SARS-CoV-2 sequencing with cloud-based analysis illustrates expedient co-ordinated surveillance of viral genomic epidemiology across six continents (preprint)

Viral sequencing has been critical in the COVID-19 pandemic response, but sequencing and bioinformatics capacity remain inconsistent. To examine the utility of a cloud-based sequencing analysis platform for SARS-CoV-2 sequencing, we conducted a cross-sectional study incorporating seven countries in July 2022. Sites submitted sequential SARS-CoV-2 sequences over two weeks to the Global Pathogen Analysis Service (GPAS). The GPAS bioinformatics cloud platform performs sequence assembly plus lineage and related sample identification. Users can share information with collaborators while retaining data ownership. Seven sites contributed sequencing reads from 5,346 clinical samples, of which 4,799/5,346 (89.8%) had a lineage identified. Omicron lineages dominated, with the vast majority being BA.5, BA.4 and BA.2, commensurate with contemporary genomic epidemiological observations. Phylogenetic analysis demonstrated low within-lineage diversity, and highly similar sequences present in globally disparate sites. A cloud-based analysis platform like GPAS addresses bioinformatics bottlenecks and facilitates collaboration in pathogen surveillance, enhancing epidemic and pandemic preparedness.

Higher dose corticosteroids in hospitalised COVID-19 patients with hypoxia but not requiring ventilatory support (RECOVERY): a randomised, controlled, open-label, platform trial (preprint)

Background: Low-dose corticosteroids have been shown to reduce mortality for hypoxic COVID-19 patients requiring oxygen or ventilatory support (non-invasive mechanical ventilation, invasive mechanical ventilation or extra-corporeal membrane oxygenation). We evaluated the use of a higher dose of corticosteroids in this patient group. Methods: This randomised, controlled, open-label platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]) is assessing multiple possible treatments in patients hospitalised for COVID-19. Eligible and consenting adult patients with clinical evidence of hypoxia (i.e. receiving oxygen or with oxygen saturation <92% on room air) were randomly allocated (1:1) to either usual care with higher dose corticosteroids (dexamethasone 20 mg once daily for 5 days followed by 10 mg once daily for 5 days or until discharge if sooner) or usual standard of care alone (which includes dexamethasone 6 mg once daily for 10 days or until discharge if sooner). The primary outcome was 28-day mortality. On 11 May 2022, the independent Data Monitoring Committee recommended stopping recruitment of patients receiving no oxygen or simple oxygen only to this comparison due to safety concerns. We report the results for these participants only. Recruitment of patients receiving ventilatory support continues. The RECOVERY trial is registered with ISRCTN (50189673) and clinicaltrials.gov ( NCT04381936 ). Findings: Between 25 May 2021 and 12 May 2022, 1272 COVID-19 patients with hypoxia and receiving no oxygen (1%) or simple oxygen only (99%) were randomly allocated to receive usual care plus higher dose corticosteroids versus usual care alone (of whom 87% received low dose corticosteroids during the follow-up period). Of those randomised, 745 (59%) were in Asia, 512 (40%) in the UK and 15 (1%) in Africa. 248 (19%) had diabetes mellitus. Overall, 121 (18%) of 659 patients allocated to higher dose corticosteroids versus 75 (12%) of 613 patients allocated to usual care died within 28 days (rate ratio [RR] 1.56; 95% CI 1.18-2.06; p=0.0020). There was also an excess of pneumonia reported to be due to non-COVID infection (10% vs. 6%; absolute difference 3.7%; 95% CI 0.7-6.6) and an increase in hyperglycaemia requiring increased insulin dose (22% vs. 14%; absolute difference 7.4%; 95% CI 3.2-11.5). Interpretation: In patients hospitalised for COVID-19 with clinical hypoxia but requiring either no oxygen or simple oxygen only, higher dose corticosteroids significantly increased the risk of death compared to usual care, which included low dose corticosteroids. The RECOVERY trial continues to assess the effects of higher dose corticosteroids in patients hospitalised with COVID-19 who require non-invasive ventilation, invasive mechanical ventilation or extra-corporeal membrane oxygenation.

Depression, Anxiety and Associated Factors among Frontline Hospital Healthcare Workers in the Fourth Wave of COVID-19: Empirical Findings from Vietnam.

