SARS-CoV-2 Viremia is Associated with COVID-19 Severity and Predicts Clinical Outcomes

Background: SARS-CoV-2 viral RNA (vRNA) is detected in the bloodstream of some patients with COVID-19 (“RNAemia”) but it is not clear whether this RNAemia reflects viremia (i.e., virus particles) and how RNAemia/viremia is related to host immune responses and outcomes. Methods: SARS-CoV-2 vRNA was quantified by ultra-sensitive RT-PCR in plasma samples (0.5-1.0 ml) from observational cohorts of 51 COVID-19 patients including 9 outpatients, 19 hospitalized (non-ICU), and 23 ICU patients, and vRNA levels compared with cross-sectional indices of COVID-19 severity and prospective clinical outcomes. We used multiple imaging methods to visualize virions in pelleted plasma. Results: SARS-CoV-2 vRNA was detected in plasma of 100%, 52.6% and 11.1% of ICU, non-ICU, and outpatients respectively. Virions were detected in plasma pellets by electron tomography and immunostaining. Plasma vRNA levels were significantly higher in ICU > non-ICU > outpatients (p6,000 copies/ml was strongly associated with mortality (HR: 10.7). Levels of vRNA were significantly associated with several inflammatory biomarkers (p<0.01) but not with plasma neutralizing antibody titers (p=0.8). Conclusions: Visualization of virus particles in plasma indicates that SARS-CoV-2 RNAemia is due, at least in part, to viremia. The levels of SARS-CoV-2 RNAemia quantified by ultrasensitive RT-PCR correlate strongly with disease severity, patient outcome and specific inflammatory biomarkers but not neutralizing antibody titers

Stressed Erythrophagocytosis as a Modifier of the Innate Immune Response to Klebsiella pneumoniae

Macrophages are main effectors of heme metabolism, increasing transiently in the liver during heightened disposal of damaged or senescent red cells (sRBC). Macrophages are also essential in defense against microbial threats, but pathologic states of heme excess may be immunosuppressive. Here, we uncover a novel mechanism whereby an acute rise in sRBC disposal by macrophages leads to an immunosuppressive phenotype following intrapulmonary Klebsiella pneumoniae infection characterized by increased extrapulmonary dissemination and reduced survival in mice. The impaired immunity to K. pneumoniae during heightened sRBC disposal is independent of iron acquisition by bacterial siderophores, as K. pneumoniae mutant lacking siderophore function recapitulates findings observed with wildtype strain. Rather, we show that sRBC disposal induces a liver transcriptomic profile notable for suppression of Stat1 and interferon-related responses during K. pneumoniae infection. Excess heme handling by macrophages recapitulates STAT1 suppression during infection that requires synergistic NRF1 and NRF2 activation but is independent of heme oxygenase-1 induction. Whereas iron is dispensable, the porphyrin moiety of heme is sufficient to mediate suppression of STAT1-dependent responses in human and mouse macrophages and promote liver dissemination of K. pneumoniae in vivo. Thus, dysfunction in cellular heme metabolism negatively regulates the STAT1 pathway with implications in host defense

A checklist is associated with increased quality of reporting preclinical biomedical research: A systematic review

<div><p>Irreproducibility of preclinical biomedical research has gained recent attention. It is suggested that requiring authors to complete a checklist at the time of manuscript submission would improve the quality and transparency of scientific reporting, and ultimately enhance reproducibility. Whether a checklist enhances quality and transparency in reporting preclinical animal studies, however, has not been empirically studied. Here we searched two highly cited life science journals, one that requires a checklist at submission (<i>Nature</i>) and one that does not (<i>Cell</i>), to identify <i>in vivo</i> animal studies. After screening 943 articles, a total of 80 articles were identified in 2013 (pre-checklist) and 2015 (post-checklist), and included for the detailed evaluation of reporting methodological and analytical information. We compared the quality of reporting preclinical animal studies between the two journals, accounting for differences between journals and changes over time in reporting. We find that reporting of randomization, blinding, and sample-size estimation significantly improved when comparing <i>Nature</i> to <i>Cell</i> from 2013 to 2015, likely due to implementation of a checklist. Specifically, improvement in reporting of the three methodological information was at least three times greater when a mandatory checklist was implemented than when it was not. Reporting the sex of animals and the number of independent experiments performed also improved from 2013 to 2015, likely from factors not related to a checklist. Our study demonstrates that completing a checklist at manuscript submission is associated with improved reporting of key methodological information in preclinical animal studies.</p></div

Outline of the study.

<p>(A) Selection of articles: Twenty consecutive articles that met the inclusion criteria among those published beginning in January for both 2013 and 2015 in <i>Nature</i> (one that implemented a pre-submission checklist) and <i>Cell</i> (one that did not) journals. This represents articles from periods of time before and after the implementation of the checklist in May 2013. (B) Flow of the analysis: To examine whether quality of reporting has improved over time, the degree of key information reported in 2015 was compared to that in 2013 in both journals combined (Objective 1). To assess whether a checklist is associated with improved quality in reporting, we first compared the changes over time observed in <i>Nature</i> (④ vs. ③). If there was significant difference, we compared time “2015 vs. 2013” in <i>Cell</i> (② vs. ①) and <i>Nature</i> vs. <i>Ce</i>ll within 2013 (③ vs. ①) and 2015 (④ vs. ②) to adjust for differences between journals and changes over time in reporting (Objective 2).</p

Distribution of reporting study designs across time.

<p>The distributions of the reporting status are presented in stacked bar graphs. The numbers inside the stacks are the number of articles corresponding to each percentage. The data for 2013 and 2015 are the total numbers of articles assessed from <i>Cell</i> and <i>Nature</i> within a given year. Fisher exact test was performed to assess the difference in reporting each methodological across time. Significant <i>P</i> values (< 0.05) are provided.</p

Data abstraction form to assess the quality and transparency in reporting.

<p>Data abstraction form to assess the quality and transparency in reporting.</p