Impact of the Alpha VOC on disease severity in SARS-CoV-2-positive adults in Sweden

Severity outcomes of SARS-CoV-2 infection in the Omicron and pre-Omicron periods, in unvaccinated first-time test positive adults less than 65 years old without comorbidity, in Sweden

BACKGROUND

The COVID-19 pandemic has had several phases with varying characteristics. We aimed to compare severity outcomes in different phases in a population with limited bias from risk factors.

METHODS

In a nationwide observational study of all unvaccinated first-time COVID-19 test positive individuals in Sweden aged 18-64 years without comorbidity, from week 45 of 2020 to week 5 of 2022, variant periods with certain variants constituting ≥ 92 % of all whole genome-sequenced cases nationwide, were compared regarding hospitalisation (with main discharge code of COVID-19), severe illness (use of high-flow nasal oxygen or admission to intensive care unit), and death due to COVID-19. Logistic regression was used to estimate odds ratios (ORs) for comparison of these outcomes between variant periods, using adjustments for variant period, age, sex, country of birth, place of residence, income, and education.

FINDINGS

The study included 789,133 individuals, including 15,145 hospitalised individuals. Among all individuals, the adjusted ORs for hospitalisation were 1.7 for the Alpha period vs the Pre-variant period (week 45-52 2020), 1.8 for the Delta period vs the Alpha period, and 0.1 for the Omicron period vs the Delta period (all comparisons significant). Among hospitalised individuals, the adjusted ORs for severe illness were 1.4 for the Alpha period vs the Pre-variant period, 1.7 for the Delta period vs the Alpha period, and 0.5 for the Omicron period vs the Delta period (all comparisons significant), and the adjusted ORs for death were 1.1 for the Alpha period vs the Pre-variant period (non-significant), 1.8 for the Delta period vs the Alpha period (significant), and 0.1 for the Omicron period vs the Delta period (non-significant).

INTERPRETATION

In this population with limited bias from risk factors, vaccination, and previous infection, disease severity increased from the pre-variant to the Delta period and then decreased with the Omicron period, among all individuals and among hospitalised individuals. These severity outcome differences should be considered when the pandemic is evaluated.

Integration of individualized and population-level molecular epidemiology data to model COVID-19 outcomes

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with enhanced transmissibility and immune escape have emerged periodically throughout the coronavirus disease 2019 (COVID-19) pandemic, but the impact of these variants on disease severity has remained unclear. In this single-center, retrospective cohort study, we examined the association between SARS-CoV-2 clade and patient outcome over a two-year period in Chicago, Illinois. Between March 2020 and March 2022, 14,252 residual diagnostic specimens were collected from SARS-CoV-2-positive inpatients and outpatients alongside linked clinical and demographic metadata, of which 2,114 were processed for viral whole-genome sequencing. When controlling for patient demographics and vaccination status, several viral clades were associated with risk for hospitalization, but this association was negated by the inclusion of population-level confounders, including case count, sampling bias, and shifting standards of care. These data highlight the importance of integrating non-virological factors into disease severity and outcome models for the accurate assessment of patient risk.

Comparing severe COVID-19 outcomes of first and second/third waves: a prospective single-centre cohort study of health-related quality of life and pulmonary outcomes 6 months after infection

OBJECTIVE

We aimed to compare long-term outcomes in intensive care unit (ICU) survivors between the first and second/third waves of the COVID-19 pandemic. More specifically, to assess health-related quality of life (HRQL) and respiratory health 6 months post-ICU and to study potential associations between patient characteristic and treatment variables regarding 6-month outcomes.

DESIGN

Prospective cohort study.

SETTING

Single-centre study of adult COVID-19 patients with respiratory distress admitted to two Swedish ICUs during the first wave (1 March 2020-1 September 2020) and second/third waves (2 September 2020- 1 August 2021) with follow-up approximately 6 months after ICU discharge.

PARTICIPANTS

Critically ill COVID-19 patients who survived for at least 90 days.

MAIN OUTCOME MEASURES

HRQL, extent of residual changes on chest CT scan and pulmonary function were compared between the waves. General linear regression and multivariable logistic regression were used to present mean score differences (MSD) and ORs with 95% CIs.

RESULTS

Of the 456 (67%) critically ill COVID-19 patients who survived at least 90 days, 278 (61%) were included in the study. Six months after ICU discharge, HRQL was similar between survivors in the pandemic waves, except that the second/third wave survivors had better role physical (MSD 20.2, 95% CI 7.3 to 33.1, p<0.01) and general health (MSD 7.2, 95% CI 0.7 to 13.6, p=0.03) and less bodily pain (MSD 12.2, 95% CI 3.6 to 20.8, p<0.01), while first wave survivors had better diffusing capacity of the lungs for carbon monoxide (OR 1.9, 95% CI 1.1 to 3.5, p=0.03).

CONCLUSIONS

This study indicates that even though intensive care treatment strategies have changed with time, there are few differences in long-term HRQL and respiratory health seems to remain at 6 months for patients surviving critical COVID-19 in the first and second/third waves of the pandemic.