(1) Background: This study aims to assess the magnitude of, and factors associated with, depression and anxiety among Vietnamese frontline hospital healthcare workers in the fourth wave of COVID-19; (2) Methods: A hospital based cross-sectional study was carried out within two weeks, October 2020, at a central COVID-19 treatment hospital. Depression and anxiety were measured with PHQ-9 and GAD-7, respectively. Bivariate and multivariate logistic regression analysis were applied to recognize variables related to depression and anxiety, respectively; (3) Results: Among 208 frontline hospital healthcare workers, overall prevalence of depressive symptoms, anxiety symptoms, and both symptoms of depression and anxiety was 38.94%, 25.48% and 24.04%, respectively, in healthcare workers. In a reduced model after using multivariate stepwise logistic regression, age (OR = 0.9, p = 0.001), marital status (OR = 7.84, p = 0.027), profession (OR = 0.39, p = 0.028), having experienced traumatic stress following a work event (OR = 46.24, p < 0.001), feeling at very high risk for COVID-19 (OR = 0.02, p < 0.04), and affected by workplace conditions (OR = 5.36, p < 0.001) were associated with the symptoms of depression. With regard to symptoms of anxiety, single status (OR: 12.18, p = 0.002), being medical technician (OR: 68.89, p < 0.001), alcohol use (OR: 6.83, p = 0.014), using pain relief medications (OR: 25.50, p = 0.047), having experienced traumatic stress following a family event (OR: 130.32, p = 0.001), having experienced traumatic stress following a work event (OR: 181.55, p = 0.002), reporting at very high risk for COVID-19 (OR: 29.64, p = 0.011), treating moderate (OR: 6.46, p = 0.038) and severe (OR: 18.96, p = 0.004) COVID-19 patients, and being significantly affected by the community (OR: 6.33, p = 0.003) were increased risk factors for the symptoms of anxiety. Meanwhile, those living with 4-5 people (OR: 0.15, p = 0.011), specializing in infectious disease (OR: 0.13, p = 0.044)/resuscitation and emergency medicine (OR: 0.04, p = 0.046), and having knowledge preparation before participating in COVID-19 (OR: 0.008, p = 0.014) were less associated with the symptoms of anxiety; (4) Conclusions: There was a relatively high prevalence among Vietnamese hospital healthcare workers exhibiting symptoms of depression and anxiety during the ongoing pandemic. Greater attention to training in psychological skills should be suggested for those belonging to a younger age group, being single/widowed/divorced, treating moderate and severe COVID-19 patients, feeling at very high risk for COVID-19, being significantly affected a lot the community or workplace conditions, or experiencing traumatic stress following a family/work event in the past week.

Associated Factors with Perceived Fear of COVID-19 among Vietnamese Hospital Healthcare Workers during Fourth Wave of the COVID-19 Pandemic: Policy Implications for Interconnected and Social- and Personal-Based Health Support.

(1) Background: The present study measures the fear of COVID-19 among hospital healthcare workers and identifies several factors associated with increasing fear of COVID-19. (2) Methods: A cross-sectional, hospital-based survey was conducted on healthcare workforce recruited from the National Hospital of Tropical Diseases from 1 October 2021 and 20 October 2021. We selected the participants who have been directly involved in diagnosing, treating, or providing nursing care to patients with COVID-19. The primary data was collected via sending the invitation directly to the participants, utilizing structured self-completed questionnaires. The seven-item fear of COVID-19 scale was used to measure the data. The responses of 208 hospital healthcare workers were included in the final analysis. (3) Results: Total score of COVID-19 fear was 19.62 (SD = 5.22). The COVID-19 fear score of 7 items ranged from 2.38 (SD = 0.83) to 3.21 (SD = 0.96). The lowest and highest scores were the item 'My hands become clammy when I think about Corona' and the item 'I am most afraid of corona' was the highest, respectively. Linear regression of the COVID-19 fear showed that the factors positively correlated with the fear of COVID-19 among hospital healthcare workers were: being influenced by the community (p = 0.001), feeling at very high risk of COVID-19 (p = 0.03), and experiencing traumatic stress with an academic event (p = 0.042). (4) Conclusions: Although these findings merit further elaboration, these preliminary findings suggest relatively great fear of the COVID-19 pandemic among Vietnamese hospital healthcare workers and that social and personal connections are necessary for maintaining the mental wellbeing.