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HLA Genotype Sequencing of Hemorrhagic Fever Survivors Human leukocyte antigen (HLA) Genotype Sequencing of EBOV/LASV 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 EBOV/LASV infection, survival and development of sequelae.
Systems Serology Measurements of Ebola/Lassa Patients and Survivors 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.
Systems Serology Measurements of Seattle COVID-19 Patients 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.
RT-PCR Measurements of Ebola/Lassa Patients RT-PCR measurements of suspected or confirmed Ebola or Lassa Fever patients in the acute phase of infection.
Blood Cell Counts of Ebola/Lassa Patients Blood cell count measurement data of suspected or confirmed Ebola or Lassa Fever patients in the acute phase of infection.
Rapid Antigen Tests of Ebola/Lassa Patients Rapid antigen test data of suspected or confirmed Ebola or Lassa Fever patients in the acute phase of infection.
Piccolo Blood Chemistry of Ebola/Lassa Patients 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 Measurements of Ebola/Lassa Patients 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.
RT-PCR Measurements of Seattle COVID-19 Patients 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.
SARS-CoV-2 Virus Sequencing 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
Lassa Virus Sequencing 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.
Ebola Virus Sequencing 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.