Outcomes of SARS-CoV-2 Omicron Variant Infections Compared With Seasonal Influenza and Respiratory Syncytial Virus Infections in Adults Attending the Emergency Department: A Multicenter Cohort Study

Severity and Long-Term Mortality of COVID-19, Influenza, and Respiratory Syncytial Virus

Importance

SARS-CoV-2, influenza, and respiratory syncytial virus (RSV) contribute to many hospitalizations and deaths each year. Understanding relative disease severity can help to inform vaccination guidance.

Objective

To compare disease severity of COVID-19, influenza, and RSV among US veterans.

Design, Setting, and Participants

This retrospective cohort study analyzed national US Veterans Health Administration electronic health record data of nonhospitalized veterans who underwent same-day testing for SARS-CoV-2, influenza, and RSV, and were diagnosed with a single infection between August 1, 2022, and March 31, 2023, or between August 1, 2023, and March 31, 2024.

Exposures

Infection with SARS-CoV-2, influenza, or RSV.

Main Outcomes and Measures

Following inverse probability weighting, the cumulative incidence and risk differences (RDs) were calculated for the primary outcomes of 30-day hospitalization, intensive care unit admission, and death, as well as the secondary outcome of long-term death extending through 180 days.

Results

Among 68 581 patients included in the 2022 to 2023 cohort (6239 [9.1%] with RSV, 16 947 [24.7%] with influenza, and 45 395 [66.2%] with COVID-19) and 72 939 in the 2023 to 2024 cohort (9748 [13.4%] with RSV, 19 242 [26.4%] with influenza, and 43 949 [60.3%] with COVID-19), the median (IQR) age was 66 (53-75) years, and 123 090 (87.0%) were male. During the 2023 to 2024 season, the 30-day risk of hospitalization was similar for COVID-19 (16.2%) and influenza (16.3%) but lower for RSV at 14.3% (RD for COVID-19 vs RSV, 1.9% [95% CI, 0.9%-2.9%]; RD for influenza vs RSV, 2.0% [95% CI, 0.8%-3.3%]). The 30-day risk of death during the 2022 to 2023 season was slightly higher for COVID-19 (1.0%) compared with influenza (0.7%) (RD, 0.4% [95% CI, 0.1%-0.6%]) or RSV (0.7%) (RD, 0.4% [95% CI, 0.1%-0.6%]) but similar during the 2023 to 2024 season. Mortality risk at 180 days was higher for COVID-19 during both seasons (2023-2024 RD for COVID-19 vs influenza, 0.8% [95% CI, 0.3%-1.2%]; RD for COVID-19 vs RSV, 0.6% [95% CI, 0.1%-1.1%]). Higher mortality in both seasons was observed for veterans without COVID-19 vaccination in the previous year compared to veterans without seasonal influenza vaccination. In contrast, among groups vaccinated against their respective infections, there were no mortality differences at any time point between COVID-19 and influenza.

Conclusions and Relevance

This cohort study showed that, during the 2022 to 2023 season, infection with SARS-CoV-2 was associated with more severe disease outcomes than influenza or RSV, whereas differences were less pronounced during the 2023 to 2024 season. During both seasons, RSV remained a milder illness, whereas COVID-19 was associated with higher long-term mortality. Vaccination attenuated differences in disease severity and long-term mortality.

4D-DIA Proteomics Uncovers New Insights into Host Salivary Response Following SARS-CoV-2 Omicron Infection

