Variant-specific symptoms of COVID-19 in a study of 1,542,510 adults in England

Risk tools for predicting long-term sequelae based on symptom profiles after known and undetected SARS-CoV-2 infections in the population

The aim was to determine the profile of long-term symptoms after known and undetected SARS-CoV-2 infections and to generate tools for risk and diagnostic assessment of Post-COVID syndrome (PCS). In the population-based Gutenberg COVID-19 Study (N = 10,250), sequential, systematic screening for SARS-CoV-2 was performed in 2020/2021. Individuals received a standardized interview on newly occurred or worsened symptoms since the infection or the pandemic. Robust Poisson regression models were fit to compare the frequency of symptoms between groups. Two scores were developed using machine learning techniques and prospectively validated in an independent cohort. Among n = 942 individuals, prevalence of long-term symptoms was 36.4% among individuals with known SARS-CoV-2 infection, 25.0% in those unknowingly infected, and 28.1% among the controls. Individuals with known infection more often reported smell (Prevalence ratio [PR] = 13.66 [95% confidence interval 4.99;37.41]) and taste disturbances (PR = 5.57 [2.62;11.81]), forgetfulness (PR = 2.88 [1.55;5.35]), concentration difficulties (PR = 2.83 [1.55;5.16], trouble with balance (PR = 2.74 [1.18;6.35]), and dyspnea (PR = 2.22 [1.18;4.19]) than controls. The risk score for predicting long-term sequelae based on symptoms during the acute infection had a cross-validated AUC of 0.74 and 0.72 when applied in an independent cohort (N = 6,570). The diagnostic score providing a probability of the presence of PCS had a cross-validated AUC of 0.66 and of 0.64 in the validation cohort (N = 3,176). Individuals with and without SARS-COV-2 infection reported persistent symptoms, but symptoms attributable to PCS were identified. The data-driven scores may help guide further diagnostic decisions in the initial management of PCS.

In-hospital Mortality Among Children and Adults Hospitalized with COVID-19 in Africa Across Pre-Delta, Delta, and Omicron SARS-CoV-2 Waves

BACKGROUND

This study examines in-hospital mortality among children and adults hospitalized with COVID-19 across the pre-Delta, Delta, and Omicron waves in the African region.

METHOD

We conducted a retrospective cohort study using individual-level data from 520,810 hospitalized children and adults in 13 African countries. Cox proportional hazards regression models were used to assess the impact of SARS-CoV-2 variants on in-hospital mortality.

FINDINGS

Among children, the risk of in-hospital mortality was comparable between pre-Delta and Delta waves (aHR 1.02, 95% CI 0.77-1.35). In adults, mortality increased by 6% during Delta wave compared with pre-Delta wave (aHR 1.06, 95% CI 1.04-1.09). During Omicron wave, mortality risk decreased significantly by 42% in children (aHR 0.58, 95% CI 0.43-0.80) and 59% in adults (aHR 0.41, 95% CI 0.40-0.43) compared to the Delta wave. Notably, the reduction in mortality risk during the Omicron wave was less pronounced for children with severe or critical COVID-19, those co-infected with HIV, and adults co-infected with both HIV and tuberculosis.

CONCLUSION

Despite a general reduction in mortality risk during Omicron wave, persistently high mortality in specific high-risk groups underscores the importance of prioritizing booster vaccinations and intensified treatment for vulnerable populations as per WHO recommendations.

The consequences of SARS-CoV-2 within-host persistence

SARS-CoV-2 causes an acute respiratory tract infection that resolves in most people in less than a month. Yet some people with severely weakened immune systems fail to clear the virus, leading to persistent infections with high viral titres in the respiratory tract. In a subset of cases, persistent SARS-CoV-2 replication results in an accelerated accumulation of adaptive mutations that confer escape from neutralizing antibodies and enhance cellular infection. This may lead to the evolution of extensively mutated SARS-CoV-2 variants and introduce an element of chance into the timing of variant evolution, as variant formation may depend on evolution in a single person. Whether long COVID is also caused by persistence of replicating SARS-CoV-2 is controversial. One line of evidence is detection of SARS-CoV-2 RNA and proteins in different body compartments long after SARS-CoV-2 infection has cleared from the upper respiratory tract. However, thus far, no replication competent virus has been cultured from individuals with long COVID who are immunocompetent. In this Review, we consider mechanisms of viral persistence, intra-host evolution in persistent infections, the connection of persistent infections with SARS-CoV-2 variants and the possible role of SARS-CoV-2 persistence in long COVID. Understanding persistent infections may therefore resolve much of what is still unclear in COVID-19 pathophysiology, with possible implications for other emerging viruses.

Post-acute sequelae of COVID-19 in people of Black ethnicities living with HIV in the United Kingdom

BackgroundThe COVID-19 pandemic disproportionately affected people of Black ethnicities, however, there are limited data on the post-acute sequelae of COVID-19 infection in these populations, and none in those with HIV.MethodsWe conducted a cross-sectional study in people of Black ethnicities with HIV in the UK. Participants were assessed for functional impairment, frailty, respiratory symptoms, anxiety and depression; they were also asked to rate aspects of their physical and mental health on a scale from 1 (poor) to 10 (excellent), both at enrolment and prior to the pandemic. We report associations with COVID-19 history and recovery status.ResultsWe enrolled 183 participants between June 2021 and October 2022, 131 (72%) of whom reported COVID-19. A history of COVID-19 was associated with a reduced ability to carry out usual activities (OR 2.54 [1.03-6.21], p = 0.04), an increase in pain, tiredness and breathlessness, and overall decline in physical health. Of those with a history of COVID-19, 111 (85%) reported to have fully recovered. Those who had not fully recovered reported poorer functional status (p < 0.001) and had higher generalised anxiety scores (p = 0.02). Objective measures of physical function were similar in those who reported no COVID-19, COVID-19 with full recovery, and COVID-19 with incomplete recovery.ConclusionsIn this cohort of Black people with HIV, participants with a history of COVID-19 reported a reduced ability to carry out activities of daily living and various other health issues. Although most people reported full recovery from COVID-19, self-reported limitations in functional status and anxiety were common sequelae.

Near-source wastewater surveillance of SARS-CoV-2, norovirus, influenza virus and RSV across five different sites in the UK

By tracking infectious diseases through sewage, municipal-scale wastewater surveillance has provided early warnings of future COVID-19 hospitalisations, identified biases in diagnostic testing, and is rapidly expanding to a broader array of pathogens. Despite applications in the targeted delivery of local interventions, near-source wastewater surveillance has received less attention and we know little about the near-source time series dynamics of contrasting pathogens. To address this, we conducted wastewater surveillance at five sites for SARS-CoV-2 and two sites for norovirus GI, norovirus GII, influenza A virus, influenza B virus, and human respiratory syncytial virus (RSV A and RSV B). Sites were selected for contrasting functions: an office, charity centre, museum, university, and care home. The key findings are (1) near-source wastewater detections were linked to local events (staff sickness, enhanced cleaning, changing populations); (2) wastewater detections decreased in the order norovirus GII > norovirus GI > SARS-CoV-2 ≈ influenza A ≈ RSV A > influenza B ≈ RSV B; (3) correlation between near-source wastewater data and national surveillance data increases as a function of catchment size and viral prevalence (examples include the SARS-CoV-2 BA.4/BA.5 variant peak at a museum and wastewater tracking the winter norovirus season); (4) strong weekday periodicity in near-source wastewater SARS-CoV-2 detections, with the correlation against COVID-19 case numbers increasing when modelling variable lag times between faecal shedding onset and clinical diagnosis (R2 = 0.45 increases to 0.84-0.86); (5) a log-linear relationship between the frequency of wastewater SARS-CoV-2 detection and log(catchment size⋅viral prevalence) (R2 = 0.6914-0.9066). Finally, we propose two use cases. Firstly, for rare or high-risk pathogens, near-source wastewater sentinel systems provide early warning of outbreaks, achieving high frequency community coverage without behaviour change and at low cost versus diagnostic testing. Secondly, for endemic pathogens, near-source wastewater reveals long-term patterns and trends, the effectiveness of local policies, and community vulnerabilities.

Estimating the effect of COVID-19 vaccination and prior infection on cycle threshold values as a proxy of SARS-CoV-2 viral load

OBJECTIVES

SARS-CoV-2 viral load could be an important parameter for transmission potential. Here, we use quantitative reverse transcription-polymerase chain reaction cycle threshold (Ct) values as a proxy for viral load. We assess the effect of COVID-19 vaccination and prior infection status on Ct value while accounting for the virus variant.

METHODS

Using Dutch SARS-CoV-2 community testing data (n = 409,925 samples) from 8 March 2021 to 31 December 2022, separate univariable linear regressions were conducted for each explanatory variable, including age, sex, testing date, variant of infection, time since symptom onset, and testing laboratory. Subsequently, causal inference analysis assessed the impact of prior infection and vaccination status on Ct values, employing inverse propensity score weighting to adjust for confounders.

RESULTS

Our findings revealed a negative correlation between age and Ct values. Additionally, we observed modest differences in Ct values between different variants of infection, with lower Ct values (indicative of higher viral load) noted for Omicron variants compared to earlier variants. In addition, our results indicated an increase in Ct value (lower viral load) with prior infection. Conversely, the impact of vaccination was less pronounced.

