Genome-based comparison between the recombinant SARS-CoV-2 XBB and its parental lineages (preprint)

Recombination is the main contributor to RNA virus evolution, and SARS-CoV-2 during the pandemic produced several recombinants. The most recent SARS-CoV-2 recombinant is the lineage labeled XBB, also known as Gryphon, which arose from BJ.1 and BM.1.1.1. Here we performed a genome-based survey aimed to compare the new recombinant with its parental lineages that never became dominant. Genetic analyses indicated that the recombinant XBB and its first descendant XBB.1 show an evolutionary condition typical of an evolutionary blind background with no further epidemiologically relevant descendant. Genetic variability and expansion capabilities are slightly higher than parental lineages. Bayesian Skyline Plot indicates that XBB reached its plateau around October 6, 2022 and after an initial rapid growth the viral population size did not further expand, and around November 10, 2022 its levels of genetic variability decreased. Simultaneously with the reduction of the XBB population size, an increase of the genetic variability of its first sub-lineage XBB.1 occurred, that in turn reached the plateau around November 9, 2022 showing a kind of vicariance with its direct progenitors. Structure analysis indicates that the affinity for ACE2 surface in XBB/XBB.1 RBDs is weaker than for BA.2 RBD. In conclusion, nowadays XBB and XBB.1 do not show evidence about a particular danger or high expansion capability. Genome-based monitoring must continue uninterrupted in order to individuate if further mutations can make XBB more dangerous or generate new subvariants with different expansion capability.

Genetic and structural data on the SARS-CoV-2 Omicron BQ.1 variant reveal its low potential for epidemiological expansion (preprint)

The BQ.1 SARS-CoV-2 variant, also known as Cerberus, is one of the most recent Omicron descendant lineages. Compared to its direct progenitor BA.5, BQ.1 carries out some additional spike mutations in some key antigenic site which confer it further immune escape ability over other circulating lineage. In such a context, here we performed a genome-based survey aimed to obtain an as complete as possible nuance of this rapidly evolving Omicron subvariant. Genetic data suggests that BQ.1 represents an evolutionary blind background, lacking of the rapid diversification which is typical of a dangerous lineage. Indeed, the evolutionary rate of BQ.1 is very similar to that of BA.5 (7.6 x 10-4 and 7 x 10-4 subs/site/year, respectively), which is circulating by several months. Bayesian Skyline Plot reconstruction, indicates low level of genetic variability, suggesting that the peak has been reached around September 3, 2022. Structure analyses performed by comparing the properties of BQ.1 and BA.5 RBD indicated that the impact of the BQ.1 mutations on the affinity for ACE2 may be modest. Likewise, immunoinformatic analyses showed modest differences between the BQ.1 and the BA5 potential B-cells epitope. In conclusion, genetic and structural analysis on SARS-CoV-2 BQ.1 suggest that, it does not show evidence about its particular dangerous or high expansion capability. The monitoring genome-based must continue uninterrupted for a better understanding of its descendant and all other lineages.

Efficacy of remdesivir-containing therapy in hospitalized COVID-19 patients: a prospective clinical experience (preprint)

ABSTRACT Objectives remdesivir is currently approved for the treatment of COVID-19. The recommendation for using remdesivir in COVID-19 was based on the in vitro and in vivo activity of this drug against SARS-CoV-2. Methods this was a prospective, observational study conducted on a large population of patients hospitalized for COVID-19. The primary endpoint of the study was to evaluate the impact of remdesivir-containing therapy on 30-day mortality; secondary endpoint was the impact of remdesivir-containing therapy on the need of high flow oxygen therapy (HFNC) or non-invasive ventilation (NIV) or mechanical ventilation. Data were analyzed after propensity score matching. Results 407 patients with SARS-CoV-2 pneumonia were consecutively enrolled. Out of these, 294 (72.2%) and 113 (27.8%) were respectively treated or not with remdesivir. Overall, 61 (14.9%) patients were treated during hospitalization with non-invasive or mechanical ventilation, while a 30-day mortality was observed in 21 (5.2%) patients with a global in-hospital mortality of 11%. Cox regression analysis, after propensity score matching, showed that therapies, including remdesivir-containing therapy, were not statistically associated with 30-day survival or mortality, while need of HFNC/NIV (HR 17.921, CI95% 0.954-336.73, p=0.044) and mechanical ventilation (HR 3.9, CI95% 5.36-16.2, p=0.003) resulted independently associated with 30-day mortality. Finally, therapies including or not remdesivir were not independently associated with a lower or higher risk of HFNC/NIV or mechanical ventilation. Conclusions this real-life experience about the remdesivir use in hospitalized patients with COVID-19 was not associated with significant increase in rates of survival or reduced use of HFNC/NIV or mechanical ventilation, compared to patients treated with other therapies not including remdesivir.

