Temporal Landscape of Human Gut Virome in SARS-CoV-2 Infection and Severity (preprint)

Background: Coronavirus Disease 2019 (COVID-19) caused by the enveloped RNA virus SARS-CoV-2 primarily affects the respiratory and gastrointestinal tracts.SARS-CoV-2 was isolated from faecal samples and active viral replication was reported in human intestinal cells. The human gut also harbors an enormous amount of resident viruses (collectively known as virome) that play a role in regulating host immunity and pathophysiology.Understanding gut virome perturbation that underlies SARS-CoV-2 infection and severity is an unmet need.Methods: We enrolled 98 COVID-19 patients with varying disease severity (3 asymptomatic, 53 mild, 34 moderate, 5 severe, 3 critical) and 78 non-COVID-19 controls matched for gender and co-morbidities. All study subjects had faecal specimens sampled at inclusion. Blood specimens were sampled for COVID-19 patients at admission to test for inflammatory markers and white cell counts. Among COVID-19 cases, 37 (38%) patients had serially faecal samples collected 2 to 3 times per week from time of hospitalization until after discharge. Using shotgun metagenomics sequencing, we sequenced and profiled the faecal RNA and DNA virome respectively. We investigated alterations and longitudinal dynamics of the gut virome in association with disease severity and blood parameters.Findings: Patients with COVID-19 showed underrepresentation of P epper mild mottle virus (RNA virus) and multiple bacteriophage lineage s (DNA viruses) and enrichment of environment-derived eukaryotic DNA viruses in faecal samples, compared to non-COVID-19 subjects. Such gut virome dysbiosis persisted up to 30 days after disease resolution. Faecal virome in SARS-CoV-2 infection harboured more stress-, inflammation- and virulence-associated gene encoding capacities including those pertaining to bacteriophage integration, DNA repair, and metabolism and virulence associated with their bacterial host. Human faecal baseline abundance of 9 virus species (1 RNA virus, Pepper chlorotic spot virus, and 8 DNA virus species) inversely correlated with disease severity of COVID-19. These viruses were also inversely associated with blood levels of pro-inflammatory proteins, white cells and neutrophils. Among the 9 COVID-19 severity-associated virus species, 4 showed inverse correlation with age; 5 showed persistent lower abundance both during disease course and after disease resolution relative to non-COVID-19 subjects. Interpretation: Both enteric RNA and DNA viromes were perturbed in COVID-19, which prolonged even after disease resolution. Gut virome may calibrate host immunity and regulate severity to SARS-CoV-2 infection. Our observation that gut viruses inversely correlated with both severity of COVID-19 and host age partly explains that older subjects are prone to severe and unfavorable COVID-19 outcomes. Our data altogether highlight the significance of human gut virome in COVID-19 disease course and potentially therapeutics.Funding Statement: This work was supported by The D. H. Chen Foundation, Center for Gut Microbiota Research (Faculty of Medicine, The Chinese University of Hong Kong) and Health and Medical Research Fund (Hong Kong, China).Declaration of Interests: None.Ethics Approval Statement: This study was approved by the Joint Chinese University of Hong Kong–New Territories East Cluster Clinical Research Ethics Committees (Reference number: 2020.076). All subjects provided informed consent to participate in this study and agreed for publication of the research results.

Genetic mechanisms of critical illness in Covid-19 (preprint)

The subset of patients who develop critical illness in Covid-19 have extensive inflammation affecting the lungs and are strikingly different from other patients: immunosuppressive therapy benefits critically-ill patients, but may harm some non-critical cases. Since susceptibility to life-threatening infections and immune-mediated diseases are both strongly heritable traits, we reasoned that host genetic variation may identify mechanistic targets for therapeutic development in Covid-19. GenOMICC (Genetics Of Mortality In Critical Care, genomicc.org) is a global collaborative study to understand the genetic basis of critical illness. Here we report the results of a genome-wide association study (GWAS) in 2790 critically-ill Covid-19 patients from 208 UK intensive care units (ICUs), representing >95% of all ICU beds. Random controls were drawn from three distinct UK population studies. We identify and replicate several novel genome-wide significant associations including variants chr19p13.3 (rs2109069, P = 3.98 x 10-12), within the gene encoding dipeptidyl peptidase 9 (DPP9), and at chr21q22.1 (rs2236757, P = 4.99 x 10-8) in the interferon receptor IFNAR2. Consistent with our focus on extreme disease in younger patients with less comorbidity, we detect a stronger signal at the known 3p21.31 locus than previous studies (rs73064425, P = 1.2 x 10-27). We identify potential targets for repurposing of existing licensed medications. Using Mendelian randomisation we found evidence in support of a causal link from low expression of IFNAR2, and high expression of TYK2, to life-threatening disease. Transcriptome-wide association in lung tissue revealed that high expression of the monocyte/macrophage chemotactic receptor CCR2 is associated with severe Covid-19. We detected genome-wide significant gene-level associations for genes with central roles in viral restriction (OAS1, OAS2, OAS3). These results identify specific loci associated with life-threatening disease, and potential targets for host-directed therapies. Randomised clinical trials will be necessary before any change to clinical practice.

