Dovilė Juozapaitė

Background: Although coronavirus disease 2019 (COVID-19) is no longer a public health emergency, it remains the most prevalent circulating infectious-like illness in Europe. Whether immunocompromising conditions (ICCs) still carry increased mortality risk during the Omicron era is unclear. Methods: We conducted a cohort study across EuCARE sites in 8 countries among adults admitted to hospital with COVID-19 between 2020 and 2023. ICCs and COVID-19 pneumonia at hospitalization were defined using clinical information and ICD-10 codes. Logistic regression and counterfactual mediation analysis was used to compare 28-day in-hospital mortality risk associated with ICCs using COVID-19 pneumonia and vaccination at hospital entry as intermediates. Proportion of the total effect of ICCs mediated and the controlled direct effects (CDEs) were calculated. We also formally tested for interaction between SARS-CoV-2 variants and ICCs for mortality risk. Results: A total of 42 488 individuals were included, of whom 1675 (3.9%) had an ICC. Fifty-five percent were male, and the median age was 67 (IQR, 52–79) years. Overall, 4344 (10.2%) individuals died in hospital. ICCs were associated with increased mortality (OR, 1.49 [95% CI, 1.25–1.79]), with no evidence for an attenuation during the Omicron phase (P value for interaction = .60). Mediation analyses showed that the total effect of ICCs was mediated by vaccination but only weakly by pneumonia. With Omicron, the excess mortality associated with ICC was higher under the scenario that everyone in the cohort was to develop COVID-19 pneumonia (CDE, 1.22 [95% CI, .09–1.65]). Conclusions: ICC remains a significant risk factor for in-hospital death, even during the Omicron era, particularly if the infection led to the development of pneumonia.

Several studies have documented reverse zoonotic transmission of SARS-CoV-2, including in farmed mink which are susceptible to human respiratory viruses and are known for serving as a reservoir capable of generating new virus variants in densely populated farms. Here, we present the results of a genomic investigation launched in response to detected human infections with mink-origin SARS-CoV-2 lineages, and show evidence of at least 14 high-confidence introductions of SARS-CoV-2 from humans into farmed mink in Lithuania where sustained transmission in farmed mink lasted up to a year. We estimated the most likely timeframes for these introductions encompassing at least six SARS-CoV-2 lineages, some of which were already extinct in humans, with Bayesian phylogenetic and molecular clock analyses. This study highlights the public health risks posed by fur farms and underscores that passive genomic surveillance systems are ineffective without the active involvement and expertise of responsible institutions.

Distinct SARS-CoV-2 lineages, discovered through various genomic surveillance initiatives, have emerged during the pandemic following unprecedented reductions in worldwide human mobility. We here describe a SARS-CoV-2 lineage - designated B.1.620 - discovered in Lithuania and carrying many mutations and deletions in the spike protein shared with widespread variants of concern (VOCs), including E484K, S477N and deletions HV69Δ, Y144Δ, and LLA241/243Δ. As well as documenting the suite of mutations this lineage carries, we also describe its potential to be resistant to neutralising antibodies, accompanying travel histories for a subset of European cases, evidence of local B.1.620 transmission in Europe with a focus on Lithuania, and significance of its prevalence in Central Africa owing to recent genome sequencing efforts there. We make a case for its likely Central African origin using advanced phylogeographic inference methodologies incorporating recorded travel histories of infected travellers.