Monocyte migration profiles define disease severity in acute COVID-19 and unique features of long COVID.

BACKGROUND: COVID-19 is associated with a dysregulated immune response but it is unclear how immune dysfunction contributes to the chronic morbidity persisting in many COVID-19 patients during convalescence (long COVID). METHODS: We assessed phenotypical and functional changes of monocytes in COVID-19 patients during hospitalisation and up to 9 months of convalescence following COVID-19, respiratory syncytial virus or influenza A. Patients with progressive fibrosing interstitial lung disease were included as a positive control for severe, ongoing lung injury. RESULTS: Monocyte alterations in acute COVID-19 patients included aberrant expression of leukocyte migration molecules, continuing into convalescence (n=142) and corresponding with specific symptoms of long COVID. Long COVID patients with unresolved lung injury, indicated by sustained shortness of breath and abnormal chest radiology, were defined by high monocyte expression of C-X-C motif chemokine receptor 6 (CXCR6) (p<0.0001) and adhesion molecule P-selectin glycoprotein ligand 1 (p<0.01), alongside preferential migration of monocytes towards the CXCR6 ligand C-X-C motif chemokine ligand 16 (CXCL16) (p<0.05), which is abundantly expressed in the lung. Monocyte CXCR6 and lung CXCL16 were heightened in patients with progressive fibrosing interstitial lung disease (p<0.001), confirming a role for the CXCR6-CXCL16 axis in ongoing lung injury. Conversely, monocytes from long COVID patients with ongoing fatigue exhibited a sustained reduction of the prostaglandin-generating enzyme cyclooxygenase 2 (p<0.01) and CXCR2 expression (p<0.05). These monocyte changes were not present in respiratory syncytial virus or influenza A convalescence. CONCLUSIONS: Our data define unique monocyte signatures that define subgroups of long COVID patients, indicating a key role for monocyte migration in COVID-19 pathophysiology. Targeting these pathways may provide novel therapeutic opportunities in COVID-19 patients with persistent morbidity.

Reconstitution of the SARS-CoV-2 ribonucleosome provides insights into genomic RNA packaging and regulation by phosphorylation.

The nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 is responsible for compaction of the ∼30-kb RNA genome in the ∼90-nm virion. Previous studies suggest that each virion contains 35 to 40 viral ribonucleoprotein (vRNP) complexes, or ribonucleosomes, arrayed along the genome. There is, however, little mechanistic understanding of the vRNP complex. Here, we show that N protein, when combined in vitro with short fragments of the viral genome, forms 15-nm particles similar to the vRNP structures observed within virions. These vRNPs depend on regions of N protein that promote protein-RNA and protein-protein interactions. Phosphorylation of N protein in its disordered serine/arginine region weakens these interactions to generate less compact vRNPs. We propose that unmodified N protein binds structurally diverse regions in genomic RNA to form compact vRNPs within the nucleocapsid, while phosphorylation alters vRNP structure to support other N protein functions in viral transcription.

The impact of COVID19 on the cervical screening programme and colposcopy services in northern ireland

Introduction/BackgroundScreening programmes are an important aspect of illness prevention. In April 2020, in response to the COVID-19 pandemic, the Northern Irish (NI) government took the decision to pause all routine cervical screening invitations. Colposcopy services continued but capacity was reduced due to infection control measures. A negative screening result is only indicative of a low risk of developing disease and relies on follow up screening to prevent progression of disease. This is in line with the World Health Organisation (WHO) and their strategy to eliminate cervical cancer as a public health problem. There is concern that this will be compromised and cause a backlog of patients when services are reintroduced.MethodologyData was collected from the largest geographical health and social care trust within NI. All patients who were invited to colposcopy following an abnormal cervical screening result from September to November 2019 were compared to those patients presenting from September to November 2020 during the peak of COVID-19. Data collected included demographics, presenting smear, time to report, method of biopsy and biopsy result.Results158 patients were included in 2019 and 87 in 2020 (45% reduction). There was a mean increase of 5 days to report the presenting smear in 2020. The most common presenting smear result was a borderline result for both years however more patients presented with severe dyskaryosis during 2020 (7% increase). A smaller time interval was seen in 2020 for colposcopy review and a mean reduction of 36 days for reporting the cervical biopsy result was seen during 2020 but no significant change in biopsy results were seen.ConclusionCOVID19 has had an impact on the timings of reporting presenting smears, smear to colposcopy interval and cervical biopsy reporting. there is no statistical difference in the individual outcomes of presenting smear and cervical biopsy.