Temporal landscape of human gut RNA and DNA virome in SARS-CoV-2 infection and severity (preprint)

Background: Coronavirus Disease 2019 (COVID-19) caused by the enveloped RNA virus SARS-CoV-2 primarily affects the respiratory and gastrointestinal tracts. SARS-CoV-2 was isolated from faecal samples and active viral replication was reported in human intestinal cells. The human gut also harbors an enormous amount of resident viruses (collectively known as the virome) that play a role in regulating host immunity and disease pathophysiology. Understanding gut virome perturbation that underlies SARS-CoV-2 infection and severity is an unmet need.Methods: We enrolled 98 COVID-19 patients with varying disease severity (3 asymptomatic, 53 mild, 34 moderate, 5 severe, 3 critical) and 78 non-COVID-19 controls matched for gender and co-morbidities. All subjects had faecal specimens sampled at inclusion. Blood specimens were collected for COVID-19 patients at admission to test for inflammatory markers and white cell counts. Among COVID-19 cases, 37 (38%) patients had serial faecal samples collected 2 to 3 times per week from time of hospitalization until after discharge. Using shotgun metagenomics sequencing, we sequenced and profiled the faecal RNA and DNA virome. We investigated alterations and longitudinal dynamics of the gut virome in association with disease severity and blood parameters.Results: Patients with COVID-19 showed underrepresentation of Pepper mild mottle virus (RNA virus) and multiple bacteriophage lineages (DNA viruses) and enrichment of environment-derived eukaryotic DNA viruses in faecal samples, compared to non-COVID-19 subjects. Such gut virome alterations persisted up to 30 days after disease resolution. Faecal virome in SARS-CoV-2 infection harboured more stress-, inflammation- and virulence-associated gene encoding capacities including those pertaining to bacteriophage integration, DNA repair, and metabolism and virulence associated with their bacterial host. Baseline fecal abundance of 10 virus species (1 RNA virus, Pepper chlorotic spot virus, and 9 DNA virus species) inversely correlated with disease COVID-19 severity. These viruses inversely correlated with blood levels of pro-inflammatory proteins, white cells and neutrophils. Among the 10 COVID-19 severity-associated DNA virus species, 4 showed inverse correlation with age; 5 showed persistent lower abundance both during disease course and after disease resolution relative to non-COVID-19 subjects.Conclusions: Both enteric RNA and DNA virome in COVID-19 patients were different from non-COVID-19 subjects, which persisted after disease resolution of COVID-19. Gut virome may calibrate host immunity and regulate severity to SARS-CoV-2 infection. Our observation that gut viruses inversely correlated with both severity of COVID-19 and host age may partly explain that older subjects are prone to severe and worse COVID-19 outcomes. Altogether our data highlight the importance of human gut virome in severity and potentially therapeutics of COVID-19.

Modelling global public health strategies in COVID-19 pandemic using deep reinforcement learning (preprint)

Rationale: Unprecedented public health measures have been used during this coronavirus 2019 (COVID-19) pandemic but with a cost to economic and social disruption. It is a challenge to implement timely and appropriate public health interventions.Objectives: This study evaluates the timing and intensity of public health policies in each country and territory in the COVID-19 pandemic, and whether machine learning can help them to find better global health strategies.Methods: Population and COVID-19 epidemiological data between 21st January 2020 to 7th April 2020 from 183 countries and 78 territories were included with the implemented public health interventions. We used deep reinforcement learning, and the model was trained to try to find the optimal public health strategies with maximizing total reward on controlling spread of COVID-19. The results proposed by the model were analyzed against the actual timing and intensity of lockdown and travel restrictions.Measurements and Main Results: Early implementation of the actual lockdown and travel restriction policies were associated with gradually groups of less severe crisis severity, relative to local index case date in each country or territory, not to 31st December 2019. However, our model suggested to initiate at least minimal intensity of lockdown or travel restriction even before index cases in each country and territory. In addition, the model mostly recommended a combination of lockdown and travel restrictions and higher intensity policies than the implemented policies by government, but did not always encourage rapid full lockdown and full border closures.Conclusion: Compared to actual government implementation, our model mostly recommended earlier and higher intensity of lockdown and travel restrictions. Machine learning may be used as a decision support tool for implementation of public health interventions during COVID-19 and future pandemics.