CONCLUSIONS

We observed an association between prior infection status and higher Ct values, suggesting a decrease in viral load, which could possibly indicate lower transmissibility.

Risk of neonatal SARS-CoV-2 infection: a retrospective cohort study based on infected mothers with gestational diabetes mellitus

Background

The COVID-19 pandemic has posed unprecedented challenges to global public health, especially for pregnant women and their offspring. However, little is known about the impact of maternal SARS-CoV-2 infection on neonatal outcomes, particularly in the context of coexisting gestational diabetes mellitus (GDM).

Methods

Hospitalized pregnant women with SARS-CoV-2 infection were retrospectively enrolled between November 2022 and January 2023, and matched with pregnant subjects free of SARS-CoV-2 infection based on their propensity scores. All women were tested for SARS-CoV-2 upon admission as part of routine procedures, then divided into groups of pregnant women with SARS-CoV-2 infection and GDM (SARS2+GDM), pregnant women with SARS-CoV-2 infection but without GDM (SARS2+noGDM), and pregnant women without SARS-CoV-2 infection or GDM (Normal group). A logistic regression model was used to study the risk of GDM, perinatal SARS-CoV-2 infection, and their interaction on neonatal SARS-CoV-2 infection.

Results

Of 378 pregnant women with SARS-CoV-2 infection, the neonatal infection rate was higher in the GDM group as compared to the SARS-CoV-2 infection only group, but both SARS-CoV-2 infection rates were lower than that of the normal control group. Logistic regression analysis identified an interaction between maternal SARS-CoV-2 infection and GDM on neonatal infection, where maternal SARS-CoV-2 infection (odds ratio [OR] = 0.31, 95%CI: 0.22-0.44) and vaccination for anti-SARS-CoV-2 (OR = 0.70, 95%CI: 0.50-0.98) were associated with lower odds of neonatal infection, while higher pre-pregnancy body mass index (BMI) (OR = 1.06, 95% CI: 1.02-1.10) and GDM (OR = 1.97, 95%CI: 1.21-3.21) were associated with higher odds of neonatal infection.

Conclusions

We demonstrate that the coexistence of GDM and perinatal SARS-CoV-2 infection was associated with an increased probability of neonatal SARS-CoV-2 infection.

Assessing the impact of SARS-CoV-2 on influenza-like illness surveillance trends in the community during the 2023/2024 winter in England

OBJECTIVES

Influenza-like-illness (ILI) is a commonly used symptom categorization in seasonal disease surveillance focusing on influenza in community and clinical settings. However, SARS-CoV-2 often causes presentation with a similar symptom profile. We explore how SARS-CoV-2-positive individuals can influence surveillance trends for the World Health Organization, the United States Centre for Disease Control, and the European Centre for Disease Control (ECDC) ILI criteria.

METHODS

Harnessing the Winter COVID-19 Infection Study in England, a cohort study, the prevalence of different ILI definitions is modeled using multilevel regression and poststratification using age and spatial stratifications with temporal smoothing. Trends over time across stratifications were compared for SARS-CoV-2 positive and negative individuals to understand differences in ILI trends. Symptom presentation across positive and negative SARS-CoV-2 cases were compared.

RESULTS

SARS-CoV-2 symptom profiles are shown to overlap with the ILI case definitions, particularly for "cough" and "fever", causing SARS-CoV-2 positive individuals to be frequently detected as ILI cases. The trend of SARS-CoV-2 positives is a substantial component of the ILI-modeled trend, driving an earlier perceived peak in prevalence. The ECDC symptom definition was most influenced by SARS-CoV-2 positive individuals.

CONCLUSIONS

Using a large community cohort we show how SARS-CoV-2 can impact ILI surveillance trends. SARS-CoV-2 makes up a substantial part of the community ILI burden and public health messaging should reflect this when discussing ILI. We show ILI is no longer a strong proxy for influenza activity alone.

Cognitive deficits and cortical volume loss in COVID-19-related hyposmia

BACKGROUND AND PURPOSE

Studies have found that up to 73% of COVID-19 patients experience hyposmia. It is unclear if the loss of smell in COVID-19 is due to damage to the peripheral or central mechanisms. This study aimed to explore the impacts of COVID-19-induced hyposmia on brain structure and cognitive functions.

METHODS

The study included 36 hyposmic (h-COV) and 21 normosmic (n-COV) participants who had recovered from mild COVID-19 infection, as well as 25 healthy controls (HCs). All participants underwent neurological examination, neuropsychiatric assessment and Sniffin' Sticks tests. High-resolution anatomical images were collected; olfactory bulb (OB) volume and cortical thickness were measured.

RESULTS

Addenbrooke's Cognitive Examination-Revised total and language sub-scores were slightly but significantly lower in the h-COV group compared to the HC group (p = 0.04 and p = 0.037). The h-COV group exhibited poorer performance in the Sniffin' Sticks test terms of discrimination score, identification score and the composite score compared to the n-COV and HC groups (p < 0.001, p = 0.001 and p = 0.002 respectively). A decrease in left and right OB volumes was observed in the h-COV group compared to the n-COV and HC groups (p = 0.003 and p = 0.006 respectively). The cortical thickness analysis revealed atrophy in the left lateral orbitofrontal cortex in the h-COV group compared to HCs. A significant low positive correlation of varying degrees was detected between discrimination and identification scores and both OB and left orbital sulci.

CONCLUSION

Temporary or permanent hyposmia after COVID-19 infection leads to atrophy in the OB and olfactory-related cortical structures and subtle cognitive problems in the long term.

Assessing the impact of severe acute respiratory syndrome coronavirus 2 infection on hematological parameters

BACKGROUND

The current study is a retrospective study designed to evaluate changes in complete blood count and coagulation parameters in adult coronavirus disease 2019 (COVID-19) patients at a prominent Saudi tertiary center to predict disease severity and mortality.

METHODS

The cohort consisted of 74 800 adult patients divided into four groups based on a COVID-19 test and the patient's sex: 35 985 in the female negative COVID-19 group, 23 278 in the male negative COVID-19 group, 8846 in the female positive COVID-19 group and 6691 in the male positive COVID-19 group.

RESULTS

Patients with COVID-19 demonstrated decreased white blood cell counts and increased red blood cell counts. Also, COVID-19-positive participants exhibited more prolonged partial thromboplastin time and lower D-dimer levels than those of COVID-19-negative subjects (p<0.05). The study also revealed gender-dependent impacts on platelet counts, implying a possible relationship with the greater infection mortality rate in men than in women (p<0.001). In addition, the study found a link between changes in coagulation test results and death in COVID-19 patients (p<0.001). The evidence regarding the effects of COVID-19 on blood cell counts and coagulation, on the other hand, is conflicting, most likely due to variances in study populations and the timing of testing postinfection.

CONCLUSIONS

According to the findings, COVID-19-related alterations in blood cell count and clotting ability may be risk factors for death.

Seroprevalence and silent infection rate during SARS-CoV-2 pandemic among children and adolescents in Western Pomerania: a multicenter, cross-sectional study-the COVIDKID study

Background

Limited data on SARS-CoV-2 seroprevalence in rural areas of northern Germany necessitate comprehensive cohort studies. We aimed to evaluate the seroprevalence, silent infection (SI) rates and risk factors for infections among children and adolescents in Western Pomerania from December 2020 to August 2022.

Methods

In this cross-sectional study, serum or plasma samples from children and adolescents (6 months to 17 years) were collected during routine blood draw. SARS-CoV-2 specific antibodies (S1 and nucleocapsid) and their neutralizing capacity were analyzed using commercially available enzyme-linked immunosorbent and neutralization assays. Socio-demographic data and information about SARS-CoV-2 infection or vaccination were obtained. Multivariable logistic regression was used to identify independent risk factors for SARS-CoV-2 infections and SI.

Results

A total of 1,131 blood samples were included into the study. Overall, SARS-CoV-2 seroprevalence was 25.1%, strongly influenced by the pandemic course, predominant virus variants, age and approval of vaccination. SI rate was 5.4% (95%-CI [3.7%-6.8%]) among unvaccinated and undiagnosed children over the entire study period with highest rates among adolescents. Main risk factor despite the time at risk for silent infections was an infected household member (Odds ratio = 9.88, 95%-CI [4.23-22.9], p < 0.001). Factors associated with overall infections (known and silent) also include the infection of a household member (Odds ratio = 17.8, 95%-CI [10.7-29.6], p < 0.001).

Conclusions

We believe that the introduction of governmental measures and systematic test strategies in schools strongly impacted on the SI rate, as we suspect that asymptomatic cases have already been identified, resulting in surprisingly low SI identified in our study.