Since late 2021, Omicron variants have dominated the epidemiological scenario as the most successful severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sublineages, driving new and breakthrough infections globally over the past two years. In this study, we investigated for the first time the host salivary response of COVID-19 patients infected with Omicron variants (BA.1, BA.2, and BA.4/5) by using an untargeted four-dimensional data-independent acquisition (4D-DIA)-based proteomics approach. We identified 137 proteins whose abundance levels differed between the COVID-19 positive and negative groups. Salivary signatures were mainly enriched in ribosomal proteins, linked to mRNAviral translation, protein synthesis and processing, immune innate, and antiapoptotic signaling. The higher abundance of 14-3-3 proteins (YWHAG, YWHAQ, YWHAE, and SFN) in saliva, first reported here, may be associated with increased infectivity and improved viral replicative fitness. We also identified seven proteins (ACTN1, H2AC2, GSN, NDKA, CD109, GGH, and PCYOX) that yielded comprehension into Omicron infection and performed outstandingly in screening patients with COVID-19 in a hospital setting. This panel also presented an enhanced anti-COVID-19 and anti-inflammatory signature, providing insights into disease severity, supported by comparisons with other proteome data sets. The salivary signature provided valuable insights into the host's response to SARS-CoV-2 Omicron infection, shedding light on the pathophysiology of COVID-19, particularly in cases associated with mild disease. It also underscores the potential clinical applications of saliva for disease screening in hospital settings. Data are available via ProteomeXchange with the identifier PXD054133.

Outcomes of COVID-19 in the Omicron-predominant wave: large-scale real-world data analysis with a comparison to influenza

PURPOSE

Studies on COVID-19 mortality during the Omicron-predominant wave have focused primarily on the inpatient/emergency room setting, and real-world data including both inpatients and outpatients are lacking.

METHODS

Patients diagnosed with COVID-19 (n = 27,440,148) or influenza (n = 8,179,641) from January 2020 to April 2023 were identified using nationwide claims data in Japan. Patients with COVID-19 in the Omicron-predominant wave were compared with their counterparts in earlier waves, and a subset of the former group (May 2022-April 2023) was compared with patients with influenza as controls.

RESULTS

The mortality rates (average number of deaths/cases per week) of COVID-19 decreased over time, being 2.7% (169/6312), 2.1% (397/18,754), 0.7% (195/28,273), and 0.4% (1613/378,848) in the wild-type-, Alpha-, Delta-, and Omicron-predominant waves, respectively. However, the number of deaths increased substantially in the Omicron-predominant wave, especially among the elderly (e.g., in the Delta- and Omicron-predominant waves, the average numbers of deaths/cases per week were < 1/5527 (< 0.01%) and 4/105,763 (< 0.01%) respectively, in patients aged 0-19, versus 101/925 (10.9%) and 1212/20,771 (5.8%), respectively, in patients aged ≥ 80). The mortality rate was lower for patients with COVID-19 than in those with influenza among those aged ≤ 39 years but higher among those aged ≥ 40 years.

CONCLUSIONS

In the Omicron-predominant wave, the mortality rate of COVID-19 decreased, but the number of patients increased, leading to a substantial increase in the number of deaths, especially among the elderly. The mortality rate of COVID-19 was higher than that of influenza in the elderly but not in the young, highlighting the need for age-specific interventions.

Burden of Acute Respiratory Infections Caused by Influenza Virus, Respiratory Syncytial Virus, and SARS-CoV-2 with Consideration of Older Adults: A Narrative Review

Influenza virus, respiratory syncytial virus (RSV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are acute respiratory infections (ARIs) that can cause substantial morbidity and mortality among at-risk individuals, including older adults. In this narrative review, we summarize themes identified in the literature regarding the epidemiology, seasonality, immunity after infection, clinical presentation, and transmission for these ARIs, along with the impact of the COVID-19 pandemic on seasonal patterns of influenza and RSV infections, with consideration of data specific to older adults when available. As the older adult population increases globally, it is of paramount importance to fully characterize the true disease burden of ARIs in order to develop appropriate mitigation strategies to minimize their impact in vulnerable populations. Challenges associated with characterizing the burden of these diseases include the shared symptomology and clinical presentation of influenza virus, RSV, and SARS-CoV-2, which complicate accurate diagnosis and highlight the need for improved testing and surveillance practices. To this end, multiple regional, national, and global virologic and disease surveillance systems have been established to provide accurate knowledge of viral epidemiology, support appropriate preparedness and response to potential outbreaks, and help inform prevention strategies to reduce disease severity and transmission. Beyond the burden of acute illness, long-term health consequences can also result from influenza virus, RSV, and SARS-CoV-2 infection. These include cardiovascular and pulmonary complications, worsening of existing chronic conditions, increased frailty, and reduced life expectancy. ARIs among older adults can also place a substantial financial burden on society and healthcare systems. Collectively, the existing data indicate that influenza virus, RSV, and SARS-CoV-2 infections in older adults present a substantial global health challenge, underscoring the need for interventions to improve health outcomes and reduce the disease burden of respiratory illnesses.Graphical abstract and video abstract available for this article.

