Descriptive comparison of admission characteristics between pandemic waves and multivariable analysis of the association of the Alpha variant (B.1.1.7 lineage) of SARS-CoV-2 with disease severity in inner London

Directions of change in intrinsic case severity across successive SARS-CoV-2 variant waves have been inconsistent

OBJECTIVES

To determine how the intrinsic severity of successively dominant SARS-CoV-2 variants changed over the course of the pandemic.

METHODS

A retrospective cohort analysis in the NHS Greater Glasgow and Clyde (NHS GGC) Health Board. All sequenced non-nosocomial adult COVID-19 cases in NHS GGC with relevant SARS-CoV-2 lineages (B.1.177/Alpha, Alpha/Delta, AY.4.2 Delta/non-AY.4.2 Delta, non-AY.4.2 Delta/Omicron, and BA.1 Omicron/BA.2 Omicron) during analysis periods were included. Outcome measures were hospital admission, ICU admission, or death within 28 days of positive COVID-19 test. We report the cumulative odds ratio; the ratio of the odds that an individual experiences a severity event of a given level vs all lower severity levels for the resident and the replacement variant after adjustment.

RESULTS

After adjustment for covariates, the cumulative odds ratio was 1.51 (95% CI: 1.08-2.11) for Alpha versus B.1.177, 2.09 (95% CI: 1.42-3.08) for Delta versus Alpha, 0.99 (95% CI: 0.76-1.27) for AY.4.2 Delta versus non-AY.4.2 Delta, 0.49 (95% CI: 0.22-1.06) for Omicron versus non-AY.4.2 Delta, and 0.86 (95% CI: 0.68-1.09) for BA.2 Omicron versus BA.1 Omicron.

CONCLUSIONS

The direction of change in intrinsic severity between successively emerging SARS-CoV-2 variants was inconsistent, reminding us that the intrinsic severity of future SARS-CoV-2 variants remains uncertain.

Role of hospital strain in determining outcomes for people hospitalised with COVID-19 in England

BACKGROUND

In England, reported COVID-19 mortality rates increased during winter 2020/21 relative to earlier summer and autumn months. This study aimed to examine the association between COVID-19-related hospital bed-strain during this time and patient outcomes.

METHODS

This was a retrospective observational study using Hospital Episode Statistics data for England. All unique patients aged ≥18 years in England with a diagnosis of COVID-19 who had a completed (discharged alive or died in hospital) hospital stay with an admission date between 1 July 2020 and 28 February 2021 were included. Bed-strain was calculated as the number of beds occupied by patients with COVID-19 divided by the maximum COVID-19 bed occupancy during the study period. Bed-strain was categorised into quartiles for modelling. In-hospital mortality was the primary outcome of interest and length of stay a secondary outcome.

RESULTS

There were 253 768 unique hospitalised patients with a diagnosis of COVID-19 during a hospital stay. Patient admissions peaked in January 2021 (n=89 047), although the crude mortality rate peaked slightly earlier in December 2020 (26.4%). After adjustment for covariates, the mortality rate in the lowest and highest quartile of bed-strain was 23.6% and 25.3%, respectively (OR 1.13, 95% CI 1.09 to 1.17). For the lowest and the highest quartile of bed-strain, adjusted mean length of stay was 13.2 days and 11.6 days, respectively in survivors and was 16.5 days and 12.6 days, respectively in patients who died in hospital.

CONCLUSIONS

High levels of bed-strain were associated with higher in-hospital mortality rates, although the effect was relatively modest and may not fully explain increased mortality rates during winter 2020/21 compared with earlier months. Shorter hospital stay during periods of greater strain may partly reflect changes in patient management over time.

SARS-CoV-2 Variants by Whole-Genome Sequencing in a University Hospital in Bangkok: First to Third COVID-19 Waves

BACKGROUND

Multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants emerged globally during the recent coronavirus disease (COVID-19) pandemic. From April 2020 to April 2021, Thailand experienced three COVID-19 waves, and each wave was driven by different variants. Therefore, we aimed to analyze the genetic diversity of circulating SARS-CoV-2 using whole-genome sequencing analysis.