Association of pre-existing depression and anxiety with Omicron variant infection

Pre-existing psychiatric disorders were linked to an increased susceptibility to COVID-19 during the initial outbreak of the pandemic, while evidence during Omicron prevalence is lacking. Leveraging data from two prospective cohorts in China, we identified incident Omicron infections between January 2023 and April 2023. Participants with a self-reported history or self-rated symptoms of depression or anxiety before the Omicron pandemic were considered the exposed group, whereas the others were considered unexposed. We employed multivariate logistic regression models to examine the association of pre-existing depression or anxiety with the risk of any or severe Omicron infection indexed by medical interventions or severe symptoms. Further, we stratified the analyses by polygenic risk scores (PRSs) for COVID-19 and repeated the analyses using the UK Biobank data. We included 10,802 individuals from the Chinese cohorts (mean age = 51.1 years, 45.6% male), among whom 7841 (72.6%) were identified as cases of Omicron infection. No association was found between any pre-existing depression or anxiety and the overall risk of Omicron infection (odds ratio [OR] =1.04, 95% confidence interval [CI] 0.95-1.14). However, positive associations were noted for severe Omicron infection, either as infections requiring medical interventions (1.26, 1.02-1.54) or with severe symptoms (≥3: 1.73, 1.51-1.97). We obtained comparable estimates when stratified by COVID-19 PRS level. Additionally, using clustering method, we identified eight distinct symptom patterns and found associations between pre-existing depression or anxiety and the patterns characterized by multiple or complex severe symptoms including cough and taste and smell decline (ORs = 1.42-2.35). The results of the UK Biobank analyses corroborated findings of the Chinese cohorts. In conclusion, pre-existing depression and anxiety was not associated with the risk of Omicron infection overall but an elevated risk of severe Omicron infection, supporting the continued efforts on monitoring and possible early intervention in this high-risk population during Omicron prevalence.

T Cell Peptide Prediction, Immune Response, and Host-Pathogen Relationship in Vaccinated and Recovered from Mild COVID-19 Subjects

COVID-19 remains a significant threat, particularly to vulnerable populations. The emergence of new variants necessitates the development of treatments and vaccines that induce both humoral and cellular immunity. This study aimed to identify potentially immunogenic SARS-CoV-2 peptides and to explore the intricate host-pathogen interactions involving peripheral immune responses, memory profiles, and various demographic, clinical, and lifestyle factors. Using in silico and experimental methods, we identified several CD8-restricted SARS-CoV-2 peptides that are either poorly studied or have previously unreported immunogenicity: fifteen from the Spike and three each from non-structural proteins Nsp1-2-3-16. A Spike peptide, LA-9, demonstrated a 57% response rate in ELISpot assays using PBMCs from 14 HLA-A*02:01 positive, vaccinated, and mild-COVID-19 recovered subjects, indicating its potential for diagnostics, research, and multi-epitope vaccine platforms. We also found that younger individuals, with fewer vaccine doses and longer intervals since infection, showed lower anti-Spike (ELISA) and anti-Wuhan neutralizing antibodies (pseudovirus assay), higher naïve T cells, and lower central memory, effector memory, and CD4hiCD8low T cells (flow cytometry) compared to older subjects. In our cohort, a higher prevalence of Vδ2-γδ and DN T cells, and fewer naïve CD8 T cells, seemed to correlate with strong cellular and lower anti-NP antibody responses and to associate with Omicron infection, absence of confusional state, and habitual sporting activity.

Variability in COVID-19 symptom presentation during pregnancy and its impact on maternal and infant outcomes across the pandemic

BACKGROUND

With the dominance of different SARS-CoV-2 variants, the severity of COVID-19 has evolved. We aimed to investigate the difference in symptom prevalence and the association between symptoms and adverse pregnancy outcomes during the dominance of Wild-type/Alpha, Delta, and Omicron.

METHODS

COVID-19 related symptom prevalence, maternal and specific neonatal outcomes of 5431 pregnant women registered in this prospective study were compared considering the dominant virus variant. Logistic regression models analyzed the association between specific symptoms and intensive care unit (ICU) admission or preterm birth.

RESULTS

Infection with the Delta variant led to an increase in the symptom burden compared to the Wild-type/Alpha variant and the highest risk for respiratory tract symptoms, feeling of sickness, headache, and dizziness/drowsiness. An infection with the Omicron variant was associated with the lowest risk of dyspnea and changes in smell/taste but the highest risk for nasal obstruction, expectoration, headaches, myalgia, and fatigue compared to the Wild-type/Alpha and Delta variant dominant periods. With the progression of the Wild-type/Alpha to the Delta variant neonatal outcomes worsened. Dyspnea and fever were strong predictors for maternal ICU admission and preterm birth independent of vaccination status or trimester of infection onset.

CONCLUSION

The symptom burden increased during the Delta period and was associated with worse pregnancy outcomes than in the Wild-type/Alpha area. During the Omicron dominance there still was a high prevalence of less severe symptoms. Dyspnea and fever can predict a severe maternal illness.

Long-COVID olfactory dysfunction: allele E4 of apolipoprotein E as a possible protective factor

BACKGROUND

 Olfactory dysfunction (OD) represents a frequent manifestation of the coronavirus disease 2019 (COVID-19). Apolipoprotein E (APOE) is a protein that interacts with the angiotensin-converting enzyme receptor, essential for viral entry into the cell. Previous publications have suggested a possible role of APOE in COVID-19 severity. As far as we know, no publications found significant associations between this disease's severity, OD, and APOE polymorphisms (E2, E3, and E4).

OBJECTIVE

 To analyze the epidemiology of OD and its relationship with APOE polymorphisms in a cohort of Long-COVID patients.

METHODS

 We conducted a prospective cohort study with patients followed in a post-COVID neurological outpatient clinic, with OD being defined as a subjective reduction of olfactory function after infection, and persistent OD being defined when the complaint lasted more than 3 months after the COVID-19 infection resolution. This cross-sectional study is part of a large research with previously reported data focusing on the cognitive performance of our sample.

RESULTS

 The final sample comprised 221 patients, among whom 186 collected blood samples for APOE genotyping. The persistent OD group was younger and had a lower hospitalization rate during the acute phase of the disease (p < 0.001). Furthermore, the APOE variant E4 allele frequency was lower in this group (p = 0.035). This study evaluated OD in an outpatient population with COVID-19. In the current literature on this disease, anosmia is associated with better clinical outcomes and the E4 allele is associated with worse outcomes.

CONCLUSION

 Our study provides new information to these correlations, suggesting APOE E4 as a protective factor for OD.

The relationship between COVID-19 and hyperglycemia: screening and monitoring hospitalized patients

BACKGROUND

Elevated blood glucose concentration, also known as hyperglycemia, has been identified as a significant factor influencing the prognosis of COVID-19, alongside the impact of the SARS-CoV-2 infection itself.

METHODS

This research is a cross-sectional investigation that examined the relationship between COVID-19 and hyperglycemia in patients admitted to Afzalipour Hospital in Kerman, Iran, from July to September 2021. A standardized data sheet was used to capture demographic data (age, gender) and laboratory information (blood sugar, arterial blood oxygen saturation, and C-reactive protein (CRP)) upon admission.

RESULTS

The present research evaluated a total of 300 individuals diagnosed with COVID-19, with an average age of 50.19 ± 15.55 years. Among these patients, the majority were male, accounting for 51.67% of the total. Hyperglycemia was seen in 21.67% of patients, but less than 20% had new-onset diabetes. Individuals exhibiting hyperglycemia were typical of advanced age (P < 0.001). Furthermore, there was a slight but statistically significant association between advanced age and elevated blood glucose concentration (R = 0.254, P < 0.001). Gender had no significant impact on the occurrence of hyperglycemia (P = 0.199). There was no significant association between CRP levels and blood glucose concentration (P = 0.524) or the incidence of hyperglycemia (P = 0.473). Although there was no significant disparity in blood oxygen saturation between individuals with or without hyperglycemia (P = 0.06), higher blood glucose concentration was correlated with lower blood oxygen saturation (R = -0.151, P < 0.001).

CONCLUSION

Considering the correlation between blood glucose concentration, advanced age, and disease severity, it is recommended to carefully screen and monitor all COVID-19 patients for hyperglycemia and new-onset diabetes. Effective management of these complications could enhance the control of patients' overall prognosis and subsequent complications.

Comparison of sinonasal symptoms in upper respiratory tract infections during the infectious diseases season of November 2023 to March 2024-a cross-sectional study

Introduction

Upper respiratory tract infections (URTIs) are among the most common reasons for patients consulting a general practitioner (GP) during the infectious diseases season, with viruses being the predominant cause. The COVID-19 pandemic has significantly impacted GPs' perception of these infections. The pandemic's progression, especially with the emergence of the Omicron variant, has complicated the diagnosis and treatment of URTIs, with evolving symptoms.

Aim

The aim of this study was to assess the differences in symptoms reported by patients with various infections, such as COVID-19, influenza, common cold, and post-viral rhinosinusitis, during the infectious diseases season of November 2023 to March 2024.

Materials and methods

The study was conducted in a primary health care clinic, providing care for a population of approximately 10,000 people, among adult patients presenting with URTI symptoms during the 2023/2024 infectious diseases season. Patients qualified for the study were swabbed for SARS-CoV-2, influenza A and B and respiratory syncytial virus (RSV) antigens. Symptoms were assessed with the use of a semi-structured questionnaire.

Results

Of the 1810 patients presenting with symptoms of URTIs, 276 patients were included in the study. Among patients with COVID-19, symptoms of nasal obstruction (p = 0.005) and nasal discharge (p = 0.001) were less common than in those with influenza or common cold. However, these nasal symptoms were significantly more frequent among patients with COVID-19 who had confirmed previous immunization (COVID-19 history or vaccination) (p = 0.028).

