Datasets

Human leukocyte antigen (HLA) Genotype Sequencing of Ebola/Lassa survivors, non-survivors, contacts and healthy controls from Sierra Leone and Nigeria using Illumina TruSight HLA v2 Sequencing Panel. HLA data will be used to determine potential risk alleles for Ebola/Lassa infection, survival and development of sequelae.

Systems Serology aims to define the features of the humoral immune response against a given pathogen. Systems Serology analysis includes measurement of the levels antigen-specific antibodies within individual patients, measurement of antibody-mediated induction of innate immune cell effector functions, measurement of binding of antigen-specific antibodies to Fc-receptors, and measurement of neutralizing activity. Samples are taken from Ebola or Lassa Fever patients, convalescent survivors, or household contacts of these patients in Sierra Leone.

Systems Serology aims to define the features of the humoral immune response against a given pathogen. Systems Serology analysis includes measurement of the levels antigen-specific antibodies within individual patients, measurement of antibody-mediated induction of innate immune cell effector functions, measurement of binding of antigen-specific antibodies to Fc-receptors, and measurement of neutralizing activity. Samples are taken from COVID-19 patients in Seattle, Washington.

Rapid antigen test data of suspected or confirmed Ebola or Lassa Fever patients in the acute phase of infection.

RT-PCR measurements of suspected or confirmed Ebola or Lassa Fever patients in the acute phase of infection.

RT-PCR measurements of SARS-CoV-2 levels for COVID-19 patients in Seattle, Washington. Complimentary dataset to Systems Serology measurments of the same patient cohort.

Blood chemistry data of suspected or confirmed Ebola or Lassa Fever patients in the acute phase of infection, collected with a Piccolo Xpress Chemistry Analyzer.

Vital measurement data of suspected or confirmed Ebola or Lassa Fever patients in the acute phase of infection, or patients and household contacts in a follow-up visit.

Blood cell count measurement data of suspected or confirmed Ebola or Lassa Fever patients in the acute phase of infection.

Virus sequencing of Lassa-infected humans and rodents from Nigeria, Sierra Leone, Liberia, Guinea, and other countries. Virus sequence data will be used to determine potential correlations between the infecting virus genome and patient survival, disease severity and development of sequelae. When multiple sequences are available for one patient, the virus has been sequenced from that patient at several points in time.

Virus sequencing of patients infected with COVID-19 from Southern California, Tijuana, New Orleans and Jordan by the SEARCH Alliance along with a large number of partners. The virus sequence data will be used to to gain insights into the emergence and spread of SARS-CoV-2. The sequencing is being performed using an amplicon-based sequencing scheme using PrimalSeq with artic nCoV-2019 scheme. Nanopore data was processed using the artic-nCoV019 pipeline with minimap2 and medaka. Illumina data was processed using iVar (Grubaguh et al. Genome Biology 2019) with bwa. Methodology is available at https://github.com/andersen-lab/HCoV-19-Genomics

Virus sequencing of acute Ebola patients from Sierra Leone, Liberia, Guinea, and other countries. Virus sequence data will be used to determine potential correlations between the infecting virus genome and patient survival, disease severity and development of sequelae. When multiple sequences are available for one patient, the virus has been sequenced from that patient at several points in time.