METHODS

A total of 33 SARS-CoV-2 positive samples from three consecutive COVID-19 waves were collected and sequenced by whole-genome sequencing, of which, 8, 10, and 15 samples were derived from the first, second, and third waves, respectively. The genetic diversity of variants in each wave and the correlation between mutations and disease severity were explored.

RESULTS

During the first wave, A.6, B, B.1, and B.1.375 were found to be predominant. The occurrence of mutations in these lineages was associated with low asymptomatic and mild symptoms, providing no transmission advantage and resulting in extinction after a few months of circulation. B.1.36.16, the predominant lineage of the second wave, caused more symptomatic COVID-19 cases and contained a small number of key mutations. This variant was replaced by the VOC alpha variant, which later became dominant in the third wave. We found that B.1.1.7 lineage-specific mutations were crucial for increasing transmissibility and infectivity, but not likely associated with disease severity. There were six additional mutations found only in severe COVID-19 patients, which might have altered the virus phenotype with an inclination toward more highly pathogenic SARS-CoV-2.

CONCLUSION

The findings of this study highlighted the importance of whole-genome analysis in tracking newly emerging variants, exploring the genetic determinants essential for transmissibility, infectivity, and pathogenicity, and helping better understand the evolutionary process in the adaptation of viruses in humans.

The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis

OBJECTIVES

The SARS-CoV-2 Alpha variant was associated with increased transmission relative to other variants present at the time of its emergence and several studies have shown an association between Alpha variant infection and increased hospitalisation and 28-day mortality. However, none have addressed the impact on maximum severity of illness in the general population classified by the level of respiratory support required, or death. We aimed to do this.

METHODS

In this retrospective multi-centre clinical cohort sub-study of the COG-UK consortium, 1475 samples from Scottish hospitalised and community cases collected between 1st November 2020 and 30th January 2021 were sequenced. We matched sequence data to clinical outcomes as the Alpha variant became dominant in Scotland and modelled the association between Alpha variant infection and severe disease using a 4-point scale of maximum severity by 28 days: 1. no respiratory support, 2. supplemental oxygen, 3. ventilation and 4. death.

RESULTS

Our cumulative generalised linear mixed model analyses found evidence (cumulative odds ratio: 1.40, 95% CI: 1.02, 1.93) of a positive association between increased clinical severity and lineage (Alpha variant versus pre-Alpha variants).

CONCLUSIONS

The Alpha variant was associated with more severe clinical disease in the Scottish population than co-circulating lineages.

COVID-19 Cluster in the Hematology/Respirology Ward of a University Hospital during the Seventh Wave of the SARS-CoV-2 Pandemic in Japan: A Descriptive Study

Objective Patients with hematological malignancies and solid organ tumors reportedly tend to have a more severe COVID-19 trajectory than do those with other diseases. We studied the clinical features and outcomes of nosocomial SARS-CoV-2 infection during the seventh wave of the pandemic. Methods This study retrospectively described the characteristics of COVID-19 clusters involving patients in the hematology/respirologyward of Kochi Medical School Hospital during the seventh wave of the pandemic of SARS-CoV-2. Patients and Materials A total of 40 individuals, including 25 patients and 15 healthcare workers, were studied. The diagnosis of SARS-CoV-2 infection was based on reverse transcription polymerase chain reaction performed on nasopharyngeal samples. Results Eleven patients had hematological diseases, and 14 had respiratory diseases. Most patients presented with a fever (n = 19) and/or sore throat (n = 10). Lower respiratory tract symptoms and pneumonia were rather infrequent, occurring in two patients. All patients received antivirals. The maximal severities were mild in 21 patients and moderate in 2. Two asymptomatic patients with SARS-CoV-2 infection did not develop symptoms of COVID-19. Cycle threshold values in nasopharyngeal samples were significantly lower in patients with COVID-19 than in those who were asymptomatic at the time of the diagnosis with SARS-CoV-2 infection. All SARS-CoV-2-infected inpatients recovered or did not develop symptoms of COVID-19. Conclusion COVID-19 vaccination, early or preemptive treatment with antivirals, and intrinsic changes in SARS-CoV-2 may have contributed to the more favorable outcomes in our series than in previously reported nosocomial clusters.