Conclusion

The incidence of individual sinonasal symptoms varies significantly depending on the aetiological agent of the URTI. This observation may not only help clinicians make the correct diagnosis, but also suggests an inflammatory response in the nasal mucosa and paranasal sinuses that is dependent on the aetiological agent. The study also indicates that this response is altered within the same virus species following immunization.

Limitations

The study's limitations include a small sample size (276 patients), focus on one season and one GP practice, and reliance on clinical signs and antigen tests. Nonetheless, the findings provide valuable insights. Further research with larger patient groups and extended follow-up periods is required to confirm these findings.

Trends in symptom prevalence and sequential onset of SARS-CoV-2 infection from 2020 to 2022 in East and Southeast Asia: a trajectory pattern exploration based on summary data

BACKGROUND

The COVID-19 pandemic's diverse symptomatology, driven by variants, underscores the critical need for a comprehensive understanding. Employing stochastic models, our study evaluates symptom sequences across SARS-CoV-2 variants on aggregated data, yielding essential insights for targeted interventions.

METHODS

We conducted a meta-analysis based on research literature published before December 9, 2022, from PubMed, LitCovid, Google Scholar, and CNKI databases, to investigate the prevalence of COVID-19 symptoms during the acute phase. Registered in PROSPERO (CRD42023402568), we performed random-effects meta-analyses using the R software to estimate pooled prevalence and 95% CI. Based on our findings, we introduced the Stochastic Progression Model and Sequential Pattern Discovery using Equivalence classes (SPADE) algorithm to analyze patterns of symptom progression across different variants.

RESULTS

Encompassing a total of 430,100 patients from east and southeast Asia, our results reveal the highest pooled estimate for cough/dry cough across wild-type, Delta, and Omicron variants, with fever (78.18%; 95% CI: 67-89%) being the most prominent symptom for the Alpha variant. Symptoms associated with the Omicron variant primarily manifested in upper respiratory tracts, cardiovascular, and neuropsychiatric systems. Stochastic models indicate early symptoms including dry cough and fever, followed by subsequent development of sleep disorders, fatigue, and more.

CONCLUSION

Our study underscores the evolving symptomatology across SARS-CoV-2 variants, emphasizing similarities in fever, cough, and fatigue. The Omicron variant presents a distinct profile characterized by milder symptoms yet heightened neuropsychological challenges. Advanced analytical models validate the observed sequential progression of symptoms, reinforcing the consistency of disease trajectory.

Residential greenspace and COVID-19 Severity: A cohort study of 313,657 individuals in Greater Manchester, United Kingdom

BACKGROUND

Greenspaces contribute positively to mental and physical well-being, promote social cohesion, and alleviate environmental stressors, such as air pollution. Ecological studies suggest that greenspace may affect incidence and severity of Coronavirus Disease 2019 (COVID-19).

OBJECTIVE

This study examines the association between residential greenspace and COVID-19 related hospitalization and death.

METHOD

In this retrospective cohort based on patient records from the Greater Manchester Care Records, all first COVID-19 cases diagnosed between March 1, 2020, and May 31, 2022 were followed until COVID-19 related hospitalization or death within 28 days. Residential greenspace availability was assessed using the Normalized Difference Vegetation Index per lower super output area in Greater Manchester. The association of greenspace with COVID-19 hospitalization and mortality were estimated using multivariate logistic regression models after adjusting for potential individual, temporal, and spatial confounders. We explored potential effect modifications of the associations with greenspace and COVID-19 severity by age, sex, body mass index, smoking, deprivation, and certain comorbidities. Combined effects of greenspace and air pollution (NO2 and PM2.5) were investigated by mutually adjusting pairs with correlation coefficients ≤ 0·7.

RESULTS

Significant negative associations were observed between greenspace availability and COVID-19 hospitalization and mortality with odds ratios [OR] (95 % Confidence Intervals [CI]) of 0·96 (0·94-0·97) and 0·84 (0·80-0·88) (per interquartile range [IQR]), respectively. These were significantly modified by deprivation (P-value for interaction < 0.05), showing that those most deprived obtained largest benefits from greenspace. Inclusion of NO2 and PM2.5 diminished associations to null for COVID-19 hospitalization, but only reduced them slightly for mortality, where inverse associations remained.

CONCLUSION

In the Greater Manchester area, residential greenspace is associated with reduced risk of hospitalization or death in individuals with COVID-19, with deprived groups obtaining the greatest benefits. Associations were strongest for COVID-19 mortality, which were robust to inclusion of air pollutants in the models.

[Post-COVID patients with persistent chemosensory symptoms are rare in the general population]

OBJECTIVE

The prevalence of long-/post-COVID-associated chemosensory symptoms is reported in the literature to be significantly higher than clinical reality reflects.

METHODS

1. N= 4062 adults acutely infected with SARS-CoV-2 and their symptoms transmitted by the Jena health office to the Robert Koch Institute between March 2020 and September 2021 were evaluated. 2. Part of the same cohort (N = 909 of 4062) answered an extensive questionnaire at least 3 months after the start of the infection, including existing chemosensory post-COVID-associated complaints. 3. Fourteen post-COVID Jena patients with chemosensory symptoms who had become acutely infected during the same period were diagnosed, treated and advised in our ENT specialist outpatient clinic.

RESULTS

The prevalence of chemosensory symptoms at the onset of infection was 19% (600/3187). About every second written respondent of the formerly acutely infected (441/890) remembered chemosensory symptoms during their COVID-19 infection. Of these, around 38% (167/441) complained of persistent chemosensory post-COVID symptoms after an average of 14.5 months. Only 2.3% (14/600) of the previously acutely infected patients with chemosensory symptoms sought medical help in a special consultation. Quantitative chemosensory damage could only be objectified in half, i.e. 1.2% (7/600) of the total cohort.

CONCLUSIONS

Despite a high prevalence of subjective chemosensory symptoms in acutely and formerly SARS-CoV-2 infected people, there is only a low need for specialized treatment, so that, unlike other post-COVID-associated complaints, the healthcare system as a whole appears to be less significantly burdened.

COVID-19 booster vaccine uptake and reduced risks for long-COVID: A cross-sectional study of a U.S. adult population

Long-COVID (having symptoms lasting 3 months or longer post-infection) is an emerging public health concern, yet research on whether COVID-19 booster vaccines can mitigate this condition is limited. This study examined associations between booster uptake and long-COVID prevalence among U.S. adults. Data were analyzed from 8757 adults aged 18 years or older with a history of COVID-19 infection from the 2022 National Health Interview Survey. Weighted prevalence and logistic regression models examined relationships between self-reported COVID-19 booster vaccination status and long-COVID, adjusting for sociodemographics and health factors. 19.5 % reported experiencing long-COVID. Individuals receiving the COVID-19 booster vaccine had significantly lower adjusted odds of long-COVID (OR 0.75, 95 % CI 0.61-0.93) compared to unvaccinated individuals. Overall, these findings suggest that COVID-19 booster vaccination is associated with a reduced prevalence of long-COVID among the U.S. adult population, underscoring the importance of optimizing booster uptake to mitigate the long-term impacts of COVID-19.

New variants of COVID-19 (XBB.1.5 and XBB.1.16, the "Arcturus"): A review of highly questioned concerns, a brief comparison between different peaks in the COVID-19 pandemic, with a focused systematic review on expert recommendations for prevention, vaccination, and treatment measures in the general population and at-risk groups

INTRODUCTION

The COVID-19 pandemic has taken many forms and continues to evolve, now around the Omicron wave, raising concerns over the globe. With COVID-19 being declared no longer a "public health emergency of international concern (PHEIC)," the COVID pandemic is still far from over, as new Omicron subvariants of interest and concern have risen since January of 2023. Mainly with the XBB.1.5 and XBB.1.16 subvariants, the pandemic is still very much "alive" and "breathing."

METHODS

This review consists of five highly concerning questions about the current state of the COVID Omicron peak. We searched four main online databases to answer the first four questions. For the last one, we performed a systematic review of the literature, with keywords "Omicron," "Guidelines," and "Recommendations."

RESULTS

A total of 31 articles were included. The main symptoms of the current Omicron wave include a characteristically high fever, coughing, conjunctivitis (with itching eyes), sore throat, runny nose, congestion, fatigue, body ache, and headache. The median incubation period of the symptoms is shorter than the previous peaks. Vaccination against COVID can still be considered effective for the new subvariants.

CONCLUSION

Guidelines recommend continuation of personal protective measures, third and fourth dose boosters, along with administration of bivalent messenger RNA vaccine boosters. The consensus antiviral treatment is combination therapy using Nirmatrelvir and Ritonavir, and the consensus for pre-exposure prophylaxis is Tixagevimab and Cilgavimab combination. We hope the present paper raises awareness for the continuing presence of COVID and ways to lower the risks, especially for at-risk groups.

