Epidemiological analysis of the first 1000 cases of SARS-CoV-2 lineage BA.1 (B.1.1.529, Omicron) compared with co-circulating Delta in Wales, UK

Transferring inpatients between wards drives large nosocomial COVID-19 outbreaks, Wales, 2020-22: a matched case-control study using routine and enhanced surveillance data

BACKGROUND

The role of the hospital environment in the spread of COVID-19 is unclear.

AIM

To measure associations between ward characteristics and outbreak size to inform mitigations.

METHODS

Wards with large (case wards) and small (control wards) outbreaks in three acute hospitals were compared. Cases were healthcare-associated COVID-19 inpatients (positive polymerase chain reaction test ≥8 days post admission). Case wards were adult medical/surgical wards with ≥10 cases within rolling 14-day periods, between April 1st, 2020 and April 30th, 2022. Control wards were equivalents with 2-9 cases. Demographic and laboratory data were extracted from routine surveillance systems. Continuous data were aggregated fortnightly and analysed as binary variables according to median values. Each case ward was compared with two control wards matched on outbreak start date (±14 days) to calculate odds ratios (ORs) and 95% confidence intervals (95% CIs) using univariable and conditional multivariable logistic regression.

FINDINGS

From 170 outbreaks (median: 5 cases; interquartile range: 2-9), 35 case wards were identified. Community admissions were lower in case wards vs control wards (5 vs 10 median admissions; P<0.01, respectively), whereas transfers between wards within the same hospital were higher (58 vs 29 median transfers; P<0.01, respectively). Wards with more transfers in the preceding fortnight were significantly more likely to experience a large outbreak (≥35 vs <35 transfers; adjusted OR: 9.08; 95% CI: 2.5-33).

CONCLUSION

We recommend safely minimizing patient movements, such as by asking clinicians to record the rationale for transfer, to reduce the likelihood of disease transmission.

Epidemiological and laboratory characteristics of Omicron infection in a general hospital in Guangzhou: a retrospective study

The COVID-19 pandemic caused by SARS-CoV-2 has emerged as a major global public health concern. In November 2022, Guangzhou experienced a significant outbreak of Omicron. This study presents detailed epidemiological and laboratory data on Omicron infection in a general hospital in Guangzhou between December 1, 2022, and January 31, 2023. Out of the 55,296 individuals tested, 12,346 were found to be positive for Omicron. The highest prevalence of positive cases was observed in the 20 to 39 age group (24.6%), while the lowest was in children aged 0 to 9 years (1.42%). Females had a higher incidence of infection than males, accounting for 56.6% of cases. The peak time of Omicron infection varied across different populations. The viral load was higher in older adults and children infected with Omicron, indicating age-related differences. Spearman's rank correlation analysis revealed positive correlations between Ct values and laboratory parameters in hospitalized patients with Omicron infection. These parameters included CRP (rs = 0.059, p = 0.009), PT (rs = 0.057, p = 0.009), INR (rs = 0.055, p = 0.013), AST (rs = 0.067, p = 0.002), LDH (rs = 0.078, p = 0.001), and BNP (rs = 0.063, p = 0.014). However, EO (Eosinophil, rs = -0.118, p < 0.001), BASO (basophil, rs = -0.093, p < 0.001), and LY (lymphocyte, rs = -0.069, p = 0.001) counts showed negative correlations with Ct values. Although statistically significant, the correlation coefficients between Ct values and these laboratory indices were very low. These findings provide valuable insights into the epidemiology of Omicron infection, including variations in Ct values across gender and age groups. However, caution should be exercised when utilizing Ct values in clinical settings for evaluating Omicron infection.

Multidisciplinary inpatient rehabilitation for older adults with COVID-19: a systematic review and meta-analysis of clinical and process outcomes

BACKGROUND

Older adults are at increased risk for disease severity and poorer prognosis following COVID-19 infection. The aim of this systematic review and meta-analysis is to explore the impact of multidisciplinary rehabilitation in the acute or post-acute hospital setting for older adults with COVID-19.

