Phenotypic evolution of SARS-CoV-2 spike during the COVID-19 pandemic.

SARS-CoV-2 variants are mainly defined by mutations in their spike. It is therefore critical to understand how the evolutionary trajectories of spike affect virus phenotypes. So far, it has been challenging to comprehensively compare the many spikes that emerged during the pandemic in a single experimental platform.

Comparative study of two Rift Valley fever virus field strains originating from Mauritania.

Rift Valley fever (RVF) is one of the major viral arthropod-borne diseases in Africa. In recent decades, RVF virus (RVFV), the causative agent of RVF, has been responsible for multiple outbreaks in West Africa with important consequences on human and animal health. In particular, an outbreak occurred in 2010 after heavy rains in the desertic region of Adrar, Mauritania.

Evaluation of risk-based travel policy for the COVID-19 epidemic in Scotland: a population-based surveillance study.

Objectives: We aimed to assess the effects of risk-based travel restrictions on (1) international travel frequency, (2) SARS-CoV-2 case importation risk, (3) national SARS-CoV-2 incidence and (4) importation of SARS-CoV-2 variants into Scotland.

Design: Population-based surveillance study.

Setting: The study utilises SARS-CoV-2 community testing from February 2021 to May 2022 in Scotland, UK and spans the introduction of the UK's 'traffic light system' policy in May 2021.

Spatially resolved single-cell atlas unveils a distinct cellular signature of fatal lung COVID-19 in a Malawian population.

Postmortem single-cell studies have transformed understanding of lower respiratory tract diseases (LRTDs), including coronavirus disease 2019 (COVID-19), but there are minimal data from African settings where HIV, malaria and other environmental exposures may affect disease pathobiology and treatment targets. In this study, we used histology and high-dimensional imaging to characterize fatal lung disease in Malawian adults with (n = 9) and without (n = 7) COVID-19, and we generated single-cell transcriptomics data from lung, blood and nasal cells. Data integration with other cohorts showed a conserved COVID-19 histopathological signature, driven by contrasting immune and inflammatory mechanisms: in US, European and Asian cohorts, by type I/III interferon (IFN) responses, particularly in blood-derived monocytes, and in the Malawian cohort, by response to IFN-γ in lung-resident macrophages.

Prediction of virus-host associations using protein language models and multiple instance learning.

Predicting virus-host associations is essential to determine the specific host species that viruses interact with, and discover if new viruses infect humans and animals. Currently, the host of the majority of viruses is unknown, particularly in microbiomes. To address this challenge, we introduce EvoMIL, a deep learning method that predicts the host species for viruses from viral sequences only.

Modulation of connexin 43 in viral infections.

Connexins are essential for intercellular communication through gap junctions and the maintenance of cellular and tissue homeostasis. Connexin 43 (Cx43) is the most ubiquitously expressed connexin. As well as regulating homeostasis, Cx43 hemichannels and gap junctions play important roles in inflammation and the immune response.

Toscana virus - an emerging Mediterranean arbovirus transmitted by sand flies.

Toscana virus (TOSV) is an emerging arthropod-borne virus (arbovirus) of medical importance that is increasing its range across much of the Mediterranean Basin, Europe and the Middle East. Transmitted by spp. sand flies, it is the most clinically relevant sand fly-borne phlebovirus.

No evidence that mutations in SARS-CoV-2 variants of concern derive from homologous fragments in gut microbiota.

Understanding the origin and evolution of mutations in SARS-CoV-2 variants of concern (VOCs) is a critical area of research. B. Cao, X.

From emergence to endemicity of highly pathogenic H5 avian influenza viruses in Taiwan.

A/goose/Guangdong/1/96-like (GsGd) highly pathogenic avian influenza (HPAI) H5 viruses cause severe outbreaks in poultry when introduced. Since emergence in 1996, control measures in most countries have suppressed local GsGd transmission following introductions, making persistent transmission in domestic birds rare. However, geographical expansion of clade 2.

Tackling coinfections.

Mechanistic understanding of the impact of coinfections is a critical knowledge gap. A workshop on coinfections highlighted key aspects required to advance this field, including identifying the coinfection priorities, creating research platforms for this type of research, promoting cross-expertise collaborations, and securing funding to support cross-kingdom pathogen research.

Efficacy of air cleaning units for preventing SARS-CoV-2 and other hospital-acquired infections on medicine for older people wards: a quasi-experimental controlled before-and-after study.

Background: Nosocomial infections are costly, and airborne transmission is increasingly recognized as important for spread. Air cleaning units (ACUs) may reduce transmission, but little research has focused on their effectiveness on open wards.

Aim: To assess whether ACUs reduce nosocomial severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), or other, infections on older adult inpatient wards.

Exploring the expanding universe of host-virus interactions mediated by viral RNA.

RNA is a central molecule in RNA virus biology; however, the interactions that it establishes with the host cell are only starting to be elucidated. In recent years, a methodology revolution has dramatically expanded the scope of host-virus interactions involving the viral RNA (vRNA). A second wave of method development has enabled the precise study of these protein-vRNA interactions in a life cycle stage-dependent manner, as well as providing insights into the interactome of specific vRNA species.

The molecular dissection of TRIM25's RNA-binding mechanism provides key insights into its antiviral activity.

TRIM25 is an RNA-binding ubiquitin E3 ligase with central but poorly understood roles in the innate immune response to RNA viruses. The link between TRIM25's RNA binding and its role in innate immunity has not been established. Thus, we utilized a multitude of biophysical techniques to identify key RNA-binding residues of TRIM25 and developed an RNA-binding deficient mutant (TRIM25-m9).

1-year health outcomes associated with systemic corticosteroids for COVID-19: a longitudinal cohort study.

Background: In patients with coronavirus disease 2019 (COVID-19) requiring supplemental oxygen, dexamethasone reduces acute severity and improves survival, but longer-term effects are unknown. We hypothesised that systemic corticosteroid administration during acute COVID-19 would be associated with improved health-related quality of life (HRQoL) 1 year after discharge.

Methods: Adults admitted to hospital between February 2020 and March 2021 for COVID-19 and meeting current guideline recommendations for dexamethasone treatment were included using two prospective UK cohort studies (Post-hospitalisation COVID-19 and the International Severe Acute Respiratory and emerging Infection Consortium).

Absolute quantitative and base-resolution sequencing reveals comprehensive landscape of pseudouridine across the human transcriptome.

Pseudouridine (Ψ) is one of the most abundant modifications in cellular RNA. However, its function remains elusive, mainly due to the lack of highly sensitive and accurate detection methods. Here, we introduced 2-bromoacrylamide-assisted cyclization sequencing (BACS), which enables Ψ-to-C transitions, for quantitative profiling of Ψ at single-base resolution.

Complete genome sequence of white sturgeon herpesvirus 2 isolated from farmed white sturgeon ().

The complete genome sequence of white sturgeon herpesvirus 2 (strain UC Davis) was determined. Comparative genomic analyses confirmed the classification of this virus in the species in the family .