Diagnostics for Public Health - Infectious Disease Surveillance and Control

AbstractAccurate diagnostics are critical in public health to ensure successful disease tracking, prevention, and control. Many of the same characteristics are desirable for diagnostic procedures in both medicine and public health: for example, low cost, high speed, low invasiveness, ease of use and interpretation, day-to-day consistency, and high accuracy. This review lays out five principles that are salient when the goal of diagnosis is to improve the overall health of a population rather than that of a particular patient, and it applies them in two important use cases: pandemic infectious disease and antimicrobial resistance.

The prevalence of feigning and concealment of Covid-19 infections in an international sample

We asked 463 participants from 21 countries whether they had feigned and/or concealed having a coronavirus infection during the pandemic period. 384 respondents (83%) reported having experienced a coronavirus infection. They were, on average, younger and reported more chronic health issues than participants who said they had never been infected. 65 (14%) admitted to having feigned the infection. Prevalence doubled (28%) when asked if they knew anyone who had feigned a coronavirus infection. Main motives for feigning were to stay at home and to obtain sick leave. As to having concealed a coronavirus infection, 56 (12%) responded affirmatively, but when asked about others, the prevalence reached 51% (n = 210). The most common reasons for concealment were to avoid letting others know and to not miss an event. Thus, both feigning and concealing infections can occur on a nontrivial scale, directly affecting prevalence rates in studies that rely on self-reported data collected from social platforms.

Histochemical Evidence for Reduced Immune Response in Nasal Mucosa of Patients with COVID-19

The primary entry point of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the nasal mucosa, where viral-induced inflammation occurs. When the immune response fails against SARS-CoV-2, understanding the altered response becomes crucial. This study aimed to compare SARS-CoV-2 immunological responses in the olfactory and respiratory mucosa by focusing on epithelia and nerves. Between 2020 and 2022, we obtained post mortem tissues from the olfactory cleft from 10 patients with histologically intact olfactory epithelia (OE) who died with or from COVID-19, along with four age-matched controls. These tissues were subjected to immunohistochemical reactions using antibodies against T cell antigens CD3, CD8, CD68, and SARS spike protein for viral evidence. Deceased patients with COVID-19 exhibited peripheral lymphopenia accompanied by a local decrease in CD3+ cells in the OE. However, SARS-CoV-2 spike protein was sparsely detectable in the OE. With regard to the involvement of nerve fibers, the present analysis suggested that SARS-CoV-2 did not significantly alter the immune response in olfactory or trigeminal fibers. On the other hand, SARS spike protein was detectable in both nerves. In summary, the post mortem investigation demonstrated a decreased T cell response in patients with COVID-19 and signs of SARS-CoV-2 presence in olfactory and trigeminal fibers.

Using SCENTinel® to predict SARS-CoV-2 infection: insights from a community sample during dominance of Delta and Omicron variants

Introduction

Based on a large body of previous research suggesting that smell loss was a predictor of COVID-19, we investigated the ability of SCENTinel®, a newly validated rapid olfactory test that assesses odor detection, intensity, and identification, to predict SARS-CoV-2 infection in a community sample.

Methods

Between April 5, 2021, and July 5, 2022, 1,979 individuals took one SCENTinel® test, completed at least one physician-ordered SARS-CoV-2 PCR test, and endorsed a list of self-reported symptoms.

Results

Among the of SCENTinel® subtests, the self-rated odor intensity score, especially when dichotomized using a previously established threshold, was the strongest predictor of SARS-CoV-2 infection. SCENTinel® had high specificity and negative predictive value, indicating that those who passed SCENTinel® likely did not have a SARS-CoV-2 infection. Predictability of the SCENTinel® performance was stronger when the SARS-CoV-2 Delta variant was dominant rather than when the SARS-CoV-2 Omicron variant was dominant. Additionally, SCENTinel® predicted SARS-CoV-2 positivity better than using a self-reported symptom checklist alone.

Discussion

These results indicate that SCENTinel® is a rapid assessment tool that can be used for population-level screening to monitor abrupt changes in olfactory function, and to evaluate spread of viral infections like SARS-CoV-2 that often have smell loss as a symptom.

The changing clinical presentation of COVID-19 in children during the course of the pandemic

AIM

To investigate the evolution of clinical symptoms of COVID-19 in children throughout the pandemic.

METHODS

In this national prospective surveillance study, symptoms in children hospitalised with COVID-19 were collected from all paediatric hospitals in Switzerland between March 2020 and March 2023. Data was analysed across four time periods, according to the predominantly circulating SARS-CoV-2 variant: T1 (wild-type), T2 (Alpha), T3 (Delta) and T4 (Omicron), as well as by age group.

RESULTS

The study included 1323 children. The proportion of children admitted to an intensive care unit remained stable throughout the pandemic. However, the pattern and frequency of clinical manifestations changed over time. Respiratory symptoms were less prevalent during T1 (wild-type), fever during T2 (Alpha) and rash during T4 (Omicron). In contrast, fever and neurological symptoms were more prevalent during T4 (Omicron). Newly described symptoms during T4 (Omicron) included conjunctivitis, laryngotracheitis and seizures. Fever was more prevalent among neonates and infants whereas respiratory symptoms were more common among infants. Gastrointestinal symptoms were more frequent among toddlers, while both toddlers and school-aged children presented with neurological symptoms more often than other age groups.

CONCLUSION

Continuous surveillance is required to detect changes in manifestations and there by be prepared for the optimal management of complications in children with COVID-19.

Outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 in a Rural Community Hospital during Omicron Predominance

Healthcare-associated infections due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has increased since the discovery of the Omicron variant. We describe a SARS-CoV-2 outbreak in the medicine-surgery unit of a rural community hospital at the time of high community transmission of Omicron variant in our county. The outbreak occurred in the medicine-surgery unit of an 89-bed rural community hospital in northern Maine. The characteristics of the patients and healthcare workers (HCWs) affected by the outbreak are described. Patient and HCW data collected as part of the outbreak investigation were used in this report. The outbreak control measures implemented are also described. A total of 24 people tested positive for SARS-CoV-2 including 11 patients and 13 HCWs. A total of 12 of the 24 (50%) persons were symptomatic, and rhinorrhea was the most common symptom noted (8/12, 67%). None of the symptomatic persons had gastrointestinal symptoms or symptoms of a loss of sense of smell or taste. All HCWs were vaccinated and 8 of the 11 patients were vaccinated. Outbreak control measures in the affected unit included implementation of full PPE (N95 respirators, eye protection, gowns and gloves) during all patient care, serial testing of employees and patients in the affected unit, cohorting positive patients, closing visitation and thorough environmental cleaning including use of ultraviolet (UV) light disinfection. This outbreak exemplifies the high transmissibility of the Omicron variant of SARS-CoV-2. The outbreak occurred despite a well-established infection control program. We noted that serial testing, use of N95 respirators during all patient care and UV disinfection were some of the measures that could be successful in outbreak control.

COVID-19 in non-hospitalised adults caused by either SARS-CoV-2 sub-variants Omicron BA.1, BA.2, BA.4/5 or Delta associates with similar illness duration, symptom severity and viral kinetics, irrespective of vaccination history

BACKGROUND

SARS-CoV-2 variant Omicron rapidly evolved over 2022, causing three waves of infection due to sub-variants BA.1, BA.2 and BA.4/5. We sought to characterise symptoms and viral loads over the course of COVID-19 infection with these sub-variants in otherwise-healthy, vaccinated, non-hospitalised adults, and compared data to infections with the preceding Delta variant of concern (VOC).

METHODS

In a prospective, observational cohort study, healthy vaccinated UK adults who reported a positive polymerase chain reaction (PCR) or lateral flow test, self-swabbed on alternate weekdays until day 10. We compared participant-reported symptoms and viral load trajectories between infections caused by VOCs Delta and Omicron (sub-variants BA.1, BA.2 or BA.4/5), and tested for relationships between vaccine dose, symptoms and PCR cycle threshold (Ct) as a proxy for viral load using Chi-squared (χ2) and Wilcoxon tests.

RESULTS

563 infection episodes were reported among 491 participants. Across infection episodes, there was little variation in symptom burden (4 [IQR 3-5] symptoms) and duration (8 [IQR 6-11] days). Whilst symptom profiles differed among infections caused by Delta compared to Omicron sub-variants, symptom profiles were similar between Omicron sub-variants. Anosmia was reported more frequently in Delta infections after 2 doses compared with Omicron sub-variant infections after 3 doses, for example: 42% (25/60) of participants with Delta infection compared to 9% (6/67) with Omicron BA.4/5 (χ2 P < 0.001; OR 7.3 [95% CI 2.7-19.4]). Fever was less common with Delta (20/60 participants; 33%) than Omicron BA.4/5 (39/67; 58%; χ2 P = 0.008; OR 0.4 [CI 0.2-0.7]). Amongst infections with an Omicron sub-variants, symptoms of coryza, fatigue, cough and myalgia predominated. Viral load trajectories and peaks did not differ between Delta, and Omicron, irrespective of symptom severity (including asymptomatic participants), VOC or vaccination status. PCR Ct values were negatively associated with time since vaccination in participants infected with BA.1 (β = -0.05 (CI -0.10-0.01); P = 0.031); however, this trend was not observed in BA.2 or BA.4/5 infections.

CONCLUSION

Our study emphasises both the changing symptom profile of COVID-19 infections in the Omicron era, and ongoing transmission risk of Omicron sub-variants in vaccinated adults.

