Transmission dynamics of COVID-19 in Ghana and the impact of public health interventions (preprint)

The study characterized COVID-19 transmission in Ghana in 2020-21 by estimating the time-varying reproduction number (R t ) and exploring its association with various public health interventions at the national and regional levels. Ghana experienced four pandemic waves with epidemic peaks in July 2020, and January, August and December, 2021. The epidemic peak was the highest nationwide in December 2021 with R t ≥2. Throughout 2020-21, per-capita cumulative case count by region increased with population size. Mobility data suggested negative correlation between R t and staying home in the first 90 days of the pandemic. The relaxation of movement restrictions and religious gatherings were not associated with increased R t in the regions with lower case burdens. R t decreased from above 1 when schools reopened in January 2021 to below 1 after vaccination rollout in March 2021. Findings indicated most public health interventions were associated with R t reduction at the national and regional levels.

The COVIDome Explorer Researcher Portal (preprint)

COVID-19 pathology involves dysregulation of diverse molecular, cellular, and physiological processes. In order to expedite integrated and collaborative COVID-19 research, we completed multi-omics analysis of hospitalized COVID-19 patients including matched analysis of the whole blood transcriptome, plasma proteomics with two complementary platforms, cytokine profiling, plasma and red blood cell metabolomics, deep immune cell phenotyping by mass cytometry, and clinical data annotation. We refer to this multidimensional dataset as the COVIDome. We then created the COVIDome Explorer, an online researcher portal where the data can be analyzed and visualized in real time. We illustrate here the use of the COVIDome dataset through a multi-omics analysis of biosignatures associated with C-reactive protein (CRP), an established marker of poor prognosis in COVID-19, revealing associations between CRP levels and damage-associated molecular patterns, depletion of protective serpins, and mitochondrial metabolism dysregulation. We expect that the COVIDome Explorer will rapidly accelerate data sharing, hypothesis testing, and discoveries worldwide.Funding: This work was supported by NIH grants R01AI150305, 3R01AI150305-01S1, R01AI145988, UL1TR002535, 3UL1TR002535-03S2, R01HL146442, R01HL149714, R01HL148151, R21HL150032, P30CA046934, R35GM124939 and RM1GM131968, as well as grants from the Boettcher Foundation and Fast Grants. Additional support was received from Chancellor’s Discovery Innovation Fund at the CU Anschutz Medical Campus, the Global Down Syndrome Foundation, the Anna and John J. Sie Foundation, and Lyda Hill Philanthropies.Conflict of Interest: KDS and JME are co-inventors on two patents related to JAK inhibition in COVID-19; JME serves in the COVID Development Advisory Board for Elly Lilly and has provided consulting services to Gilead Sciences Inc. JME serves on the Cell Reports Advisory Board.

The COVIDome Explorer Researcher Portal (preprint)

SUMMARY COVID-19 pathology involves dysregulation of diverse molecular, cellular, and physiological processes. In order to expedite integrated and collaborative COVID-19 research, we completed multi-omics analysis of hospitalized COVID-19 patients including matched analysis of the whole blood transcriptome, plasma proteomics with two complementary platforms, cytokine profiling, plasma and red blood cell metabolomics, deep immune cell phenotyping by mass cytometry, and clinical data annotation. We refer to this multidimensional dataset as the COVIDome. We then created the COVIDome Explorer, an online researcher portal where the data can be analyzed and visualized in real time. We illustrate here the use of the COVIDome dataset through a multi-omics analysis of biosignatures associated with C-reactive protein (CRP), an established marker of poor prognosis in COVID-19, revealing associations between CRP levels and damage-associated molecular patterns, depletion of protective serpins, and mitochondrial metabolism dysregulation. We expect that the COVIDome Explorer will rapidly accelerate data sharing, hypothesis testing, and discoveries worldwide.