Reconstitution of the SARS-CoV-2 ribonucleosome provides insights into genomic RNA packaging and regulation by phosphorylation

The nucleocapsid (N) protein of SARS-CoV-2 is responsible for compaction of the ∼30-kb RNA genome in the ∼90-nm virion. Previous studies suggest that each virion contains 35-40 viral ribonucleoprotein (vRNP) complexes, or ribonucleosomes, arrayed along the genome. There is, however, little mechanistic understanding of the vRNP complex. Here, we show that N protein, when combined in vitro with short fragments of the viral genome, forms 15-nm particles similar to the vRNP structures observed within virions. These vRNPs depend on regions of N protein that promote protein-RNA and protein-protein interactions. Phosphorylation of N protein in its disordered serine/arginine (SR) region weakens these interactions to generate less compact vRNPs. We propose that unmodified N protein binds structurally diverse regions in genomic RNA to form compact vRNPs within the nucleocapsid, while phosphorylation alters vRNP structure to support other N protein functions in viral transcription.

Tendances récentes des dépenses de santé dans les pays de l’OCDE, et réactions aux chocs économiques et épidémiques Recent trends and structure of health spending in OECD countries in the light of economic and public health shocks

L’analyse de l’évolution récente des dépenses de santé met en évidence les deux chocs : la crise économique de 2008, et l’impact récent de la maladie à coronavirus 2019 (COVID-19) en 2020. Alors que les économies des pays de l’Organisation de coopération et de développement économiques (OCDE) se sont contractées fortement en 2008 et 2009, la part des dépenses de santé est restée relativement stable. En 2020, avec les fermetures généralisées et autres mesures de santé publique limitant drastiquement l’activité économique, de nombreuses économies de l’OCDE ont connu un déclin en chute libre. La nécessité d’accroître les dépenses de santé, notamment de la part des gouvernements, face à la pandémie, a engendré une croissance des dépenses de santé la plus rapide jamais enregistrée au sein de la zone OCDE au cours des 15 dernières années.

Tendances récentes des dépenses de santé dans les pays de l’OCDE, et réactions aux chocs économiques et épidémiques

Resumé L’analyse de l’évolution récente des dépenses de santé met en évidence les deux chocs : la crise économique de 2008, et l’impact récent de la maladie à coronavirus 2019 (COVID-19) en 2020. Alors que les économies des pays de l’Organisation de coopération et de développement économiques (OCDE) se sont contractées fortement en 2008 et 2009, la part des dépenses de santé est restée relativement stable. En 2020, avec les fermetures généralisées et autres mesures de santé publique limitant drastiquement l’activité économique, de nombreuses économies de l’OCDE ont connu un déclin en chute libre. La nécessité d’accroître les dépenses de santé, notamment de la part des gouvernements, face à la pandémie, a engendré une croissance des dépenses de santé la plus rapide jamais enregistrée au sein de la zone OCDE au cours des 15 dernières années. Summary Analysis of recent trends in health spending show the two shocks : the economic crisis in 2008 and the recent impact of the COVID 19 in 2020. While OECD economies contracted sharply in 2008 and 2009, the share of health in the economy remained relatively stable. In 2020, with widespread lockdowns and other public health measures severely restricting economic output and consumer spending, many OECD economies went into freefall in 2020. The need to increase health spending, particularly by governments, in response to the pandemic is likely to have led to the fastest growth in OECD health spending in the last 15 years.

Impact of COVID-19 on Key Performance Indicators of the National Hip Fracture Database and the Management of Hip Fracture Patients.