TRIAL REGISTRATION

NCT04750356.

Clinical Manifestations of Infections with the Omicron Sub-Lineages BA.1, BA.2, and BA.5: A Retrospective Follow-Up Analysis of Public Health Data from Mecklenburg-Western Pomerania, Germany

The Omicron variants BA.1, BA.2, and BA.5 caused several waves of SARS-CoV-2 in Germany in 2022. In this comparative study, public health data on SARS-CoV-2 infections from Mecklenburg-Western Pomerania, Germany, between January and October 2022 were examined retrospectively using Pearson's chi-squared tests and Fisher's exact tests for testing for statistical significance. Compared to BA.5 infections, BA.1 and BA.2 infections affected younger individuals aged up to 19 years significantly more often, whereas BA.5 infections occurred significantly more frequently in patients between 40 and 59 years of age when compared to BA.1 and BA.2. Infections with all three variants predominantly caused flu-like symptoms; nevertheless, there were significant differences between the reported symptoms of BA.1, BA.2, and BA.5 infections. Especially, the symptoms of 'fever', 'severe feeling of sickness', 'loss of taste', and 'loss of smell' were significantly more often present in patients with BA.5 infections compared to BA.1 and BA.2 cases. Additionally, BA.2 and BA.5 cases reported significantly more often the symptoms of 'runny nose' and 'cough' than BA.1-infected cases. Our findings indicate remarkable differences in the clinical presentations among the sub-lineages, especially in BA.5 infections. Furthermore, the study demonstrates a powerful tool to link epidemiological data with genetic data in order to investigate their potential impact on public health.

Risk perception as a motivational resource during the COVID-19 pandemic: the role of vaccination status and emerging variants

BACKGROUND

People's perceived risk of being infected and having severe illness was conceived as a motivational source of adherence to behavioral measures during the COVID-19 crisis.

METHODS

We used online self-reported data, spanning 20 months of the COVID-19 crisis in Belgium (n = 221,791; 34.4% vaccinated; July 2020 - March 2022) to study the association between risk perception and motivation.

RESULTS

Both perceived infection probability and severity fluctuated across time as a function of the characteristics of emerging variants, with unvaccinated persons perceiving decreasingly less risk compared to vaccinated ones. Perceived severity (and not perceived probability) was the most critical predictor of autonomous motivation for adherence to health-protective measures, a pattern observed at both the between-day and between-person level among both vaccinated and unvaccinated individuals. An integrated process model further indicated that on days with higher hospitalization load, participants reported being more adherent because risk severity and autonomous motivation for adherence were more elevated on these days.

CONCLUSIONS

These findings suggest that risk severity served as a critical and dynamic resource for adherence to behavioral measures because it fostered greater autonomous regulation.

Virus-mediated cell fusion of SARS-CoV-2 variants

SARS-CoV-2 has the ability to form large multi-nucleated cells known as syncytia. Little is known about how syncytia affect the dynamics of the infection or severity of the disease. In this manuscript, we extend a mathematical model of cell-cell fusion assays to estimate both the syncytia formation rate and the average duration of the fusion phase for five strains of SARS-CoV-2. We find that the original Wuhan strain has the slowest rate of syncytia formation (6.4×10-4/h), but takes only 4.0 h to complete the fusion process, while the Alpha strain has the fastest rate of syncytia formation (0.36 /h), but takes 7.6 h to complete the fusion process. The Beta strain also has a fairly fast syncytia formation rate (9.7×10-2/h), and takes the longest to complete fusion (8.4 h). The D614G strain has a fairly slow syncytia formation rate (2.8×10-3/h), but completes fusion in 4.0 h. Finally, the Delta strain is in the middle with a syncytia formation rate of 3.2×10-2/h and a fusing time of 6.1 h. We note that for these SARS-CoV-2 strains, there appears to be a tradeoff between the ease of forming syncytia and the speed at which they complete the fusion process.

Identification of differences in the magnitude and specificity of SARS-CoV-2 nucleocapsid antibody responses in naturally infected and vaccinated individuals

As there are limited data on B-cell epitopes for the nucleocapsid protein in SARS-CoV-2, we sought to identify the immunodominant regions within the N protein, recognized by patients with varying severity of natural infection with the Wuhan strain (WT), delta, omicron, and in those who received the Sinopharm vaccines, which is an inactivated, whole virus vaccine. Using overlapping peptides representing the N protein, with an in-house ELISA, we mapped the immunodominant regions within the N protein, in seronegative (n = 30), WT infected (n = 30), delta infected (n = 30), omicron infected + vaccinated (n = 20) and Sinopharm (BBIBP-CorV) vaccinees (n = 30). We then investigated the sensitivity and specificity of these immunodominant regions and analyzed their conservation with other SARS-CoV-2 variants of concern, seasonal human coronaviruses, and bat Sarbecoviruses. We identified four immunodominant regions aa 29-52, aa 155-178, aa 274-297, and aa 365-388, which were highly conserved within SARS-CoV-2 and the bat coronaviruses. The magnitude of responses to these regions varied based on the infecting SARS-CoV-2 variants, >80% of individuals gave responses above the positive cut-off threshold to many of the four regions, with some differences with individuals who were infected with different VoCs. These regions were found to be 100% specific, as none of the seronegative individuals gave any responses. As these regions were highly specific with high sensitivity, they have a potential to be used to develop diagnostic assays and to be used in development of vaccines.

Vaccine Effectiveness against SARS-CoV-2 Infection during the Circulation of Alpha, Delta, or Omicron Variants: A Retrospective Cohort Study in a Tertiary Hospital in Serbia

The COVID-19 pandemic prompted rapid vaccine development and deployment worldwide. Despite widespread vaccination efforts, understanding the effectiveness of vaccines in hospitalized patients remains a critical concern. This retrospective cohort study, conducted at a tertiary healthcare centre in Serbia, tracked patients hospitalized during different waves of COVID-19 variants-Alpha, Delta, and Omicron. Data collection included demographics, comorbidities, symptoms, and vaccination status. Among 3593 patients, those with prior exposure to COVID-19 cases or hospital treatment showed higher positivity rates. Symptom prevalence varied across waves, with coughs persisting. Patients without chronic diseases were more frequent among those testing negative. Vaccine effectiveness varied, with Sinopharm demonstrating a 45.6% effectiveness initially and Pfizer-BioNTech showing an effectiveness of up to 74.8% within 0-84 days after the second dose. Mixed-dose strategies, notably Sinopharm as a primary dose followed by a Pfizer-BioNTech booster, suggested increased protection. Despite substantial vaccination availability, a significant portion of hospitalized patients remained unvaccinated. This study underscores the dynamic nature of vaccine effectiveness and advocates for booster strategies to address evolving challenges in combating COVID-19, particularly in hospitalized patients.

Limitations of the Cough Sound-Based COVID-19 Diagnosis Artificial Intelligence Model and its Future Direction: Longitudinal Observation Study

BACKGROUND

The outbreak of SARS-CoV-2 in 2019 has necessitated the rapid and accurate detection of COVID-19 to manage patients effectively and implement public health measures. Artificial intelligence (AI) models analyzing cough sounds have emerged as promising tools for large-scale screening and early identification of potential cases.

OBJECTIVE

This study aimed to investigate the efficacy of using cough sounds as a diagnostic tool for COVID-19, considering the unique acoustic features that differentiate positive and negative cases. We investigated whether an AI model trained on cough sound recordings from specific periods, especially the early stages of the COVID-19 pandemic, were applicable to the ongoing situation with persistent variants.

METHODS

We used cough sound recordings from 3 data sets (Cambridge, Coswara, and Virufy) representing different stages of the pandemic and variants. Our AI model was trained using the Cambridge data set with subsequent evaluation against all data sets. The performance was analyzed based on the area under the receiver operating curve (AUC) across different data measurement periods and COVID-19 variants.

RESULTS

The AI model demonstrated a high AUC when tested with the Cambridge data set, indicative of its initial effectiveness. However, the performance varied significantly with other data sets, particularly in detecting later variants such as Delta and Omicron, with a marked decline in AUC observed for the latter. These results highlight the challenges in maintaining the efficacy of AI models against the backdrop of an evolving virus.

CONCLUSIONS

While AI models analyzing cough sounds offer a promising noninvasive and rapid screening method for COVID-19, their effectiveness is challenged by the emergence of new virus variants. Ongoing research and adaptations in AI methodologies are crucial to address these limitations. The adaptability of AI models to evolve with the virus underscores their potential as a foundational technology for not only the current pandemic but also future outbreaks, contributing to a more agile and resilient global health infrastructure.