Cardiac Damage in Patients Infected with Different SARS-CoV-2 Variants of Concern

Coronavirus Disease 2019 causes significant morbidity, and different variants of concern (VOCs) can impact organ systems differently. We conducted a single-center retrospective cohort analysis comparing biomarkers and clinical outcomes in hospitalized patients infected with the wild-type or Alpha (wt/Alpha) VOC against patients infected with the Omicron VOC. We included 428 patients infected with the wt/Alpha VOC and 117 patients infected with the Omicron VOC. The Omicron cohort had higher maximal median high-sensitivity Troponin-T (hs-TnT) levels (wt/Alpha: 12.8 ng/L, IQR 6.6-29.5 vs. Omicron: 27.8 ng/L, IQR 13.7-54.0; p < 0.001) and N-terminal prohormone of brain natriuretic peptide (NT-proBNP) (wt/Alpha: 256 ng/L, IQR 74.5-913.5 vs. Omicron: 825 ng/L, IQR 168-2759; p < 0.001) levels. This remained true for patients under 65 years of age and without pre-existing cardiovascular disease (hs-TnT (wt/Alpha: 6.1 ng/L, IQR 2.5-10.25 vs. Omicron: 8.6 ng/L, IQR 6.2-15.7; p = 0.007) and NT-proBNP (wt/Alpha: 63 ng/L, IQR 25-223.75 vs. Omicron: 158 ng/L, IQR 75.5-299.5; p = 0.006)). In-hospital mortality was similar between the two groups (wt/Alpha: 53 or 12.7% vs. Omicron: 9 or 7.7%; p = 0.132) and more patients infected with wt/Alpha VOC required intensive care admission (wt/Alpha: 93 or 22.2% vs. Omicron: 14 or 12%; p = 0.014). Increased cardiac biomarkers were correlated with a higher risk of mortality and ICU admission in both groups. Herein, we detected higher levels of cardiac biomarkers in hospitalized patients infected with the Omicron VOC when compared to wt/Alpha, being indicative of higher cardiac involvement. Although hs-TnT and NT-proBNP levels were higher in the Omicron cohort and both markers were linked to in hospital mortality in both groups, the mortality rates were similar.

Near real-time severe acute respiratory illness surveillance characterising influenza and COVID-19 epidemiology in hospitalised adults, 2021-22

OBJECTIVES

We report the findings of a novel enhanced syndromic surveillance that characterised influenza- and SARS-CoV-2-associated severe acute respiratory illness (SARI) in the 2021/2022 winter season.

METHODS

Prospective cohort study of adults admitted to the Queen Elizabeth University Hospital, Glasgow, with a severe acute respiratory illness. Patient demographics, clinical history, admission details, and outcomes were recorded. Data were available to Public Health Scotland (PHS) and clinicians weekly.

RESULTS

Between November 2021 and May 2022, 1063 hospitalised SARI episodes in 1037 adult patients were identified. Median age was 72.0 years, and 44.5% were male. Most (82.6%) SARI cases had ≥1 co-morbidity; chronic lung disease (50.0%) and malignancy (22.5%) were the most frequently reported. Overall, 229 (22%) and 33 (3%) SARI episodes were SARS-CoV-2 and influenza A PCR positive, respectively. 74.7%, 6.5% and 43.0% SARI episodes received antibiotics, antivirals, and steroids, respectively (54.5%, 11.0% and 51.3% among COVID-19 patients). 1.1% required mechanical ventilation and 7.8% died. Male sex, multimorbidity, frailty, respiratory rate >30, low GCS and chest X-ray consolidation were predictive of in-hospital mortality.