METHODS

The Cochrane library, EMBASE, Cinahl and Medline (via EBSCO), PubMed, and Web of Science were systematically searched in June 2022 and a repeat search was completed in March 2023. Screening, data extraction and quality appraisal were conducted independently by two reviewers. Studies reporting outcomes for older adults following multidisciplinary rehabilitation (provided by two or more Health and Social Care Professionals) were included. Both observational and experimental study designs were included. The primary outcome was functional ability. Secondary outcomes included discharge disposition, acute hospital and rehabilitation unit length of stay, mortality, primary and secondary healthcare utilisation, and long-term effects of COVID-19.

RESULTS

Twelve studies met the inclusion criteria, comprising a total of 570 older adults. Where reported, older adults stayed in the acute hospital for a mean of 18 days (95%CI, 13.35- 23.13 days) and in rehabilitation units for 19 days (95%CI, 15.88-21.79 days). There was a significant improvement in functional ability among older adults with COVID-19 who received multidisciplinary rehabilitation (REM, SMD = 1.46, 95% CI 0.94 to 1.98). The proportion of older adults who were discharged directly home following rehabilitation ranged from 62 to 97%. Two studies reported a 2% inpatient mortality rate of older persons during rehabilitative care. No study followed up patients after the point of discharge and no study reported on long term effects of COVID-19.

CONCLUSIONS

Multidisciplinary rehabilitation may result in improved functional outcomes on discharge from rehabilitation units/centres for older adults with COVID-19. Findings also highlight the need for further research into the long-term effect of rehabilitation for older adults following COVID-19. Future research should comprehensively describe multidisciplinary rehabilitation in terms of disciplines involved and the intervention provided.

SARS-CoV-2 Vaccine Breakthrough Infections of Omicron and Delta Variants in Healthcare Workers

Understanding SARS-CoV-2 breakthrough infections in vaccinated healthcare workers is of key importance in mitigating the effects of the COVID-19 pandemic in healthcare facilities. An observational prospective cohort study was conducted in vaccinated employees with acute SARS-CoV-2 infection between October 2021 and February 2022. Serological and molecular testing was performed to determine SARS-CoV-2 viral load, lineage, antibody levels, and neutralizing antibody titers. A total of 571 (9.7%) employees experienced SARS-CoV-2 breakthrough infections during the enrolment period, of which 81 were included. The majority (n = 79, 97.5%) were symptomatic and most (n = 75, 92.6%) showed Ct values < 30 in RT-PCR assays. Twenty-four (30%) remained PCR-positive for > 15 days. Neutralizing antibody titers were strongest for the wildtype, intermediate for Delta, and lowest for Omicron variants. Omicron infections occurred at higher anti-RBD-IgG serum levels (p = 0.00001) and showed a trend for higher viral loads (p = 0.14, median Ct difference 4.3, 95% CI [-2.5-10.5]). For both variants, viral loads were significantly higher in participants with lower anti-RBD-IgG serum levels (p = 0.02). In conclusion, while the clinical course of infection with both the Omicron and Delta variants was predominantly mild to moderate in our study population, waning immune response over time and prolonged viral shedding were observed.

Interaction of Laurusides 1 and 2 with the 3C-like Protease (Mpro) from Wild-Type and Omicron Variant of SARS-CoV-2: A Molecular Dynamics Study

