several technical and non-technical obstacles. © 2022 IEEE.

A multi-country phase 2 study to evaluate the suitcase lab for rapid detection of SARS-CoV-2 in seven Sub-Saharan African countries: Lessons from the field.

BACKGROUND: The COVID-19 pandemic led to severe health systems collapse, as well as logistics and supply delivery shortages across sectors. Delivery of PCR related healthcare supplies continue to be hindered. There is the need for a rapid and accessible SARS-CoV-2 molecular detection method in low resource settings. OBJECTIVES: To validate a novel isothermal amplification method for rapid detection of SARS-CoV-2 across seven sub-Sharan African countries. STUDY DESIGN: In this multi-country phase 2 diagnostic study, 3,231 clinical samples in seven African sites were tested with two reverse transcription Recombinase-Aided Amplification (RT-RAA) assays (based on SARS-CoV-2 Nucleocapsid (N) gene and RNA-dependent RNA polymerase (RdRP) gene). The test was performed in a mobile suitcase laboratory within 15 min. All results were compared to a real-time RT-PCR assay. Extraction kits based on silica gel or magnetic beads were applied. RESULTS: Four sites demonstrated good to excellent agreement, while three sites showed fair to moderate results. The RdRP gene assay exhibited an overall PPV of 0.92 and a NPV of 0.88. The N gene assay exhibited an overall PPV of 0.93 and a NPV 0.88. The sensitivity of both RT-RAA assays varied depending on the sample Ct values. When comparing sensitivity between sites, values differed considerably. For high viral load samples, the RT-RAA assay sensitivity ranges were between 60.5 and 100% (RdRP assay) and 25 and 98.6 (N assay). CONCLUSION: Overall, the RdRP based RT-RAA test showed the best assay accuracy. This study highlights the challenges of implementing rapid molecular assays in field conditions. Factors that are important for successful deployment across countries include the implementation of standardized operation procedures, in-person continuous training for staff, and enhanced quality control measures.

Quels sont les facteurs liés au vécu douloureux des patients atteints de rhumatisme inflammatoire chronique pendant la pandémie de la COVID-19 ?

Introduction La pandémie de Coronavirus a entraîné de nombreuses conséquences sur le bien-être, l'accès aux soins et le maintien thérapeutique chez les patients atteints de maladies chroniques. L'objectif de cette étude est d'évaluer l'impact du confinement sur le vécu douloureux des patients atteints de rhumatisme inflammatoire chronique (RIC) et les éventuels facteurs associés. Patients et méthodes Une étude transversale a été menée auprès de patients atteints de RIC à l'aide d'un questionnaire en ligne fournissant les caractéristiques des patients et de leur maladie et la douleur globale qu'ils avaient ressentie avant et pendant la période de confinement, en utilisant l'échelle visuelle analogique (EVA). Système d'analyse statistique IBM SPSS Statistics V20.0.0 a été utilisé pour analyser les données de l'étude. Nous avons effectué une analyse univariée puis multivariée pour rechercher les facteurs liés à la perception de la douleur pendant le confinement. Les valeurs qualitatives ont été analysées par le test du Chi2. Les valeurs quantitatives ont été analysées par le test de Student lorsque les mesures étaient normalement distribuées ou par un test non paramétrique (Mann-Whitney U) lorsque les mesures n'étaient pas normalement distribuées (le test de Kolmogorov-Smirnov a été utilisé pour tester la normalité). Résultats Parmi les 350 patients ayant répondu au questionnaire, la polyarthrite rhumatoïde représentait 62,3 %, la spondylarthropathie 34,3 % et le RIC indifférenciée 3,4 %. La douleur causée par le RIC pendant le confinement a été rapportée par 79,1 % des patients. L'EVA de la douleur a augmenté de manière significative pendant la pandémie (4,6 ± 2,8 et 5,4 ± 3 avant et pendant le confinement ;p < 0,001). En analyse multivariée, les facteurs impliqués dans la douleur étaient l'impact négatif du Coronavirus sur l'accès aux soins rhumatologiques, la mauvaise observance thérapeutique, la qualité du sommeil perturbée et l'impact psychologique négatif. Discussion Cette étude montre les difficultés rencontrées par les patients pour assurer un suivi régulier auprès de leurs rhumatologues et la forte prévalence de l'arrêt des traitements. L'expérience de la douleur pendant la pandémie serait déterminée par des facteurs liés aux patients eux-mêmes et à l'interruption du suivi de leur RIC. La plupart des patients ont réclamé des difficultés à consulter leur rhumatologue pour plusieurs raisons : les problèmes de transport et la crainte de contracter le Coronavirus sur le chemin de l'hôpital et une peur générale d'attraper la COVID-19 à l'hôpital même. Ce constat est alarmant et laisse craindre des poussées de RIC plus fréquentes en période post-pandémique. Conclusion L'enquête a montré que cette pandémie a augmenté l'expérience douloureuse chez les patients ayant un RIC. Les facteurs influençant le vécu douloureux doivent être pris en compte pour aider les patients à faire face à leurs RIC et à cette crise sanitaire mondiale.