Check out this selection of four articles from CoVICIS researchers over the last four years for insights from cohort studies in Italy and Switzerland on genomic epidemiology of SAR-CoV-2 variants, post-COVID recovery, and humoral and cellular immune responses.
Genomic epidemiology of the main SARS-Cov-2 variants circulating in Italy during the omicron Era
Bergna A, Lai A, Sagradi F, Menzo S, Mancini N, Bruzzone B, et al. Genomic Epidemiology of the main SARS-CoV-2 variants circulating in Italy during the omicron era. Authorea. August 26, 2024. doi: 10.22541/au.172471040.00213827/v1.
Research by 14 Italian universities under the CoVICIS Horizon Europe grant (Nr 101046041) has published a detailed investigation of the clinical and epidemiological characteristics of COVID-19 patients that reconstructs the genomic epidemiology of main SARS-CoV-2 Omicron sub-lineages in Italy in 2022. Since early 2022 the Omicron variant has rapidly spread worldwide, becoming the dominant variant to date.
These analyses dissect the epidemiological dynamics of Omicron sub-lineages in Italy over a period of great epidemiological change in the COVID-19 epidemic. In brief, the spread rate of the studied variant was found to exceed its evolutionary rate. No single sub-lineage had sufficient time to differentiate into large clusters, but only into small and fragmented groups sharing the same recent ancestor.
Compared to previous variants, the Omicron variant showed a high number of mutations, with an average of 50 substitutions throughout the genome, more than half of which are localized in the spike protein. These characteristics are responsible for a higher binding affinity to the ACE2 receptor and greater immune escape from neutralizing and monoclonal antibodies. This variant further evolved rapidly, giving rise to an array of multiple lineages and sub-lineages with specific mutational profiles. The intrinsic characteristic of the Omicron variant and the current absence of containment measures have allowed for a rapid spread and evolution of Omicron.
This study included more than 8,000 samples collected during the year 2022 in five Italian regions, accounting for more than 33% of the Italian population. The full study can be found here.
Recovery and symptom trajectories up to two years after SARS-CoV-2 infection: population based, longitudinal cohort study
Ballouz T, Menges D, Anagnostopoulos A, Domenghino A, Aschmann HE, Frei A, et al. Recovery and symptom trajectories up to two years after SARS-CoV-2 infection: population based, longitudinal cohort study. BMJ. 2023 May 31;381:e074425. doi: 10.1136/bmj-2022-074425.
A study of the general population in Zurich, Switzerland, evaluating longer term symptoms and health outcomes associated with post-covid-19 found that while most people recover or improve after infection, up to 18% of infected individuals are adversely affected by post-Covid-19 condition 24 months after infection.
Clinical trials are needed to establish effective interventions to reduce the burden of post-covid-19 condition. Although the people whose experience was studied had varying recovery trajectories, 5.2% had worse health and 4.4% had alternating periods of recovery and health impairment over time. Almost 10% experienced the highest excess risks for altered taste or smell and/or post-exertional malaise, with fatigue, dyspnoea, and reduced concentration and memory also at higher excess risk.
Effective interventions are needed to reduce the burden of post-covid-19 condition. The full study can be found here.
Post COVID-19 condition after Wildtype, Delta, and Omicron SARS-CoV-2 infection and prior vaccination: Pooled analysis of two population-based cohorts
Ballouz T, Menges D, Kaufmann M, Amati R, Frei A, von Wyl V, et al. Post COVID-19 condition after Wildtype, Delta, and Omicron SARS-CoV-2 infection and prior vaccination: Pooled analysis of two population-based cohorts. PLoS One. 2023 Feb 22;18(2):e0281429. doi: 10.1371/journal.pone.0281429.
Post COVID-19 condition (PCC) is an important complication of SARS-CoV-2 infection, affecting millions worldwide. This study aimed to evaluate the prevalence and severity of post COVID-19 condition (PCC) with novel SARS-CoV-2 variants and after prior vaccination.
Vaccinated individuals infected with Omicron and Delta variants of COVID-19 were less likely to develop PCC compared to non-vaccinated Wildtype-infected individuals. Number of vaccine doses and timing of last vaccination seemed to make no difference in PCC prevalence. The prevalence of PCC-related symptoms among vaccinated, Omicron-infected individuals was lower across severity levels. Four clusters of diverse systemic, neurocognitive, cardiorespiratory, and musculoskeletal symptoms were identified, with similar patterns across variants.
The risk of PCC appears to be lowered with infection by the Omicron variant and after prior vaccination. This evidence is crucial to guide future public health measures and vaccination strategies. The full study can be found here.
Heterogenous humoral and cellular immune responses with distinct trajectories post SARS-CoV-2 infection in a population-based cohort
Menges D, Zens KD, Ballouz T, Caduff N, Llanas-Cornejo D, Aschmann HE, Det al. Heterogenous humoral and cellular immune responses with distinct trajectories post-SARS-CoV-2 infection in a population-based cohort. Nat Commun. 2022 Aug 18;13(1):4855. doi: 10.1038/s41467-022-32573-w.
To better understand the development of SARS-CoV-2-specific immunity over time, a detailed evaluation of humoral and cellular responses is required. In this study, researchers characterize anti-Spike (S) IgA and IgG in a representative population-based cohort of 431 SARS-CoV-2-infected individuals up to 217 days after diagnosis, demonstrating that 85% develop and maintain anti-S responses. In a subsample of 64 participants, researchers assessed anti-Nucleocapsid (N) IgG, neutralizing antibody activity, and T cell responses to Membrane (M), N, and S proteins. In contrast to S-specific antibody responses, anti-N IgG levels decline substantially over time and neutralizing activity toward Delta and Omicron variants is low to non-existent within just weeks of Wildtype SARS-CoV-2 infection. Virus-specific T cells are detectable in most participants, albeit more variable than antibody responses. Cluster analyses of the co-evolution of antibody and T cell responses within individuals identify five distinct trajectories characterized by specific immune patterns and clinical factors. These findings demonstrate the relevant heterogeneity in humoral and cellular immunity to SARS-CoV-2 while also identifying consistent patterns where antibody and T cell responses may work in a compensatory manner to provide protection. The full study can be found here.