Laurus nobilis (bay laurel) is a natural source of biological compounds, and some of its extracts and phytocompounds are also endowed with antiviral activity toward the family of the severe acute respiratory syndrome (SARS)-associated β-coronaviruses. Some glycosidic laurel compounds such as laurusides were proposed as inhibitors of important protein targets of SARS-CoV-2, which clearly recalls their potential as anti-COVID-19 drugs. Due to the frequent genomic variations of the β-coronaviruses and the consequent importance of evaluating a new drug candidate with respect to the variants of the target β-coronavirus, we decided to investigate at an atomistic level the molecular interactions of the potential laurel-derived drugs laurusides 1 and 2 (L01 and L02, respectively) toward a well-conserved and crucial target, the 3C-like protease (Mpro), using the enzymes of both the wild-type of SARS-CoV-2 and of the more recent Omicron variant. Thus, we performed molecular dynamic (MD) simulations of laurusides—SARS-CoV-2 protease complexes to deepen the knowledge on the stability of the interaction and compare the effects of the targeting among the two genomic variants. We found that the Omicron mutation does not significantly impact the lauruside binding and that L02 connects more stably with respect to L01 in the complexes from both variants, even though both compounds prevalently interact within the same binding pocket. Although purely in silico, the current study highlights the potential role of bay laurel phytocompounds in the antiviral and specifically anti-coronavirus research and shows their potential binding toward Mpro, corroborating the important commitment of bay laurel as functional food and disclosing novel scenarios of lauruside-based antiviral therapies.

Prevalence of Olfactory Dysfunction with the Omicron Variant of SARS-CoV-2: A Systematic Review and Meta-Analysis

The omicron variant is thought to cause less olfactory dysfunction than previous variants of SARS-CoV-2, but the reported prevalence differs greatly between populations and studies. Our systematic review and meta-analysis provide information regarding regional differences in prevalence as well as an estimate of the global prevalence of olfactory dysfunction based on 62 studies reporting information on 626,035 patients infected with the omicron variant. Our estimate of the omicron-induced prevalence of olfactory dysfunction in populations of European ancestry is 11.7%, while it is significantly lower in all other populations, ranging between 1.9% and 4.9%. When ethnic differences and population sizes are considered, the global prevalence of omicron-induced olfactory dysfunction in adults is estimated to be 3.7%. Omicron's effect on olfaction is twofold to tenfold lower than that of the alpha or delta variants according to previous meta-analyses and our analysis of studies that directly compared the prevalence of olfactory dysfunction between omicron and previous variants. The profile of the prevalence differences between ethnicities mirrors the results of a recent genome-wide association study that connected a gene locus encoding an odorant-metabolizing enzyme, UDP glycosyltransferase, to the extent of COVID-19-related loss of smell. Our analysis is consistent with the hypothesis that this enzyme contributes to the observed population differences.

Prevalence of Olfactory Dysfunction with the Omicron Variant of SARS-CoV-2: A Systematic Review and Meta-analysis

The omicron variant is thought to cause less olfactory dysfunction than previous variants of SARS-CoV-2, but the reported prevalence differs greatly between populations and studies. Our systematic review and meta-analysis provide information about regional differences in prevalence as well as an estimate of the global prevalence of olfactory dysfunction based on 62 studies reporting on 626,035 patients infected with the omicron variant. Our estimate of the omicron-induced prevalence of olfactory dysfunction in populations of European ancestry is 11.7%, while it is significantly lower in all other populations, ranging between 1.9% and 4.9%. When ethnic differences and population sizes are taken into account, the global prevalence of omicron-induced olfactory dysfunction in adults is estimated at 3.7%. Omicron’s effect on olfaction is twofold to tenfold lower than that of the alpha or delta variant, according to previous meta-analyses and our analysis of studies that directly compared prevalence of olfactory dysfunction between omicron and previous variants. The profile of prevalence differences between ethnicities mirrors the results of a recent genome-wide association study that implicated a gene locus encoding an odorant-metabolizing enzyme, UDP glycosyltransferase, to be linked to the extent of COVID-related loss of smell. Our analysis is consistent with the hypothesis that this enzyme contributes to the observed population differences.

Influencing factors of nucleic acid negative conversion in patients with mild and common COVID-19 induced by the Omicron variant of SARS-COV-2

OBJECTIVE

To observe the clinical characteristics of mild and common COVID-19 patients infected with the Omicron variant, and to analyze related factors affecting the time to negative conversion of viral nucleic acid detection.

