Quantifying COVID-19 recovery process from a human mobility perspective: An intra-city study in Wuhan.

The COVID-19 pandemic has brought huge challenges to sustainable urban and community development. Although some recovery signals and patterns have been uncovered, the intra-city recovery process remains underexploited. This study proposes a comprehensive approach to quantify COVID-19 recovery leveraging fine-grained human mobility records. Taking Wuhan, a typical COVID-19 affected megacity in China, as the study area, we identify accurate recovery phases and select appropriate recovery functions in a data-driven manner. We observe that recovery characteristics regarding duration, amplitude, and velocity exhibit notable differences among urban blocks. We also notice that the recovery process under a one-wave outbreak lasts at least 84 days and has an S-shaped form best fitted with four-parameter Logistic functions. More than half of the recovery variance can be well explained and estimated by common variables from auxiliary data, including population, economic level, and built environments. Our study serves as a valuable reference that supports data-driven recovery quantification for COVID-19 and other crises.

Pan-Genome Analysis Reveals The Molecular Targets of Identification and Virulence Detection in Mucoralean Fungi (preprint)

Mucoralean fungi offer various pathogens to cause mucormycosis, especially in immunodeficient patients. Over the past decades, both the morbidity and mortality of mucormycosis have increased rapidly, particularly in developing countries. Nowadays, mucormycosis more often happens in India for the COVID-19 pandemic and its backward diagnostic techniques. Our epidemiologic outcomes show several identifications of Mucoralean fungi are limited to genus, while Rhizopus species, Mucor species and Lichtheimia species have high proportions. To find more molecular targets to make rapid and accurate identifications of Mucorales genus and species, Pan-genome analysis and Phylogenetic tree are conducted with four Mucorales isolates we sequenced and 43 fungi from NCBI. A few Mucorales-specific genes have been found such as STE/STE20 protein kinase, GH36 and sel1 repeat protein. Mucorales genus-specific genes are also found in Lichtheimia species and Cunninghamella species, which covered cellular structure, biochemistry metabolism, molecular processing, and signal transduction. Reported proteins related to the virulence of Mucorales species were run with Orthofinder and 112092, cotH3, gcn4 and igp1 have shown the potential to be the direct identification as well as the virulence detection of Mucorales species. The molecular biological techniques need to be promoted, for which our study provide hypothesis and feasibility analysis.

Coordination and Cooperation are Essential: A Call for a Global Network to Enhance Integrated Human Health Risk Resilience Based on China’s COVID-19 Pandemic Coping Practice

More than a year after its appearance and still rampant around the world, the COVID-19 pandemic has highlighted tragically how poorly the world is prepared to handle systemic risks in an increasingly hyper-connected global social-ecological system. The absence or clear inadequacy of global governance arrangements and mechanisms is painfully distinct and obvious. In this short article, we summarize a set of COVID-19 pandemic-related analyses and lessons that are inspired by Chinese practice. First, strong government response is one of the most important methods to control a pandemic. Second, countries should be concerned about human-to-frozen goods-to-human transmission. Third, sharing resources and experiences through cooperation is crucial to ensure an adequate health response. Based on these insights, we stress the critical importance of coordination and cooperation, and call for a global network to enhance integrated human health risk resilience.

Plasma cell-free DNA promise disease monitoring and tissue injury assessment of COVID-19 (preprint)

COVID-19 is a huge threat to global health. Due to the lack of definitive etiological therapeutics currently, effective disease monitoring is of high clinical value for better healthcare and management of the large number of COVID-19 patients. In this study, we recruited 37 COVID-19 patients, collected 176 blood samples upon diagnosis and during treatment, and analyzed cell-free DNA (cfDNA) in these samples. We report gross abnormalities in cfDNA of COVID-19 patients, including elevated GC content, altered molecule size and end motif patterns. More importantly, such cfDNA characteristics reflect patient-specific physiological conditions during treatment. Further analysis on tissue origin tracing of cfDNA reveals frequent tissue injuries in COVID-19 patients, which is supported by clinical diagnoses. Hence, we demonstrate the translational merit of cfDNA as valuable analyte for effective disease monitoring, as well as tissue injury assessment in COVID-19 patients.

Economic Burden of Public Health Care Was Higher Than That of Hospitalization and Treatment Associated With COVID-19 in China (preprint)

Background: During the coronavirus disease 2019 (COVID-19) pandemic, it is essential to evaluate the socioeconomic burden imposed on the Chinese health care system.Methods: We prospectively collected information from the Center for Disease Control and Prevention and the designated hospitals to determine the cost of public health care and hospitalization due to COVID-19. We estimated the resource use and direct medical costs per confirmed case and the costs associated with public health care per thousand people at the national level.Results: The average costs per case for specimen collection and nucleic acid testing (NAT) were $29.49 and $53.44, respectively, while the average cost of NAT for high-risk populations was $297.94 per capita. The average costs per thousand people for epidemiological surveys, disinfectant, health education and centralized isolation were $49.54, $247.01, $90.22 and $543.72, respectively. A single hospitalization for COVID-19 in China cost an average of $3,792.69 ($2,754.82-$5,393.76) in direct medical costs incurred only during hospitalization, while the total costs associated with hospitalization were estimated to have reached nearly $31,229.39 million in China as of 20 May 2020. The cost of public health care ($6.81 billion) was 20 times that of hospitalization.Conclusions: This study highlights the magnitude of resources needed to control the COVID-19 pandemic and treat COVID-19 cases. Public health measures implemented by the Chinese government have been valuable with regard to reducing the infection rate and may be cost-effective ways to control emerging infectious diseases.