SARS-CoV-2 shifting transmission dynamics and hidden reservoirs limited the efficacy of public health interventions in Italy (preprint)

We investigated SARS-CoV-2 transmission dynamics in Italy, one of the countries hit hardest by the pandemic, using phylodynamic analysis of viral genetic and epidemiological data. We observed the co-circulation of at least 13 different SARS-CoV-2 lineages over time, which were linked to multiple importations and characterized by large transmission clusters concomitant with a high number of infections. Subsequent implementation of a three-phase nationwide lockdown strategy greatly reduced infection numbers and hospitalizations. Yet we present evidence of sustained viral spread among sporadic clusters acting as "hidden reservoirs" during summer 2020. Mathematical modelling shows that increased mobility among residents eventually catalyzed the coalescence of such clusters, thus driving up the number of infections and initiating a new epidemic wave. Our results suggest that the efficacy of public health interventions is, ultimately, limited by the size and structure of epidemic reservoirs, which may warrant prioritization during vaccine deployment.

Retinal involvement and ocular findings in COVID‐19 pneumonia patients (preprint)

Background: changes in immune and coagulation systems and possible viral spread through blood-brain barrier have been described in SARS-CoV-2 infection. In this study, we evaluate the possible retinal involvement and ocular findings in severe COVID-19 pneumonia patients. Methods: a cross sectional study was conducted on 46 patients affected by severe COVID-19 who were hospitalized in one Intensive Care Unit (ICU) and in two Infectious Diseases wards, including a bedside eye screening, corneal sensitivity assessment and retinography. Results: a total of 43 SARS-CoV-2 positive pneumonia patients affected with COVID-19 pneumonia were included, 25 males and 18 females, with a median age of 70 [IQR 59-78]. Except for one patient with unilateral posterior chorioretinitis of opportunistic origin, of whom aqueous tap was negative for SARS-CoV-2, no further retinal manifestation related to COVID-19 infection was found in our cohort. We found 3 patients (7%) with bilateral conjunctivitis in whom PCR analysis on conjunctival swab provided negative results for SARS-CoV-2. No alterations of corneal sensitivity were found. Conclusion: we demonstrated the absence of retinal involvement in SARS-CoV-2 pneumonia patients. Ophthalmologic evaluation in COVID-19, particularly in patients hospitalized in an ICU setting, may be useful to reveal systemic co-infections by opportunistic pathogens.

CURB-65 plus Hypoalbuminemia: a new score system for prediction of the in-hospital mortality risk in patients with SARS-CoV-2 pneumonia (preprint)

Introduction: There is the need of a simple but highly reliable score system for stratifying the risk of mortality and Intensive Care Unit (ICU) transfer in patients with SARS-CoV-2 pneumonia at the Emergency Room. Purpose: In this study, the ability of CURB-65, extended CURB-65, PSI and CALL scores and C-Reactive Protein (CRP) to predict intra-hospital mortality and ICU admission in patients with SARS-CoV-2 infection were evaluated.Methods: During March-May 2020, a retrospective, single-center study including all consecutive adults patients with diagnosis of SARS-CoV-2 pneumonia was conducted. Clinical, laboratory and radiological data as well as CURB-65, expanded CURB-65, PSI and CALL scores were calculated based on data recorded at hospital admission. Results: Overall, 224 patients with documented SARS-CoV-2 infection were included in the study. As for intra-hospital mortality (24/224, 11%), PSI performed better than all the other tested scores, which showed lower AUC values (AUC=0.890 for PSI versus AUC=0.885, AUC=0.858 and AUC=0.743 for expanded CURB-65, CURB-65 and CALL scores, respectively). Of note, the addition of hypoalbuminemia to the CURB-65 score increased the prediction value of intra-hospital mortality (AUC=0.905). All the tested scores performed worse in predicting the need of ICU transfer (26/224, 12%), with the best AUC for extended CURB-65 score (AUC= 0.708).Conclusion: The addition of albumin level to the easy-to-calculate CURB-65 score at hospital admission is able to improve the quality of prediction of intra-hospital mortality in patients with SARS-CoV-2 pneumonia.

Co-infection of SARS-CoV-2 with Chlamydia or Mycoplasma pneumoniae: a case series and review of the literature (preprint)

The novel coronavirus SARS-CoV-2 has spread all over the world causing a global pandemic and representing a great medical challenge. Nowadays, there is limited knowledge on the rate of co-infections with other respiratory pathogens, with viral co-infection being the most representative agents. Co-infection with Mycoplasma pneumoniae has been described both in adults and pediatrics whereas only 2 cases of Chlamydia pneumoniae have been reported in a large US study so far. In the present report, we describe a series of 7 patients where co-infection with C. pneumoniae (n=5) or M. pneumoniae (n=2) and SARS-CoV-2 was detected in a large teaching hospital in Rome. An extensive review of the updated literature regarding the co-infection between SARS-CoV-2 and these atypical pathogens is also performed.