METHODS

Clinical data of 1781 patients with coronavirus disease 2019 (COVID-19) admitted to a cabin hospital in Shanghai from April 12 to May 26, 2022, were retrospectively analyzed, including age, gender, height, weight, clinical symptoms, comorbid diseases, COVID-19 vaccination, treatment, and nucleic acid negative conversion time. Univariate and multivariate logistic regression analyses were used to analyze the influencing factors of nucleic acid negative conversion time.

RESULTS

Among the 1781 patients, 995 were male and 786 were female, with a median age of 39 (30, 52) years. There were 727 patients (40.8%) with overweight and obesity [body mass index (BMI) > 24 kg/cm 2) and 413 patients (23.2%) had comorbid diseases. 205 cases (11.5%) were not vaccinated while 1576 cases were vaccinated. There were 1233 cases (69.2%) with one or more symptoms. The main clinical symptoms were cough (60.3%), expectoration (50.4%) and fever (36.9%). 1444 cases (81.0%) were treated with Chinese medicine, 78 cases (4.4%) were treated with western medicine, 14 cases (0.8%) were treated with integrated Chinese and western medicine, and 245 cases (13.8%) did not receive any medical treatment. All patients improved and were discharged. The median nucleic acid negative conversion time was 10.3 (7.4, 12.4) d. Univariate and multivariate analysis showed that, age ≥ 60 years ( OR＝1.537, 95% CI: 1.116 - 2.115, P<0.01), BMI > 24 kg/cm 2 ( OR＝1.344, 95% CI: 1.106 - 1.634, P<0.01 ) and hypertension ( OR＝1.518, 95% CI: 1.094 - 2.106, P<0.05) were independent risk factors for prolonged nucleic acid negative conversion. COVID-19 vaccination ( OR=0.548, 95% CI: 0.398 - 0.755, P<0.01) was a protective factor, that is, vaccination shortened the time for the nucleic acid test to become negative.

CONCLUSIONS

The symptoms of the Omicron variant infection were relatively mild and occult. Age ≥ 60 years old, comorbid hypertension, no vaccination and BMI > 24 kg/cm 2 are independent influencing factors for prolonged nucleic acid negative conversion.

Machine learning-based scoring system to predict in-hospital outcomes in patients hospitalized with COVID-19

BACKGROUND

The evolution of patients hospitalized with coronavirus disease 2019 (COVID-19) is still hard to predict, even after several months of dealing with the pandemic.

AIMS

To develop and validate a score to predict outcomes in patients hospitalized with COVID-19.

METHODS

All consecutive adults hospitalized for COVID-19 from February to April 2020 were included in a nationwide observational study. Primary composite outcome was transfer to an intensive care unit from an emergency department or conventional ward, or in-hospital death. A score that estimates the risk of experiencing the primary outcome was constructed from a derivation cohort using stacked LASSO (Least Absolute Shrinkage and Selection Operator), and was tested in a validation cohort.

RESULTS

Among 2873 patients analysed (57.9% men; 66.6±17.0 years), the primary outcome occurred in 838 (29.2%) patients: 551 (19.2%) were transferred to an intensive care unit; and 287 (10.0%) died in-hospital without transfer to an intensive care unit. Using stacked LASSO, we identified 11 variables independently associated with the primary outcome in multivariable analysis in the derivation cohort (n=2313), including demographics (sex), triage vitals (body temperature, dyspnoea, respiratory rate, fraction of inspired oxygen, blood oxygen saturation) and biological variables (pH, platelets, C-reactive protein, aspartate aminotransferase, estimated glomerular filtration rate). The Critical COVID-19 France (CCF) risk score was then developed, and displayed accurate calibration and discrimination in the derivation cohort, with C-statistics of 0.78 (95% confidence interval 0.75-0.80). The CCF risk score performed significantly better (i.e. higher C-statistics) than the usual critical care risk scores.

CONCLUSIONS

The CCF risk score was built using data collected routinely at hospital admission to predict outcomes in patients with COVID-19. This score holds promise to improve early triage of patients and allocation of healthcare resources.