CONCLUSION

Near real-time hospitalised SARI syndromic surveillance characterised the evolving clinical epidemiology of SARS-CoV-2 and influenza, high antimicrobial use, and predictors of inpatient mortality among hospitalised SARI patients.

Rosini Silva A, Brites C, Angelo da Silva Miyaguti N, Raposo Passos Mansoldo F, Vaz Nunes S, Henrique Godoy Sanches P, Regiani Cataldi T, Pais de Carvalho C, Reis da Silva A, Ribeiro da Rosa J, Magalhães Borges M, Vilarindo Oliveira W, Canevari TC, Beatriz Vermelho A, Nogueira Eberlin M, M. Porcari A. Mass Spectrometry-Based Metabolomics Reveals a Salivary Signature for Low-Severity COVID-19

Omics approaches were extensively applied during the coronavirus disease 2019 (COVID-19) pandemic to understand the disease, identify biomarkers with diagnostic and prognostic value, and discover new molecular targets for medications. COVID-19 continues to challenge the healthcare system as the virus mutates, becoming more transmissible or adept at evading the immune system, causing resurgent epidemic waves over the last few years. In this study, we used saliva from volunteers who were negative and positive for COVID-19 when Omicron and its variants became dominant. We applied a direct solid-phase extraction approach followed by non-target metabolomics analysis to identify potential salivary signatures of hospital-recruited volunteers to establish a model for COVID-19 screening. Our model, which aimed to differentiate COVID-19-positive individuals from controls in a hospital setting, was based on 39 compounds and achieved high sensitivity (85%/100%), specificity (82%/84%), and accuracy (84%/92%) in training and validation sets, respectively. The salivary diagnostic signatures were mainly composed of amino acids and lipids and were related to a heightened innate immune antiviral response and an attenuated inflammatory profile. The higher abundance of thyrotropin-releasing hormone in the COVID-19 positive group highlighted the endocrine imbalance in low-severity disease, as first reported here, underscoring the need for further studies in this area.

Intensive care unit-acquired infections more common in patients with COVID-19 than with influenza

Intensive care unit-acquired infections are complicating events in critically ill patients. In this study we analyzed the incidence, microbiological patterns, and outcome in patients with COVID-19 versus influenza in the intensive care unit (ICU). We included all adult patients treated with invasive mechanical ventilation due to (1) COVID-19 between January 2020 and March 2022, and (2) influenza between January 2015 and May 2023 at Sahlgrenska University Hospital, Sweden. Of the 480 participants included in the final analysis, 436 had COVID-19. The incidence rates of ICU-acquired infections were 31.6/1000 and 9.9/1000 ICU-days in the COVID-19 and influenza cohorts, respectively. Ventilator-associated lower respiratory tract infections were most common in both groups. In patients with COVID-19, corticosteroid treatment was associated with an increased risk of ICU-acquired infections and with higher 90-day mortality in case of infection. Furthermore, ICU-acquired infection was associated with a prolonged time in the ICU, with more difficult-to-treat gram-negative infections in late versus early ventilator-associated lower respiratory tract infections. Further research is needed to understand how the association between corticosteroid treatment and incidence and outcome of ICU-acquired infections varies across different patient categories.

Severity of Respiratory Syncytial Virus vs COVID-19 and Influenza Among Hospitalized US Adults

Importance

On June 21, 2023, the Centers for Disease Control and Prevention recommended the first respiratory syncytial virus (RSV) vaccines for adults aged 60 years and older using shared clinical decision-making. Understanding the severity of RSV disease in adults can help guide this clinical decision-making.

Objective

To describe disease severity among adults hospitalized with RSV and compare it with the severity of COVID-19 and influenza disease by vaccination status.

Design, Setting, and Participants

In this cohort study, adults aged 18 years and older admitted to the hospital with acute respiratory illness and laboratory-confirmed RSV, SARS-CoV-2, or influenza infection were prospectively enrolled from 25 hospitals in 20 US states from February 1, 2022, to May 31, 2023. Clinical data during each patient's hospitalization were collected using standardized forms. Data were analyzed from August to October 2023.

