Spike S1 domain interactome in non-pulmonary systems: A role beyond the receptor recognition

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes Coronavirus Disease 2019 (COVID-19), which, since 2019 in China, has rapidly become a worldwide pandemic. The aggressiveness and global spread were enhanced by the many SARS-CoV-2 variants that have been isolated up to now. These mutations affect mostly the viral glycoprotein Spike (S), the capsid protein mainly involved in the early stages of viral entry processes, through the recognition of specific receptors on the host cell surface. In particular, the subunit S1 of the Spike glycoprotein contains the Receptor Binding Domain (RBD) and it is responsible for the interaction with the angiotensin-converting enzyme 2 (ACE2). Although ACE2 is the primary Spike host receptor currently studied, it has been demonstrated that SARS-CoV-2 is also able to infect cells expressing low levels of ACE2, indicating that the virus may have alternative receptors on the host cells. The identification of the alternative receptors can better elucidate the pathogenicity and the tropism of SARS-CoV-2. Therefore, we investigated the Spike S1 interactomes, starting from host membrane proteins of non-pulmonary cell lines, such as human kidney (HK-2), normal colon (NCM460D), and colorectal adenocarcinoma (Caco-2). We employed an affinity purification-mass spectrometry (AP-MS) to pull down, from the membrane protein extracts of all cell lines, the protein partners of the recombinant form of the Spike S1 domain. The purified interactors were identified by a shotgun proteomics approach. The lists of S1 potential interacting proteins were then clusterized according to cellular localization, biological processes, and pathways, highlighting new possible S1 intracellular functions, crucial not only for the entrance mechanisms but also for viral replication and propagation processes.

Clinical Characteristics and Potential Risk Factors Associated with the SARS-CoV-2 Infection: Survey on a Health Care Workers (HCWs) Population in Northern Italy.

During the two years of the COVID-19 pandemic, more than 400 million cases all over the world have been identified. Health care workers were among the first to deal with this virus and consequently a high incidence of infection was reported in this population. The aim of the survey was to investigate health care workers' (HCWs) clinical characteristics and potential risk factors associated with the SARS-CoV-2 infection in a referral hospital in Northern Italy after the first and second waves of the pandemic. We administered a questionnaire during the flu vaccination campaign that took place at the end of 2020; among 1386 vaccinated HCWs, data was collected and analyzed for 1065 subjects. 182 HCWs (17%) declared that they had tested positive on at least a molecular or a serological test since the beginning of the pandemic. Comparing the infected vs. not infected HCWs, median age, BMI, smoking habit, presence of hypertension or other comorbidities were not significantly different, while having worked in a COVID ward was associated with the infection (ORadj = 1.54, 95% CI: 1.07-2.20). Respondents declared that more than 70% of contacts occurred in the hospital with patients or colleagues, while about 15% in domestic environments. Among the infected, the most reported symptoms were fever (62.1%), asthenia (60.3%), anosmia/ageusia (53.5%), arthralgia/myalgia (48.3%), headache or other neurological symptoms (46.6%), cough (43.1%) and flu-like syndrome (41.4%). The percentage of subjects who have been infected with SARS-CoV-2 seems to be higher in HCWs than in the general population; hence, in hospitals, protective measures and preventive strategies to avoid the spreading of the contagion remain crucial.

Global ecological analysis of COVID-19 mortality and comparison between "the East" and "the West".

Although SARS-CoV-2 was first reported in China and neighbouring countries, the pandemic quickly spread around the globe. This paper explores national drivers of the pandemic and the radically different epidemiology and response in the West and in the East. We studied coronavirus disease (COVID-19) mortality until 31st December 2020, using an ecological study design, considering baseline characteristics and responses that might account for the uneven impact of the pandemic. A multivariable regression model was developed to explore key determinants. Key variables in the West were contrasted with those in the East, and speed of response was examined. Worldwide, 2.24 million COVID-19 deaths were documented in 2020. Western countries reported a median mortality 114 times that of the East (684 vs. 6.0 per million). Significant correlates of mortality in countries with at least 1 million population were median age, obesity prevalence, and democracy index; political stability and experience of SARS in 2002-2003 were protective; health system variables and income inequality were not associated. Outputs of the model were consistent when adjusted for stringency index, timeliness of stay-at-home requirements, and geographical autocorrelation. The West experiences a much higher COVID-19 mortality than the East. Despite structural advantages in the West, delays in national responses early on resulted in a loss of control over the spread of SARS-CoV-2. Although the early success of the East was sustained in the second half of 2020, the region remains extremely vulnerable to COVID-19 until enough people are immunized.

Long-chain polyphosphates impair SARS-CoV-2 infection and replication.

