In the Acknowledgements section of this Article, the grant number 'SQ2019FY010009' should have been '2019FY101500'; this has been corrected online.

bioRxiv preprint 2 Emerging and re-emerging infectious diseases, such as SARS, MERS, Zika and highly 25 pathogenic influenza present a major threat to public health 1-3 . Despite intense research 26 effort, how, when and where novel diseases appear are still the source of considerable 27 uncertainly. A severe respiratory disease was recently reported in the city of Wuhan, 28 Hubei province, China. At the time of writing, at least 62 suspected cases have been 29 reported since the first patient was hospitalized on December 12 nd 2019. Epidemiological 30 investigation by the local Center for Disease Control and Prevention (CDC) suggested 31 that the outbreak was associated with a sea food market in Wuhan. We studied seven 32 patients who were workers at the market, and collected bronchoalveolar lavage fluid 33 (BALF) from one patient who exhibited a severe respiratory syndrome including fever, 34 dizziness and cough, and who was admitted to Wuhan Central Hospital on December 35 26 th 2019. Next generation metagenomic RNA sequencing 4 identified a novel RNA virus 36 from the family Coronaviridae designed WH-Human-1 coronavirus (WHCV). 37 Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that 38 WHCV was most closely related (89.1% nucleotide similarity similarity) to a group of 39 Severe Acute Respiratory Syndrome (SARS)-like coronaviruses (genus Betacoronavirus, 40 subgenus Sarbecovirus) previously sampled from bats in China and that have a history 41 of genomic recombination. This outbreak highlights the ongoing capacity of viral spill-42 over from animals to cause severe disease in humans. 43 44 Seven patients, comprising five men and two women, were hospitalized at the Central 45 : bioRxiv preprint 3 patients was 43, ranging from 31 to 70 years old. The clinical characteristics of the patients 47 are shown in Table 1. Fever and cough were the most common symptoms. All patients had 48 fever with body temperatures ranging from 37.2 o C to 40 o C. Patients 1, 2, 5, 6 and 7 had 49 cough, while patients 1, 2 and 7 presented with severe cough with phlegm at onset of illness. 50 Patients 4 and 5 also complained of chest tightness and dyspnea. Patients 1, 3, 4 and 6 51 experienced dizziness and patient 3 felt weakness. No neurological symptoms were observed 52 in any of the patients. Bacterial culture revealed the presence of Streptococcus bacteria in 53 throat swabs from patients 3, 4 and 7. Combination antibiotic, antiviral and glucocorticoid 54 therapy were administered. Unfortunately, patient 1 and 4 showed respiratory failure: patient 55 1 was given high flow noninvasive ventilation, while patient 4 was provided with nasal/face 56 mask ventilation (Table 1). 57Epidemiological investigation by the Wuhan CDC revealed that all the suspected cases 58 were linked to individuals working in a local indoor seafood market. Notably, in addition to 59 fish and shell fish, a variety of live wild animals including hedgehogs, badgers, snakes, and 60 birds (turtledoves) were available for sale in th...

Background COVID-19 is an infectious disease characterized by multiple respiratory and extrapulmonary manifestations, including gastrointestinal symptoms. Although recent studies have linked gut microbiota to infectious diseases such as influenza, little is known about the role of the gut microbiota in COVID-19 pathophysiology. Methods To better understand the host-gut microbiota interactions in COVID-19, we characterized the gut microbial community and gut barrier function using metagenomic and metaproteomic approaches in 63 COVID-19 patients and 8 non-infected controls. Both immunohematological parameters and transcriptional profiles were measured to reflect the immune response in COVID-19 patients. Results Altered gut microbial composition was observed in COVID-19 patients, which was characterized by decreased commensal species and increased opportunistic pathogenic species. Severe illness was associated with higher abundance of four microbial species (i.e., Burkholderia contaminans, Bacteroides nordii, Bifidobacterium longum, and Blautia sp. CAG 257), six microbial pathways (e.g., glycolysis and fermentation), and 10 virulence genes. These severity-related microbial features were further associated with host immune response. For example, the abundance of Bu. contaminans was associated with higher levels of inflammation biomarkers and lower levels of immune cells. Furthermore, human-origin proteins identified from both blood and fecal samples suggested gut barrier dysfunction in COVID-19 patients. The circulating levels of lipopolysaccharide-binding protein increased in patients with severe illness and were associated with circulating inflammation biomarkers and immune cells. Besides, proteins of disease-related bacteria (e.g., B. longum) were detectable in blood samples from patients. Conclusions Our results suggest that the dysbiosis of the gut microbiome and the dysfunction of the gut barrier might play a role in the pathophysiology of COVID-19 by affecting host immune homeostasis.

Aims To assess the effects of atmospheric N deposition on the C budget of an alpine meadow ecosystem on the Qinghai-Tibetan Plateau, it is necessary to explore the responses of soil-atmosphere carbon dioxide (CO 2 ) exchange to N addition.Methods Based on a multi-form, low-level N addition experiment, soil CO 2 effluxes were monitored weekly using the static chamber and gas chromatograph technique. Soil variables and aboveground biomass were measured monthly to examine the key driving factors of soil CO 2 efflux.Results The results showed that low-level N input tended to decrease soil moisture, whereas medium-level N input maintained soil moisture. Three-year N additions slightly increased soil inorganic N pools, especially the soil NH 4 + -N pool. N applications significantly increased aboveground biomass and soil CO 2 efflux; moreover, this effect was more significant from NH 4 + -N than from NO 3 − -N fertilizer. In addition, the soil CO 2 efflux was mainly driven by soil temperature, followed by aboveground biomass and NH 4 + -N pool. Conclusions These results suggest that chronic atmospheric N deposition will stimulate soil CO 2 efflux in the alpine meadow on the Qinghai-Tibetan Plateau by increasing available N content and promoting plant growth.

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