Comparative analysis of symptom profile and risk of death associated with infection by SARS-CoV-2 and its variants in Hong Kong

The recurrent multiwave nature of coronavirus disease 2019 (COVID-19) necessitates updating its symptomatology. We characterize the effect of variants on symptom presentation, identify the symptoms predictive and protective of death, and quantify the effect of vaccination on symptom development. With the COVID-19 cases reported up to August 25, 2022 in Hong Kong, an iterative multitier text-matching algorithm was developed to identify symptoms from free text. Multivariate regression was used to measure associations between variants, symptom development, death, and vaccination status. A least absolute shrinkage and selection operator technique was used to identify a parsimonious set of symptoms jointly associated with death. Overall, 70.9% (54 450/76 762) of cases were symptomatic with 102 symptoms identified. Intrinsically, the wild-type and delta variant caused similar symptoms among unvaccinated symptomatic cases, whereas the wild-type and omicron BA.2 subvariant had heterogeneous patterns, with seven symptoms (fatigue, fever, chest pain, runny nose, sputum production, nausea/vomiting, and sore throat) more frequent in the BA.2 cohort. With ≥2 vaccine doses, BA.2 was more likely than delta to cause fever among symptomatic cases. Fever, blocked nose, pneumonia, and shortness of breath remained jointly predictive of death among unvaccinated symptomatic elderly in the wild-type-to-omicron transition. Number of vaccine doses required for reducing occurrence varied by symptoms. We substantiate that omicron has a different clinical presentation compared to previous variants. Syndromic surveillance can be bettered with reduced reliance on symptom-based case identification, increased weighing on symptoms predictive of death in outcome prediction, individual-based risk assessment in care homes, and incorporating free-text symptom reporting.

Employee investigation and contact tracing program in a pediatric cancer hospital to mitigate the spread of COVID-19 among the workforce, patients, and caregivers

Background

Case investigations and contact tracing are essential disease control measures used by health departments. Early in the pandemic, they were seen as a key strategy to stop COVID-19 spread. The CDC urged rapid action to scale up and train a large workforce and collaborate across public and private agencies to halt COVID-19 transmission.

Methods

We developed a program for case investigation and contact tracing that followed CDC and local health guidelines, compliant with the Occupational Safety and Health Administration (OSHA) regulations and tailored to the needs and resources of our institution. Program staff were trained and assessed for competency before joining the program.

Results

From March 2020 to May 2021, we performed 838 COVID-19 case investigations, which led to 136 contacts. Most employees reported a known SARS-CoV-2 exposure from the community (n = 435) or household (n = 343). Only seven (5.1%) employees were determined as more likely than not to have SARS-CoV-2 infection related to workplace exposure, and when so, lapses in following the masking recommendations were identified. Between June 2021-February 2022, our program adjusted to the demand of the different waves, particularly omicron, by significantly reducing the amount of data collected. No transmission from employees to patients or caregivers was observed during this period.

Conclusion

Prompt implementation of case investigation and contact tracing is possible, and it effectively reduces workplace exposures. This approach can be adapted to suit the specific needs and requirements of various healthcare settings, particularly those serving the most vulnerable patient populations.

Extracting symptoms from free-text responses using ChatGPT among COVID-19 cases in Hong Kong

OBJECTIVES

To investigate the feasibility and performance of Chat Generative Pretrained Transformer (ChatGPT) in converting symptom narratives into structured symptom labels.

METHODS

We extracted symptoms from 300 deidentified symptom narratives of COVID-19 patients by a computer-based matching algorithm (the standard), and prompt engineering in ChatGPT. Common symptoms were those with a prevalence >10% according to the standard, and similarly less common symptoms were those with a prevalence of 2-10%. The precision of ChatGPT was compared with the standard using sensitivity and specificity with 95% exact binomial CIs (95% binCIs). In ChatGPT, we prompted without examples (zero-shot prompting) and with examples (few-shot prompting).

RESULTS

In zero-shot prompting, GPT-4 achieved high specificity (0.947 [95% binCI: 0.894-0.978]-1.000 [95% binCI: 0.965-0.988, 1.000]) for all symptoms, high sensitivity for common symptoms (0.853 [95% binCI: 0.689-0.950]-1.000 [95% binCI: 0.951-1.000]), and moderate sensitivity for less common symptoms (0.200 [95% binCI: 0.043-0.481]-1.000 [95% binCI: 0.590-0.815, 1.000]). Few-shot prompting increased the sensitivity and specificity. GPT-4 outperformed GPT-3.5 in response accuracy and consistent labelling.

DISCUSSION

This work substantiates ChatGPT's role as a research tool in medical fields. Its performance in converting symptom narratives to structured symptom labels was encouraging, saving time and effort in compiling the task-specific training data. It potentially accelerates free-text data compilation and synthesis in future disease outbreaks and improves the accuracy of symptom checkers. Focused prompt training addressing ambiguous descriptions impacts medical research positively.

The relative prevalence of the Omicron variant within SARS-CoV-2 infected cohorts in different countries: A systematic review

The Omicron variant of SARS-CoV-2 was detected in October 2021 and exhibited high transmissibility, immune evasion, and reduced severity when compared to the earlier variants. The lesser vaccine effectiveness against Omicron and its reduced severity created vaccination hesitancy among the public. This review compiled data reporting the relative prevalence of Omicron as compared to the early variants to give an insight into the existing variants, which may shape the decisions regarding the targets of the newly developed vaccines. Complied data revealed more than 90% prevalence within the infected cohorts in some countries. The BA.1 subvariant predominated over the BA.2 during the early stages of the Omicron wave. Moreover, BA.4/BA.5 subvariants were detected in South Africa, USA and Italy between October 2021 and April 2022. It is therefore important to develop vaccines that protect against Omicron as well as the early variants, which are known to cause more severe complications.

SARS-CoV-2 infection in immunosuppression evolves sub-lineages which independently accumulate neutralization escape mutations

One mechanism of variant formation may be evolution during long-term infection in immunosuppressed people. To understand the viral phenotypes evolved during such infection, we tested SARS-CoV-2 viruses evolved from an ancestral B.1 lineage infection lasting over 190 days post-diagnosis in an advanced HIV disease immunosuppressed individual. Sequence and phylogenetic analysis showed two evolving sub-lineages, with the second sub-lineage replacing the first sub-lineage in a seeming evolutionary sweep. Each sub-lineage independently evolved escape from neutralizing antibodies. The most evolved virus for the first sub-lineage (isolated day 34) and the second sub-lineage (isolated day 190) showed similar escape from ancestral SARS-CoV-2 and Delta-variant infection elicited neutralizing immunity despite having no spike mutations in common relative to the B.1 lineage. The day 190 isolate also evolved higher cell-cell fusion and faster viral replication and caused more cell death relative to virus isolated soon after diagnosis, though cell death was similar to day 34 first sub-lineage virus. These data show that SARS-CoV-2 strains in prolonged infection in a single individual can follow independent evolutionary trajectories which lead to neutralization escape and other changes in viral properties.

Evaluating the accessibility and capacity of SARS-CoV-2 vaccination and analyzing convenience-related factors during the Omicron variant epidemic in Beijing, China

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination service system lacks standardized indicators to assess resource allocation. Moreover, data on specific vaccination-promoting measures is limited. This study aimed to evaluate vaccination accessibility and capacity and investigate convenience-related factors in China during the Omicron variant epidemic. We collected information on SARS-CoV-2 vaccination services among vaccination sites in Beijing. Analysis was performed using nearest neighbor, Ripley's K, hot spot analysis, and generalized estimating equations. Overall, 299 vaccination sites were included. The demand for the SARS-CoV-2 vaccine increased with the increase in daily new cases, and the number of staff administering vaccines should be increased in urban areas at the beginning of the epidemic. Providing vaccination for both children and adults, extending vaccination service hours, and offering a wider range of vaccine categories significantly increased the doses of vaccines administered (all P < .05). The provision of mobile vaccination vehicles effectively increased the doses of vaccines administered to individuals aged ≥ 60 years (P < .05). The allocation of SARS-CoV-2 vaccination services should be adjusted according to geographic location, population size, and vaccination demands. Simultaneous provision of vaccination services for children and their guardians, flexible service hours, prompt innovative vaccine production, and tailored vaccination strategies can foster vaccination uptake.

Oxygen Therapy During Activities of Daily Living Rehabilitation and Outcome in Patients With Severe-to-critical COVID-19

Objective

To primarily study the duration of supplemental oxygen use while performing ADLs (activities of daily living) and associations leading to a more prolonged oxygen therapy during these tasks. Secondary objectives include (1) studying the presence of COVID-19 related complications during inpatient rehabilitation and after discharge and (2) describing functional outcomes of participants after supplemental oxygen liberation and hospital discharge.

Design

Explorative prospective observational cohort study.

Setting

Rehabilitation center within a tertiary hospital, caring for post-COVID patients.

Participants

Twenty-three (N=23) community-dwelling persons with severe-to-critical COVID-19 disease and ongoing oxygen therapy needs. There was a preponderance of men (69.6%), with mean age of 69.5 (range 46-85) years.

Interventions

Inpatient pulmonary rehabilitation.

Main Outcome Measures

The primary outcome was the duration of supplemental oxygen use (from initiation till wean) for ambulation, toileting, dressing, and showering. Secondary outcomes included the presence of COVID-19 related complications (during rehabilitation and after discharge) and post-discharge functional status.

Results

After rehabilitation center transfer, all subjects only required oxygen therapy during task(s) performance, and not at rest. ADLs that took the shortest and longest time for supplemental oxygen weaning were dressing (mean 38.4±SD 17.1 days) and showering (mean 47.7±SD 18.1 days), respectively. The mean duration of oxygen therapy application was 48.6±SD 18.3 days. On multivariable analysis, mechanical ventilation and exertional desaturation were significantly associated with prolonged duration for oxygen therapy in all ADLs.