The Trans-omics Landscape of COVID-19 (preprint)

The outbreak of coronavirus disease 2019 (COVID-19) has been causing a global health emergency. Although previous studies investigated COVID-19 at different omics levels, the molecular hallmarks of COVID-19, especially in those patients without comorbidities, have not been fully investigated. Here, we presented a trans-omics landscape for COVID-19 based on integrative analysis of genomic, transcriptomic, proteomic, metabolomic and lipidomic profiles from blood samples of 231 COVID-19 patients, ranging from asymptomatic to critically ill, importantly excluding those with any comorbidities. Notably, we found neutrophils heterogeneity existed between asymptomatic and critically ill patients. Expression discordance of inflammatory cytokines at mRNA and protein levels in asymptomatic patients could possibly be explained by post-transcriptional regulation by RNA binding proteins (RBPs) and microRNAs. Neutrophils over-activation, induced arginine depletion, and tryptophan metabolites accumulation contributed to T/NK cell dysfunction in critical patients. Anti-virus interferons were gradually suppressed along with disease severity. Overall, our study systematically revealed multi-omics characteristics of COVID-19, and the data we generated could hopefully help illuminate COVID-19 pathogenesis and provide valuable clues about potential therapeutic strategies for COVID-19.

Effects of policies and containment measures on control of COVID-19 epidemic in Chongqing.

BACKGROUND: Coronavirus disease 2019 (COVID-19) is an emerging, rapidly evolving disease that spreads through the respiratory system and is highly contagious. In March 2020, the World Health Organization declared the COVID-19 outbreak a pandemic. In China, the pandemic was controlled after 2 mo through effective policies and containment measures. Describing the detailed policies and containment measures used to control the epidemic in Chongqing will provide a reference for the prevention and control of COVID-19 in other areas of the world. AIM: To explore the effects of different policies and containment measures on the control of the COVID-19 epidemic in Chongqing. METHODS: Epidemiological data on COVID-19 in Chongqing were prospectively collected from January 21 to March 15, 2020. The policies and prevention measures implemented by the government during the epidemic period were also collected. Trend analysis was performed to explore the impact of the main policy measures on the effectiveness of the control of COVID-19 in Chongqing. RESULTS: As of March 15, the cumulative incidence of COVID-19 in Chongqing was 1.84/100000 (576 cases) and the infection fatality rate was 1.04% (6/576). The spread of COVID-19 was controlled by effective policies that involved establishing a group for directing the COVID-19 epidemic control effort; strengthening guidance and supervision; ensuring the supply of daily necessities and medical supplies and equipment to residents; setting up designated hospitals; implementing legal measures; and enhancing health education. Medical techniques were implemented to improve the recovery rate and control the epidemic. Policies such as "the lockdown of Wuhan", "initiating a first-level response to major public health emergencies", and "implementing the closed management of residential communities" significantly curbed the spread of COVID-19. Optimizing the diagnosis process, shortening the diagnosis time, and constructing teams of clinical experts facilitated the provision of "one team of medical experts for each patient" treatment for severe patients, which significantly improved the recovery rate and reduced the infection fatality rate. CONCLUSION: The prevention policies and containment measures implemented by the government and medical institutions are highly effective in controlling the spread of the epidemic and increasing the recovery rate of COVID-19 patients.

The Trans-omics Landscape of COVID-19 (preprint)

System-wide molecular characteristics of COVID-19, especially in those patients without comorbidities, have not been fully investigated. We compared extensive molecular profiles of blood samples from 231 COVID-19 patients, ranging from asymptomatic to critically ill, importantly excluding those with any comorbidities. Amongst the major findings, asymptomatic patients were characterized by highly activated anti-virus interferon, T/natural killer (NK) cell activation, and transcriptional upregulation of inflammatory cytokine mRNAs. However, given very abundant RNA binding proteins (RBPs), these cytokine mRNAs could be effectively destabilized hence preserving normal cytokine levels. In contrast, in critically ill patients, cytokine storm due to RBPs inhibition and tryptophan metabolites accumulation contributed to T/NK cell dysfunction. A machine-learning model was constructed which accurately stratified the COVID-19 severities based on their multi-omics features. Overall, our analysis provides insights into COVID-19 pathogenesis and identifies targets for intervening in treatment.

Time-series plasma cell-free DNA analysis reveals disease severity of COVID-19 patients (preprint)

Symptoms of coronavirus disease 2019 (COVID-19) range from asymptomatic to severe pneumonia and death. Detection of individuals at high risk for critical condition is crucial for control of the disease. Herein, for the first time, we profiled and analyzed plasma cell-free DNA (cfDNA) of mild and severe COVID-19 patients. We found that in comparison between mild and severe COVID-19 patients, Interleukin-37 signaling was one of the most relevant pathways; top significantly altered genes included POTEH, FAM27C, SPATA48, which were mostly expressed in prostate and testis; adrenal glands, small intestines and liver were tissues presenting most differentially expressed genes. Our data thus revealed potential tissue involvement, provided insights into mechanism on COVID-19 progression, and highlighted utility of cfDNA as a noninvasive biomarker for disease severity inspections.