Pre-Omicron Vaccine Breakthrough Infection Induces Superior Cross-Neutralization against SARS-CoV-2 Omicron BA.1 Compared to Infection Alone

SARS-CoV-2 variants raise concern because of their high transmissibility and their ability to evade neutralizing antibodies elicited by prior infection or by vaccination. Here, we compared the neutralizing abilities of sera from 70 unvaccinated COVID-19 patients infected before the emergence of variants of concern (VOCs) and of 16 vaccine breakthrough infection (BTI) cases infected with Gamma or Delta against the ancestral B.1 strain, the Gamma, Delta and Omicron BA.1 VOCs using live virus. We further determined antibody levels against the Nucleocapsid (N) and full Spike proteins, the receptor-binding domain (RBD) and the N-terminal domain (NTD) of the Spike protein. Convalescent sera featured considerable variability in the neutralization of B.1 and in the cross-neutralization of different strains. Their neutralizing capacity moderately correlated with antibody levels against the Spike protein and the RBD. All but one convalescent serum failed to neutralize Omicron BA.1. Overall, convalescent sera from patients with moderate disease had higher antibody levels and displayed a higher neutralizing ability against all strains than patients with mild or severe forms of the disease. The sera from BTI cases fell into one of two categories: half the sera had a high neutralizing activity against the ancestral B.1 strain as well as against the infecting strain, while the other half had no or a very low neutralizing activity against all strains. Although antibody levels against the spike protein and the RBD were lower in BTI sera than in unvaccinated convalescent sera, most neutralizing sera also retained partial neutralizing activity against Omicron BA.1, suggestive of a better cross-neutralization and higher affinity of vaccine-elicited antibodies over virus-induced antibodies. Accordingly, the IC50: antibody level ratios were comparable for BTI and convalescent sera, but remained lower in the neutralizing convalescent sera from patients with moderate disease than in BTI sera. The neutralizing activity of BTI sera was strongly correlated with antibodies against the Spike protein and the RBD. Together, these findings highlight qualitative differences in antibody responses elicited by infection in vaccinated and unvaccinated individuals. They further indicate that breakthrough infection with a pre-Omicron variant boosts immunity and induces cross-neutralizing antibodies against different strains, including Omicron BA.1.

Biological Properties of SARS-CoV-2 Variants: Epidemiological Impact and Clinical Consequences

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a virus that belongs to the coronavirus family and is the cause of coronavirus disease 2019 (COVID-19). As of May 2022, it had caused more than 500 million infections and more than 6 million deaths worldwide. Several vaccines have been produced and tested over the last two years. The SARS-CoV-2 virus, on the other hand, has mutated over time, resulting in genetic variation in the population of circulating variants during the COVID-19 pandemic. It has also shown immune-evading characteristics, suggesting that vaccinations against these variants could be potentially ineffective. The purpose of this review article is to investigate the key variants of concern (VOCs) and mutations of the virus driving the current pandemic, as well as to explore the transmission rates of SARS-CoV-2 VOCs in relation to epidemiological factors and to compare the virus's transmission rate to that of prior coronaviruses. We examined and provided key information on SARS-CoV-2 VOCs in this study, including their transmissibility, infectivity rate, disease severity, affinity for angiotensin-converting enzyme 2 (ACE2) receptors, viral load, reproduction number, vaccination effectiveness, and vaccine breakthrough.

Clinical outcomes associated with SARS-CoV-2 Omicron (B.1.1.529) variant and BA.1/BA.1.1 or BA.2 subvariant infection in southern California

ABTRACT

Epidemiologic surveillance has revealed decoupling of COVID-19 hospitalizations and deaths from case counts following emergence of the Omicron (B.1.1.529) SARS-CoV-2 variant globally. However, assessment of the relative severity of Omicron variant infections presents challenges because of differential acquired immune protection against Omicron and prior variants, and because longer-term changes have occurred in testing and healthcare practices. Here we show that Omicron variant infections were associated with substantially reduced risk of progression to severe clinical outcomes relative to time-matched Delta (B.1.617.2) variant infections within a large, integrated healthcare system in southern California. Adjusted hazard ratios (aHRs) for any hospital admission, symptomatic hospital admission, intensive care unit admission, mechanical ventilation, and death comparing cases with Omicron versus Delta variant infection were 0.59 (95% confidence interval: 0.51-0.69), 0.59 (0.51-0.68), 0.50 (0.29-0.87), 0.36 (0.18-0.72), and 0.21 (0.10-0.44) respectively. This reduced severity could not be explained by differential history of prior infection among cases with Omicron or Delta variant infection, and was starkest among cases not previously vaccinated against COVID-19 (aHR=0.40 [0.33-0.49] for any hospital admission and 0.14 [0.07-0.28] for death). Infections with the Omicron BA.2 subvariant were not associated with differential risk of severe outcomes in comparison to BA.1/BA.1.1 subvariant infections. Lower risk of severe clinical outcomes among cases with Omicron variant infection should inform public health response amid establishment of the Omicron variant as the dominant SARS-CoV-2 lineage globally.