Coronavirus disease 2019 (COVID-19) is a mild to moderate respiratory tract infection, however, a subset of patients progress to severe disease and respiratory failure. The mechanism of protective immunity in mild forms and the pathogenesis of severe COVID-19 associated with increased neutrophil counts and dysregulated immune responses remain unclear. In a dual-center, two-cohort study, we combined single-cell RNA-sequencing and single-cell proteomics of whole-blood and peripheral-blood mononuclear cells to determine changes in immune cell composition and activation in mild versus severe COVID-19 (242 samples from 109 individuals) over time. HLA-DR hi CD11c hi inflammatory monocytes with an interferon-stimulated gene signature were elevated in mild COVID-19. Severe COVID-19 was marked by occurrence of neutrophil precursors, as evidence of emergency myelopoiesis, dysfunctional mature neutrophils, and HLA-DR lo monocytes. Our study provides detailed insights into the systemic immune response to SARS-CoV-2 infection and reveals profound alterations in the myeloid cell compartment associated with severe COVID-19.

Abstract. The global methane (CH 4 ) budget is becoming an increasingly important component for managing realistic pathways to mitigate climate change. This relevance, due to a shorter atmospheric lifetime and a stronger warming potential than carbon dioxide, is challenged by the still unexplained changes of atmospheric CH 4 over the past decade. Emissions and concentrations of CH 4 are continuing to increase, making CH 4 the second most important human-induced greenhouse gas after carbon dioxide. Two major difficulties in reducing uncertainties come from the large variety of diffusive CH 4 sources that overlap geographically, and from the destruction of CH 4 by the very short-lived hydroxyl radical (OH). To address these difficulties, we have established a consortium of multi-disciplinary scientists under the umbrella of the Global Carbon Project to synthesize and stimulate research on the methane cycle, and producing regular (∼ biennial) updates of the global methane budget. This consortium includes atmospheric physicists and chemists, biogeochemists of surface and marine emissions, and socio-economists who study anthropogenic emissions. Following Kirschke et al. (2013), we propose here the first version of a living review paper that integrates results of top-down studies (exploiting atmospheric observations within an atmospheric inverse-modelling framework) and bottom-up models, inventories and data-driven approaches (including process-based models for estimating land surface emissions and atmospheric chemistry, and inventories for anthropogenic emissions, data-driven extrapolations). . Top-down inversions consistently infer lower emissions in China (∼ 58 Tg CH 4 yr −1 , range 51-72, −14 %) and higher emissions in Africa (86 Tg CH 4 yr −1 , range 73-108, +19 %) than bottom-up values used as prior estimates. Overall, uncertainties for anthropogenic emissions appear smaller than those from natural sources, and the uncertainties on source categories appear larger for top-down inversions than for bottom-up inventories and models.The most important source of uncertainty on the methane budget is attributable to emissions from wetland and other inland waters. We show that the wetland extent could contribute 30-40 % on the estimated range for wetland emissions. Other priorities for improving the methane budget include the following: (i) the development of process-based models for inland-water emissions, (ii) the intensification of methane observations at local scale (flux measurements) to constrain bottom-up land surface models, and at regional scale (surface networks and satellites) to constrain top-down inversions, (iii) improvements in the estimation of atmospheric loss by OH, and (iv) improvements of the transport models integrated in top-down inversions.

12Diagnostic testing for COVID-19 is central to controlling the global pandemic. Recently, To and 13 colleagues reported that 20 of 23 (87%) patients who had SARS-CoV-2 detected by reverse-14 transcriptase PCR (RT-PCR) in nasopharyngeal swabs (NPS) or sputum also had SARS-CoV-2 15 detectable in saliva (1). The use of saliva has several advantages compared to collection of NPS. In 16 particular, the close contact involved in swab collection poses a risk to healthcare workers, and 17 collection of saliva may reduce this risk. Further, saliva collection does not require specialised 18 consumables, causes less patient discomfort, and may be a useful sample for self-collection (2). 20We further investigated the feasibility and utility of saliva collection from ambulatory patients 21 presenting to a dedicated COVID-19 screening clinic at the Royal Melbourne Hospital (RMH), 22Melbourne, Australia. Between 25 th March and 1 st April 2020, 622 patients were tested for COVID-23 19 through the screening clinic. All patients had NPS, and 522/622 (83.9%) patients also provided 24 saliva. Patients were asked to pool saliva in their mouth for 1-2 minutes prior to collection, and gently 25 spit 1-2 mL of saliva into a 25mL collection pot. Neat saliva specimens were transported to the 26 laboratory where an approximate 1:1 ratio of liquid Amies media was immediately added. We 27 specifically chose to use liquid Amies media in order to: (i) evaluate the use of an alternative transport 28 media in the face of global shortages of viral transport medium (VTM), and (ii) to preserve VTM in 29 our own laboratory. The median time from sample collection to addition of media was 180 minutes 30 (range 55 -537 minutes). NPS and saliva specimens underwent nucleic acid extraction on the Qiagen 31 EZ1 platform (QIAGEN, Hilden, Germany). An extraction volume of 200uL of the sample was used, 32 with RNA eluted in 60uL. Reverse-transcriptase PCR (RT-PCR) testing was performed using a 33 multiplex RT-PCR test for SARS-CoV-2 and other seasonal coronaviruses (Coronavirus Typing (8-34 well) assay, AusDiagnostics, Mascot, Australia). All positive NPS samples for SARS-CoV-2 35 underwent confirmatory testing at a local reference laboratory (the Victorian Infectious Diseases 36 Reference Laboratory) using previously published primers (3). 38Overall, 39/622 (6.3%; 95% confidence interval [CI] 4.6%-8.5%) patients had PCR-positive NPS, and 39 33/39 patients (84.6%; 95% CI 70.0%-93.1%) had SARS-CoV-2 detected in saliva. The median cycle 40 threshold (Ct) value was significantly lower in NPS than saliva ( Figure 1A), suggestive of higher viral 41 loads in NPS, and in both samples, there was a correlation between Ct value and days from symptom 42 onset ( Figure 1B). To assess specificity, a subset of saliva specimens from 50 patients with PCR-43 negative swabs was also tested. Of note, SARS-CoV-2 was detected in 1/50 (2%; 95% CI 0.1%-44 11.5%) of these saliva samples, which may reflect differing quality of NPS collection. 46To date, studies assessing the utilit...

Atmospheric new particle formation (NPF) is an important global phenomenon that is nevertheless sensitive to ambient conditions. According to both observation and theoretical arguments, NPF usually requires a relatively high sulfuric acid (HSO) concentration to promote the formation of new particles and a low preexisting aerosol loading to minimize the sink of new particles. We investigated NPF in Shanghai and were able to observe both precursor vapors (HSO) and initial clusters at a molecular level in a megacity. High NPF rates were observed to coincide with several familiar markers suggestive of HSO-dimethylamine (DMA)-water (HO) nucleation, including sulfuric acid dimers and HSO-DMA clusters. In a cluster kinetics simulation, the observed concentration of sulfuric acid was high enough to explain the particle growth to ~3 nanometers under the very high condensation sink, whereas the subsequent higher growth rate beyond this size is believed to result from the added contribution of condensing organic species. These findings will help in understanding urban NPF and its air quality and climate effects, as well as in formulating policies to mitigate secondary particle formation in China.

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