BACKGROUND:  A hospital's performance regarding the management of hip fractures is based on six key performance indicators (KPIs) which are recorded onto the National Hip Fracture Database (NHFD). The aim of this study was to assess the overall impact of coronavirus disease 2019 (COVID-19) on the management and outcomes of hip fracture patients against a similar period in 2019 by utilizing the KPIs. METHOD:  Retrospective data collection of hip fracture patients during a six-week (pre-COVID) period in 2019 and a six-week (COVID-19) period in a single orthopedic unit. The following parameters were compared; patient age, time to theater, surgeon operating time, total time in the operating room, time from ward to recovery, time from hospital presentation to theater, and total time from presentation to hospital discharge. RESULTS:  Some 38 patients in the pre-COVID-19 period vs. 27 patients with hip fractures in the COVID-19 period were included in the study. Time from diagnosis to theater and surgeon operating time were similar in both groups. The mean length of stay was 9.3 days vs. a mean of 31.34 days (p = 0.0004) in the COVID-19 and pre-COVID-19 groups respectively. A 30-day mortality was 22.2% (n = 6) in the COVID-19 group vs. 5.3% (n = 2) in the pre-COVID-19 group. CONCLUSION:  Our study demonstrates that the combination of surgical stress and COVID-19 leads to higher mortality rates. Our hospital's structural reorganization during the pandemic has shown progress in achieving important KPIs and improved short-term outcomes for hip fracture and trauma patients.

Impact of COVID-19 on the Onset and Progression of Alzheimer's Disease and Related Dementias: A Roadmap for Future Research.

COVID-19 causes lasting neurological symptoms in some survivors. Like other infections, COVID-19 may increase risk of cognitive impairment. This perspective highlights four knowledge gaps about COVID-19 that need to be filled to avoid this possible health issue. The first is the need to identify the COVID-19 symptoms, genetic polymorphisms and treatment decisions associated with risk of cognitive impairment. The second is the absence of model systems in which to test hypotheses relating infection to cognition. The third is the need for consortia for studying both existing and new longitudinal cohorts in which to monitor long term consequences of COVID-19 infection. A final knowledge gap discussed is the impact of the isolation and lack of social services brought about by quarantine/lockdowns on people living with dementia and their caregivers. Research into these areas may lead to interventions that reduce the overall risk of cognitive decline for COVID-19 survivors.

Phosphorylation modulates liquid-liquid phase separation of the SARS-CoV-2 N protein

The nucleocapsid (N) protein of coronaviruses serves two major functions: compaction of the RNA genome in the virion and regulation of viral gene transcription in the infected cell (1-3) . The N protein contains two globular RNA-binding domains surrounded by regions of intrinsic disorder (4) . Phosphorylation of the central disordered region is required for normal viral genome transcription (5,6) , which occurs in a cytoplasmic structure called the replication transcription complex (RTC) (7-11) . It is not known how phosphorylation controls N protein function. Here we show that the N protein of SARS-CoV-2, together with viral RNA, forms biomolecular condensates (12-15) . Unmodified N protein forms partially ordered gel-like structures that depend on multivalent RNA-protein and protein-protein interactions. Phosphorylation reduces a subset of these interactions, generating a more liquid-like droplet. We speculate that distinct oligomeric states support the two functions of the N protein: unmodified protein forms a structured oligomer that is suited for nucleocapsid assembly, and phosphorylated protein forms a liquid-like compartment for viral genome processing. Inhibitors of N protein phosphorylation could therefore serve as antiviral therapy.

Phosphoregulation of Phase Separation by the SARS-CoV-2 N Protein Suggests a Biophysical Basis for its Dual Functions.

The nucleocapsid (N) protein of coronaviruses serves two major functions: compaction of the RNA genome in the virion and regulation of viral gene transcription. It is not clear how the N protein mediates such distinct functions. The N protein contains two RNA-binding domains surrounded by regions of intrinsic disorder. Phosphorylation of the central disordered region promotes the protein's transcriptional function, but the underlying mechanism is not known. Here, we show that the N protein of SARS-CoV-2, together with viral RNA, forms biomolecular condensates. Unmodified N protein forms partially ordered gel-like condensates and discrete 15-nm particles based on multivalent RNA-protein and protein-protein interactions. Phosphorylation reduces these interactions, generating a more liquid-like droplet. We propose that distinct oligomeric states support the two functions of the N protein: unmodified protein forms a structured oligomer that is suited for nucleocapsid assembly, and phosphorylated protein forms a liquid-like compartment for viral genome processing.