Conclusion

The duration of needful oxygen therapy was dissimilar for different ADLs. Showering, which required the longest duration of supplemental oxygen wean, might prove to be the rate-limiting ADL for discharge home.

A Danish questionnaire study of acute symptoms of SARS-CoV-2 infection by variant, vaccination status, sex and age

It is not well-described how the acute symptoms of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) differ by variant, vaccination, sex and age. A cross-sectional questionnaire study linked to national testing- and registry data was conducted among 148,874 SARS-CoV-2 first time reverse transcription polymerase chain reaction (RT-PCR) test-positive individuals and corresponding date-matched symptomatic test-negative controls. Major SARS-CoV-2 variants (Index/wild type, Alpha, Delta and Omicron) were defined using periods of predominance. Risk differences (RDs) were estimated for each of 21 predefined acute symptoms comparing: (1) test-positive and -negative individuals, by variant period, (2) vaccinated and unvaccinated test-positives, by variant period, (3) individuals tested positive during the Omicron and Delta periods, by vaccination status, and (4) vaccinated Omicron test-positive and -negative individuals, by age and sex. Compared to pre-Omicron, RDs between test-positive and test-negative individuals during the Omicron period were lower for most symptoms. RDs for altered sense of smell (dysosmia) and taste (dysgeusia) were highest for Delta (RD = 50.8 (49.4-52.0) and RD = 54.7 (53.4-56.0), respectively) and lowest for Omicron (RD = 12.8 (12.1-13.5) and RD = 11.8 (11.1-12.4), respectively). Across variants, vaccinated individuals reported fewer symptoms. During Omicron, females and 30-59 year-old participants reported more symptoms.

A multi-country analysis of COVID-19 hospitalizations by vaccination status

BACKGROUND

Individuals vaccinated against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), when infected, can still develop disease that requires hospitalization. It remains unclear whether these patients differ from hospitalized unvaccinated patients with regard to presentation, coexisting comorbidities, and outcomes.

METHODS

Here, we use data from an international consortium to study this question and assess whether differences between these groups are context specific. Data from 83,163 hospitalized COVID-19 patients (34,843 vaccinated, 48,320 unvaccinated) from 38 countries were analyzed.

FINDINGS

While typical symptoms were more often reported in unvaccinated patients, comorbidities, including some associated with worse prognosis in previous studies, were more common in vaccinated patients. Considerable between-country variation in both in-hospital fatality risk and vaccinated-versus-unvaccinated difference in this outcome was observed.

CONCLUSIONS

These findings will inform allocation of healthcare resources in future surges as well as design of longer-term international studies to characterize changes in clinical profile of hospitalized COVID-19 patients related to vaccination history.

FUNDING

This work was made possible by the UK Foreign, Commonwealth and Development Office and Wellcome (215091/Z/18/Z, 222410/Z/21/Z, 225288/Z/22/Z, and 220757/Z/20/Z); the Bill & Melinda Gates Foundation (OPP1209135); and the philanthropic support of the donors to the University of Oxford's COVID-19 Research Response Fund (0009109). Additional funders are listed in the "acknowledgments" section.

Odds of COVID-19-associated asthma exacerbations in children higher during Omicron wave

BACKGROUND

We aimed to determine the association of COVID-19 variant wave with asthma exacerbations in children with asthma.

METHODS

We conducted a retrospective cross-sectional study of children in the Western Pennsylvania COVID-19 Registry (WPACR). We extracted data for all children in the WPACR with asthma and compared their acute clinical presentation and outcomes during the Pre-Delta (7/1/20-6/30/21), Delta (8/1/21-12/14/21), and Omicron (12/15/21-8/30/22) waves. We conducted multivariable logistic regression analyses of SARS-CoV-2-associated asthma exacerbations, adjusting for characteristics that have been associated with COVID-19 outcomes in prior studies.

RESULTS

Among 573 children with asthma in the WPACR during the study period, the proportion of children with COVID-19 who had an asthma exacerbation was higher during the Omicron wave than during the prior two variant waves (40.2% vs. 22.6% vs. 26.2%, p = 0.002; unadjusted OR = 2.12 [95% confidence interval (CI) = 1.39-3.22], p < 0.001). In our multivariable regression models, the odds of an asthma exacerbation were 2.8 times higher during the Omicron wave than during prior waves (adjusted OR = 2.80 [95% CI = 1.70-4.61]). Results were similar after additionally adjusting for asthma severity but were no longer significant after additionally adjusting for poor asthma control.

CONCLUSION

The proportion of children with asthma experiencing an asthma exacerbation during SARS-CoV-2 infection was higher during Omicron than prior variant waves, adding to the body of evidence that COVID-19-associated respiratory symptoms vary by variant. These findings provide additional support for vaccination and prevention.

[Persistent olfactory impairment after COVID-19-recommendations of the Working Group on Olfactology and Gustology of the German Society of Oto-rhino-laryngology, Head and Neck Surgery]

This article does not intend to comprehensively review the existing literature on coronavirus disease 2019 (COVID-19)-associated smell disorders, but aims to summarize scientific evidence for otorhinolaryngological practice and provide recommendations for diagnosis and treatment of persistent smell disorders following COVID-19.

Association of SARS-CoV-2 viral load with abnormal laboratory characteristics and clinical outcomes in hospitalised COVID-19 patients

We conducted a retrospective, analytical cross-sectional and single-centre study that included 190 hospitalised COVID-19 patients in the Fujian Provincial Hospital South Branch between December 2022 and January 2023 to analyse the correlation of viral loads of throat swabs with clinical progression and outcomes. To normalise the Ct value as quantification of viral loads, we used RNase P gene as internal control gene and subtracted the Ct value of SARS-CoV-2 N gene from the Ct value of RNase P gene, termed △Ct. Most patients were discharged (84.2%), and only 10 (5.6%) individuals who had a lower △Ct value died. The initial △Ct value of participants was also significantly correlated with some abnormal laboratory characteristics, and the duration time of SARS-CoV-2 was longer in patients with severe symptoms and a lower △Ct value at admission. Our study suggested that the △Ct value may be used as a predictor of disease progression and outcomes in hospitalised COVID-19 patients.

SARS-CoV-2 Variant-Specific Gastrointestinal Symptoms of COVID-19: 2023 Update

The gastrointestinal (GI) tract may be a significant entrance or interaction site for SARS-CoV-2; therefore, the gut mucosal immune system participates in virus interaction as a first-line physical and immunological defense, leading to GI involvement and symptoms. This review focuses on the GI symptoms associated with SARS-CoV-2 infection while providing specific results on variant-specific signs and syndromes related to coronavirus disease 2019 (COVID-19). The pattern of symptoms changed during the virus evolution, since the data provided a current and thorough picture of the symptoms experienced by SARS-CoV-2 infected people, and variations in symptom patterns occurred as the Alpha, Delta, and Omicron variants have spread. Since the beginning of the pandemic, GI symptoms have been linked to SARS-CoV-2 infections, even though most infected people do not report them. For example, diarrhea (28.2%) was the most frequently reported GI symptom in the early phase of the pandemic. The most observed GI tract symptoms during COVID-19 were anorexia (loss of appetite), nausea, vomiting, diarrhea, and abdominal pain, usually in at least one-third of the patients. Mesenteric ischemia and GI bleeding were less observed but more severe. While GI symptoms are not associated with increased mortality, they complicate the disease, increase the duration of the illness, and result in worse outcomes. Nevertheless, it is accepted that symptoms between variants differ significantly, i.e., the Omicron variant causes milder COVID-19 than the Delta. Still, the rate of GI symptoms has declined in the following variant-dominated phases of the pandemic (Alpha: 19.4%, Delta: 17.9%, Omicron: 13.8%), which was also demonstrated for other GI signs associated with COVID-19.

Meta-Analysis of COVID-19 Metabolomics Identifies Variations in Robustness of Biomarkers

The global COVID-19 pandemic resulted in widespread harms but also rapid advances in vaccine development, diagnostic testing, and treatment. As the disease moves to endemic status, the need to identify characteristic biomarkers of the disease for diagnostics or therapeutics has lessened, but lessons can still be learned to inform biomarker research in dealing with future pathogens. In this work, we test five sets of research-derived biomarkers against an independent targeted and quantitative Liquid Chromatography-Mass Spectrometry metabolomics dataset to evaluate how robustly these proposed panels would distinguish between COVID-19-positive and negative patients in a hospital setting. We further evaluate a crowdsourced panel comprising the COVID-19 metabolomics biomarkers most commonly mentioned in the literature between 2020 and 2023. The best-performing panel in the independent dataset-measured by F1 score (0.76) and AUROC (0.77)-included nine biomarkers: lactic acid, glutamate, aspartate, phenylalanine, β-alanine, ornithine, arachidonic acid, choline, and hypoxanthine. Panels comprising fewer metabolites performed less well, showing weaker statistical significance in the independent cohort than originally reported in their respective discovery studies. Whilst the studies reviewed here were small and may be subject to confounders, it is desirable that biomarker panels be resilient across cohorts if they are to find use in the clinic, highlighting the importance of assessing the robustness and reproducibility of metabolomics analyses in independent populations.