Demographic and clinical characteristics and outcomes of COVID-19 patients admitted to a university hospital in the west of Iran: a retrospective study in the third wave

COVID-19 is a disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The characteristics of this infectious disease vary from a country to another and from one peak to the next. The aim of the present study was to describe the COVID-19 patients hospitalized in Kermanshah, a city in the west of Iran, in the third peak of the disease and to identify in-hospital mortality determinants in this disease. Methods: In this retrospective study, the clinical and demographic characteristics, laboratory findings, prescribed treatments and outcome of all COVID-19 patients (definitive, suspected, and probable) were collected from the medical records department of Farabi Hospital affiliated with Kermanshah University of Medical Sciences, Kermanshah, Iran from 22 October to 20 November 2020. Results: In total, 665 COVID-19 patients (265 females and 400 males, mean age: 58.7 years) were enrolled, including 479 confirmed, 15 probable, and 30 suspected cases. About 84% of the patients presented with low oxygen saturation levels. The most common comorbidities were hypertension (15%), diabetes (10%), and cardiovascular disease (3%). The median (IQR) length of hospital stay was 6 (Nojomi et al., 2021; Flores-Vega et al., 2022; Fattahi et al., 2021; Cusinato et al., 2022; Avatef Fazeli et al., 2021 (4., 5., 6., 7., 8.)) and 7 (Javadi Mamaghani et al., 2021; Abdolahnejad et al., 2022; Nojomi et al., 2021; Flores-Vega et al., 2022; Fattahi et al., 2021; Cusinato et al., 2022; Avatef Fazeli et al., 2021; Sayad et al., 2021; Hesni et al., 2022; Buttenschøn et al., 2022; Smits et al., 2022; Rosenberger et al., 2021; Shi et al., 2022 (2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12., 13., 14.)) day in discharged and deceased patients, respectively. Eighty-two out of 655 patients admitted to the hospital and 39of the 60 patients admitted to the ICU died. In total, in-hospital mortality rate was 12.33%. Regarding lab variables, in the adjusted model, no significant difference was observed between discharged and deceased patients.The results of multivariable logistic regression showed that each one-unit increase in oxygen saturation (SPO2) increased the odds of survival by 0.88 times (aOR 0.88, 95% CI 0.78-0.99, p = 0.043). Moreover, each one-day increase in the length of ICU stay reduced the odds of mortality by 0.49 times (aOR 0.82, 95% CI 0.26-0.95, p = 0.035). Conclusion: Hospitalized COVID-19 patients were generally more ill during the third peak so that about 85% of the patients had SPO2 ≤ 93%. The in-hospital mortality rate was also high. Demographic and paraclinical variables (except SPO2 level) were not suitable predictors of mortality.

Severity of COVID-19 among Hospitalized Patients: Omicron Remains a Severe Threat for Immunocompromised Hosts

The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in the general population in the context of a relatively high immunity gained through the early waves of coronavirus disease 19 (COVID-19), and vaccination campaigns. Despite this context, a significant number of patients were hospitalized, and identifying the risk factors associated with severe disease in the Omicron era is critical for targeting further preventive, and curative interventions. We retrospectively analyzed the individual medical records of 1501 SARS-CoV-2 positive hospitalized patients between 13 December 2021, and 13 February 2022, in Belgium, of which 187 (12.5%) were infected with Delta, and 1036 (69.0%) with Omicron. Unvaccinated adults showed an increased risk of moderate/severe/critical/fatal COVID-19 (crude OR 1.54; 95% CI 1.09-2.16) compared to vaccinated patients, whether infected with Omicron or Delta. In adults infected with Omicron and moderate/severe/critical/fatal COVID-19 (n = 323), immunocompromised patients showed an increased risk of in-hospital mortality related to COVID-19 (adjusted OR 2.42; 95% CI 1.39-4.22), compared to non-immunocompromised patients. The upcoming impact of the pandemic will be defined by evolving viral variants, and the immune system status of the population. The observations support that, in the context of an intrinsically less virulent variant, vaccination and underlying patient immunity remain the main drivers of severe disease.