Inorganic polyphosphates (polyPs) are linear polymers composed of repeated phosphate (PO4 3-) units linked together by multiple high-energy phosphoanhydride bonds. In addition to being a source of energy, polyPs have cytoprotective and antiviral activities. Here, we investigated the antiviral activities of long-chain polyPs against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. In molecular docking analyses, polyPs interacted with several conserved amino acid residues in angiotensin-converting enzyme 2 (ACE2), the host receptor that facilitates virus entry, and in viral RNA-dependent RNA polymerase (RdRp). ELISA and limited proteolysis assays using nano- LC-MS/MS mapped polyP120 binding to ACE2, and site-directed mutagenesis confirmed interactions between ACE2 and SARS-CoV-2 RdRp and identified the specific amino acid residues involved. PolyP120 enhanced the proteasomal degradation of both ACE2 and RdRp, thus impairing replication of the British B.1.1.7 SARS-CoV-2 variant. We thus tested polyPs for functional interactions with the virus in SARS-CoV-2-infected Vero E6 and Caco2 cells and in primary human nasal epithelial cells. Delivery of a nebulized form of polyP120 reduced the amounts of viral positive-sense genomic and subgenomic RNAs, of RNA transcripts encoding proinflammatory cytokines, and of viral structural proteins, thereby presenting SARS-CoV-2 infection in cells in vitro.

The experience of the health care workers of a severely hit SARS-CoV-2 referral Hospital in Italy: incidence, clinical course and modifiable risk factors for COVID-19 infection.

BACKGROUND: During the COVID-19 pandemic, the health care workers (HCWs) at the frontline have been largely exposed to infected patients, running a high risk of being infected by the SARS-CoV-2 virus.Since limiting transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in health care setting is crucial to avoid the community spread of SARS-CoV-2, we want to share our experience as an early hit hospital where standard infection control practices have been conscientiously applied and effective. We believe that our example, as first and hardest hit country, might be a warning and aid not only for those who have been hit later, but also for a second fearful wave of contagion. In addition, we want to offer an insight on modifiable risk factors for HWs-related infection. METHODS: Demographic, lifestyle, work-related and comorbidities data of 1447 HCWs, which underwent a nasopharyngeal swab for SARS-CoV-2, were retrospectively collected. For the 164 HCWs positive for SARS-CoV-2, data about safety in the workplace, symptoms and clinical course of COVID-19 were also collected. Cumulative incidence of SARS-CoV-2 infection was estimated. Risk factors for SARS-CoV-2 infection were assessed using a multivariable Poisson regression. RESULTS: The cumulative incidence of SARS-CoV-2 infection among the screened HCWs was 11.33% (9.72-13.21). Working in a COVID-19 ward, being a former smoker (versus being a person who never smoked) and BMI was positively associated with SARS-CoV-2 infection, whereas being a current smoker was negatively associated with this variable. CONCLUSIONS: Assuming an equal accessibility and proper use of personal protective equipment of all the HCWs of our Hospital, the great and more prolonged contact with COVID-19 patients remains the crucial risk factor for SARS-CoV-2. Therefore, increased and particular care needs to be focused specifically on the most exposed HCWs groups, which should be safeguarded. Furthermore, in order to limit the risk of asymptomatic spread of SARS-CoV-2 infection, the HCWs mild symptoms of COVID-19 should be considered when evaluating the potential benefits of universal staff testing.

Calcineurin Inhibitor-Based Immunosuppression and COVID-19: Results from a Multidisciplinary Cohort of Patients in Northern Italy.

The role of immunosuppression in SARS-CoV-2-related disease (COVID-19) is a matter of debate. We here describe the course and the outcome of COVID-19 in a cohort of patients undergoing treatment with calcineurin inhibitors. In this monocentric cohort study, data were collected from the COVID-19 outbreak in Italy up to April 28th 2020. Patients were followed at our hospital for solid organ transplantation or systemic rheumatic disorders (RMDs) and were on calcineurin inhibitor (CNI)-based therapy. Selected patients were referred from the North of Italy. The aim of our study was to evaluate the clinical course of COVID-19 in this setting. We evaluated 385 consecutive patients (220 males, 57%; median age 61 years, IQR 48-69); 331 (86%) received solid organ transplantation and 54 (14%) had a RMD. CNIs were the only immunosuppressant administered in 47 patients (12%). We identified 14 (4%) COVID-19 patients, all transplanted, mainly presenting with fever (86%) and diarrhea (71%). Twelve patients were hospitalized and two of them died, both with severe comorbidities. No patients developed acute respiratory distress syndrome or infectious complications. The surviving 10 patients are now fully recovered. The clinical course of COVID-19 patients on CNIs is generally mild, and the risk of superinfection seems low.