Exposures

RSV, SARS-CoV-2, or influenza infection.

Main Outcomes and Measures

Using multivariable logistic regression, severity of RSV disease was compared with COVID-19 and influenza severity, by COVID-19 and influenza vaccination status, for a range of clinical outcomes, including the composite of invasive mechanical ventilation (IMV) and in-hospital death.

Results

Of 7998 adults (median [IQR] age, 67 [54-78] years; 4047 [50.6%] female) included, 484 (6.1%) were hospitalized with RSV, 6422 (80.3%) were hospitalized with COVID-19, and 1092 (13.7%) were hospitalized with influenza. Among patients with RSV, 58 (12.0%) experienced IMV or death, compared with 201 of 1422 unvaccinated patients with COVID-19 (14.1%) and 458 of 5000 vaccinated patients with COVID-19 (9.2%), as well as 72 of 699 unvaccinated patients with influenza (10.3%) and 20 of 393 vaccinated patients with influenza (5.1%). In adjusted analyses, the odds of IMV or in-hospital death were not significantly different among patients hospitalized with RSV and unvaccinated patients hospitalized with COVID-19 (adjusted odds ratio [aOR], 0.82; 95% CI, 0.59-1.13; P = .22) or influenza (aOR, 1.20; 95% CI, 0.82-1.76; P = .35); however, the odds of IMV or death were significantly higher among patients hospitalized with RSV compared with vaccinated patients hospitalized with COVID-19 (aOR, 1.38; 95% CI, 1.02-1.86; P = .03) or influenza disease (aOR, 2.81; 95% CI, 1.62-4.86; P < .001).

Conclusions and Relevance

Among adults hospitalized in this US cohort during the 16 months before the first RSV vaccine recommendations, RSV disease was less common but similar in severity compared with COVID-19 or influenza disease among unvaccinated patients and more severe than COVID-19 or influenza disease among vaccinated patients for the most serious outcomes of IMV or death.

Model-based analysis of the incidence trends and transmission dynamics of COVID-19 associated with the Omicron variant in representative cities in China

BACKGROUND

In 2022, Omicron outbreaks occurred at multiple sites in China. It is of great importance to track the incidence trends and transmission dynamics of coronavirus disease 2019 (COVID-19) to guide further interventions.

METHODS

Given the population size, economic level and transport level similarities, two groups of outbreaks (Shanghai vs. Chengdu and Sanya vs. Beihai) were selected for analysis. We developed the SEAIQRD, ARIMA, and LSTM models to seek optimal modeling techniques for waves associated with the Omicron variant regarding data predictive performance and mechanism transmission dynamics, respectively. In addition, we quantitatively modeled the impacts of different combinations of more stringent interventions on the course of the epidemic through scenario analyses.

RESULTS

The best-performing LSTM model showed better prediction accuracy than the best-performing SEAIQRD and ARIMA models in most cases studied. The SEAIQRD model had an absolute advantage in exploring the transmission dynamics of the outbreaks. Regardless of the time to inflection point or the time to Rt curve below 1.0, Shanghai was later than Chengdu (day 46 vs. day 12/day 54 vs. day 14), and Sanya was later than Beihai (day 16 vs. day 12/day 20 vs. day 16). Regardless of the number of peak cases or the cumulative number of infections, Shanghai was higher than Chengdu (34,350 vs. 188/623,870 vs. 2,181), and Sanya was higher than Beihai (1,105 vs. 203/16,289 vs. 3,184). Scenario analyses suggested that upgrading control level in advance, while increasing the index decline rate and quarantine rate, were of great significance for shortening the time to peak and Rt below 1.0, as well as reducing the number of peak cases and final affected population.

CONCLUSIONS

The LSTM model has great potential for predicting the prevalence of Omicron outbreaks, whereas the SEAIQRD model is highly effective in revealing their internal transmission mechanisms. We recommended the use of joint interventions to contain the spread of the virus.