High attack rate in a large care home outbreak of SARS-CoV-2 BA.2.86, East of England, August 2023

Distinct evolution of SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 lineages combining increased fitness and antibody evasion

The unceasing circulation of SARS-CoV-2 leads to the continuous emergence of novel viral sublineages. Here, we isolate and characterize XBB.1, XBB.1.5, XBB.1.9.1, XBB.1.16.1, EG.5.1.1, EG.5.1.3, XBF, BA.2.86.1 and JN.1 variants, representing >80% of circulating variants in January 2024. The XBB subvariants carry few but recurrent mutations in the spike, whereas BA.2.86.1 and JN.1 harbor >30 additional changes. These variants replicate in IGROV-1 but no longer in Vero E6 and are not markedly fusogenic. They potently infect nasal epithelial cells, with EG.5.1.3 exhibiting the highest fitness. Antivirals remain active. Neutralizing antibody (NAb) responses from vaccinees and BA.1/BA.2-infected individuals are markedly lower compared to BA.1, without major differences between variants. An XBB breakthrough infection enhances NAb responses against both XBB and BA.2.86 variants. JN.1 displays lower affinity to ACE2 and higher immune evasion properties compared to BA.2.86.1. Thus, while distinct, the evolutionary trajectory of these variants combines increased fitness and antibody evasion.

Memory T cells effectively recognize the SARS-CoV-2 hypermutated BA.2.86 variant

T cells are critical in mediating the early control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) breakthrough infection. However, it remains unknown whether memory T cells can effectively cross-recognize new SARS-CoV-2 variants with a broad array of mutations, such as the emergent hypermutated BA.2.86 variant. Here, we report in two separate cohorts, including healthy controls and individuals with chronic lymphocytic leukemia, that SARS-CoV-2 spike-specific CD4+ and CD8+ T cells induced by prior infection or vaccination demonstrate resilient immune recognition of BA.2.86. In both cohorts, we found largely preserved SARS-CoV-2 spike-specific CD4+ and CD8+ T cell magnitudes against mutated spike epitopes of BA.2.86. Functional analysis confirmed that both cytokine expression and proliferative capacity of SARS-CoV-2 spike-specific T cells to BA.2.86-mutated spike epitopes are similarly sustained. In summary, our findings indicate that memory CD4+ and CD8+ T cells continue to provide cell-mediated immune recognition to highly mutated emerging variants such as BA.2.86.

Distinct evolution of SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 lineages combining increased fitness and antibody evasion

The unceasing circulation of SARS-CoV-2 leads to the continuous emergence of novel viral sublineages. Here, we isolated and characterized XBB.1, XBB.1.5, XBB.1.9.1, XBB.1.16.1, EG.5.1.1, EG.5.1.3, XBF, BA.2.86.1 and JN.1 variants, representing >80% of circulating variants in January 2024. The XBB subvariants carry few but recurrent mutations in the spike, whereas BA.2.86.1 and JN.1 harbor >30 additional changes. These variants replicated in IGROV-1 but no longer in Vero E6 and were not markedly fusogenic. They potently infected nasal epithelial cells, with EG.5.1.3 exhibiting the highest fitness. Antivirals remained active. Neutralizing antibody (NAb) responses from vaccinees and BA.1/BA.2-infected individuals were markedly lower compared to BA.1, without major differences between variants. An XBB breakthrough infection enhanced NAb responses against both XBB and BA.2.86 variants. JN.1 displayed lower affinity to ACE2 and higher immune evasion properties compared to BA.2.86.1. Thus, while distinct, the evolutionary trajectory of these variants combines increased fitness and antibody evasion.

SARS-CoV-2 BA.2.86 enters lung cells and evades neutralizing antibodies with high efficiency

BA.2.86, a recently identified descendant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.2 sublineage, contains ∼35 mutations in the spike (S) protein and spreads in multiple countries. Here, we investigated whether the virus exhibits altered biological traits, focusing on S protein-driven viral entry. Employing pseudotyped particles, we show that BA.2.86, unlike other Omicron sublineages, enters Calu-3 lung cells with high efficiency and in a serine- but not cysteine-protease-dependent manner. Robust lung cell infection was confirmed with authentic BA.2.86, but the virus exhibited low specific infectivity. Further, BA.2.86 was highly resistant against all therapeutic antibodies tested, efficiently evading neutralization by antibodies induced by non-adapted vaccines. In contrast, BA.2.86 and the currently circulating EG.5.1 sublineage were appreciably neutralized by antibodies induced by the XBB.1.5-adapted vaccine. Collectively, BA.2.86 has regained a trait characteristic of early SARS-CoV-2 lineages, robust lung cell entry, and evades neutralizing antibodies. However, BA.2.86 exhibits low specific infectivity, which might limit transmissibility.

Detection of SARS-CoV-2 BA.2.86 by lateral flow devices

We evaluated the performance of 12 lateral flow devices by assessing their analytical sensitivity for SARS-CoV-2 variant BA.2.86. Kits from ACON, Orient Gene, Xiamen Biotime, Getein, and SureScreen detected variant BA.2.86 to sufficient sensitivity levels, comparable to those observed with previous Omicron variants. The stocks of lateral flow devices currently held by the UK government do not currently need changing for deployment for this variant.

The Value of the COVID-19 Yorkshire Rehabilitation Scale in the Assessment of Post-COVID among Residents of Long-Term Care Facilities

The COVID-19 Yorkshire Rehabilitation Scale (C19-YRS) is a patient-reported outcome measure designed to assess the long-term effects of COVID-19. The scale was validated and is commonly used in the general population. In this study, we assess the utility of the C19-YRS in evaluating the post-COVID burden among residents of long-term care facilities with a mean age of 79. C19-YRS and Barthel index evaluations were performed among 144 residents of long-term care facilities reporting new or worsened symptoms or functioning three months after convalescence from COVID-19. The C19-YRS-based screening showed that 70.9% of COVID-19 convalescents had ≥1 complaint three months after recovery. The highest C19-YRS-scored symptoms (indicating a higher burden) were breathlessness, fatigue, and cognitive and continence problems; however, symptomatology was very heterogeneous, revealing a high complexity of the disease in older persons. The mean total C19-YRS score was higher in hospitalized patients (n = 78) than in the outpatient group (n = 66) (p = 0.02). The functioning subscale of the C19-YRS strongly correlated with the Barthel index, with r = -0.8001 (p < 0.0001). A moderately strong correlation existed between retrospectively reported C19-YRS-based functioning and the Barthel index score reported before illness (r = 0.7783, p < 0.0001). The C19-YRS is instrumental in evaluating the consequences of COVID-19 among long-term-care residents. The assessment allows for a broad understanding of rehabilitation needs.

SARS-CoV-2 BA.2.86 ("Pirola"): Is it Pi or Just Another Omicron Sublineage?

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