Real-world effectiveness of steroids in severe COVID-19: a retrospective cohort study

INTRODUCTION

Randomised controlled trials have shown that steroids reduce the risk of dying in patients with severe Coronavirus disease 2019 (COVID-19), whilst many real-world studies have failed to replicate this result. We aim to investigate real-world effectiveness of steroids in severe COVID-19.

METHODS

Clinical, demographic, and viral genome data extracted from electronic patient record (EPR) was analysed from all SARS-CoV-2 RNA positive patients admitted with severe COVID-19, defined by hypoxia at presentation, between March 13th 2020 and May 27th 2021. Steroid treatment was measured by the number of prescription-days with dexamethasone, hydrocortisone, prednisolone or methylprednisolone. The association between steroid > 3 days treatment and disease outcome was explored using multivariable cox proportional hazards models with adjustment for confounders (including age, gender, ethnicity, co-morbidities and SARS-CoV-2 variant). The outcome was in-hospital mortality.

RESULTS

1100 severe COVID-19 cases were identified having crude hospital mortality of 15.3%. 793/1100 (72.1%) individuals were treated with steroids and 513/1100 (46.6%) received steroid ≤ 3 days. From the multivariate model, steroid > 3 days was associated with decreased hazard of in-hospital mortality (HR: 0.47 (95% CI: 0.31-0.72)).

CONCLUSION

The protective effect of steroid treatment for severe COVID-19 reported in randomised clinical trials was replicated in this retrospective study of a large real-world cohort.

COVID-19 in the 47 countries of the WHO African region: a modelling analysis of past trends and future patterns

Background

COVID-19 has affected the African region in many ways. We aimed to generate robust information on the transmission dynamics of COVID-19 in this region since the beginning of the pandemic and throughout 2022.

Methods

For each of the 47 countries of the WHO African region, we consolidated COVID-19 data from reported infections and deaths (from WHO statistics); published literature on socioecological, biophysical, and public health interventions; and immunity status and variants of concern, to build a dynamic and comprehensive picture of COVID-19 burden. The model is consolidated through a partially observed Markov decision process, with a Fourier series to produce observed patterns over time based on the SEIRD (denoting susceptible, exposed, infected, recovered, and dead) modelling framework. The model was set up to run weekly, by country, from the date the first infection was reported in each country until Dec 31, 2021. New variants were introduced into the model based on sequenced data reported by countries. The models were then extrapolated until the end of 2022 and included three scenarios based on possible new variants with varying transmissibility, severity, or immunogenicity.

Findings

Between Jan 1, 2020, and Dec 31, 2021, our model estimates the number of SARS-CoV-2 infections in the African region to be 505·6 million (95% CI 476·0–536·2), inferring that only 1·4% (one in 71) of SARS-CoV-2 infections in the region were reported. Deaths are estimated at 439 500 (95% CI 344 374–574 785), with 35·3% (one in three) of these reported as COVID-19-related deaths. Although the number of infections were similar between 2020 and 2021, 81% of the deaths were in 2021. 52·3% (95% CI 43·5–95·2) of the region's population is estimated to have some SARS-CoV-2 immunity, given vaccination coverage of 14·7% as of Dec 31, 2021. By the end of 2022, we estimate that infections will remain high, at around 166·2 million (95% CI 157·5–174·9) infections, but deaths will substantially reduce to 22 563 (14 970–38 831).

Interpretation

The African region is estimated to have had a similar number of COVID-19 infections to that of the rest of the world, but with fewer deaths. Our model suggests that the current approach to SARS-CoV-2 testing is missing most infections. These results are consistent with findings from representative seroprevalence studies. There is, therefore, a need for surveillance of hospitalisations, comorbidities, and the emergence of new variants of concern, and scale-up of representative seroprevalence studies, as core response strategies.

Funding

None.