Alterations in T and B cell function persist in convalescent COVID-19 patients.

BACKGROUND: Emerging studies indicate that some coronavirus disease 2019 (COVID-19) patients suffer from persistent symptoms, including breathlessness and chronic fatigue; however, the long-term immune response in these patients presently remains ill-defined. METHODS: Here, we describe the phenotypic and functional characteristics of B and T cells in hospitalized COVID-19 patients during acute disease and at 3-6 months of convalescence. FINDINGS: We report that the alterations in B cell subsets observed in acute COVID-19 patients were largely recovered in convalescent patients. In contrast, T cells from convalescent patients displayed continued alterations with persistence of a cytotoxic program evident in CD8+ T cells as well as elevated production of type 1 cytokines and interleukin-17 (IL-17). Interestingly, B cells from patients with acute COVID-19 displayed an IL-6/IL-10 cytokine imbalance in response to Toll-like receptor activation, skewed toward a pro-inflammatory phenotype. Whereas the frequency of IL-6+ B cells was restored in convalescent patients irrespective of clinical outcome, the recovery of IL-10+ B cells was associated with the resolution of lung pathology. CONCLUSIONS: Our data detail lymphocyte alterations in previously hospitalized COVID-19 patients up to 6 months following hospital discharge and identify 3 subgroups of convalescent patients based on distinct lymphocyte phenotypes, with 1 subgroup associated with poorer clinical outcome. We propose that alterations in B and T cell function following hospitalization with COVID-19 could affect longer-term immunity and contribute to some persistent symptoms observed in convalescent COVID-19 patients. FUNDING: Provided by UKRI, Lister Institute of Preventative Medicine, the Wellcome Trust, The Kennedy Trust for Rheumatology Research, and 3M Global Giving.

Qualitative Data Collection in an Era of Social Distancing

Qualitative researchers face unique opportunities and challenges as a result of the disruption of COVID-19. Although the pandemic represents a unique opportunity to study the crisis itself, social distancing mandates are restricting traditional face-to-face investigations of all kinds. In this article, we describe options and resources for researchers who find themselves needing to alter their study designs from face-to-face qualitative data collection to a “socially distant” method. Although technologies are constantly changing, we review the latest videoconferencing services available to researchers and provide guidance on what services might best suit a project’s needs. We describe options for various platforms and applications including information about enhanced security applications for researchers collecting sensitive patient health information. Concerns about these technologies including security of the platform and logistical needs such as computer equipment are also discussed. Special attention is given to ethical issues when transitioning research efforts to online venues.

Phosphorylation modulates liquid-liquid phase separation of the SARS-CoV-2 N protein.

The nucleocapsid (N) protein of coronaviruses serves two major functions: compaction of the RNA genome in the virion and regulation of viral gene transcription in the infected cell 1-3 . The N protein contains two globular RNA-binding domains surrounded by regions of intrinsic disorder 4 . Phosphorylation of the central disordered region is required for normal viral genome transcription 5,6 , which occurs in a cytoplasmic structure called the replication transcription complex (RTC) 7-11 . It is not known how phosphorylation controls N protein function. Here we show that the N protein of SARS-CoV-2, together with viral RNA, forms biomolecular condensates 12-15 . Unmodified N protein forms partially ordered gel-like structures that depend on multivalent RNA-protein and protein-protein interactions. Phosphorylation reduces a subset of these interactions, generating a more liquid-like droplet. We speculate that distinct oligomeric states support the two functions of the N protein: unmodified protein forms a structured oligomer that is suited for nucleocapsid assembly, and phosphorylated protein forms a liquid-like compartment for viral genome processing. Inhibitors of N protein phosphorylation could therefore serve as antiviral therapy.