Dr Kayla Barnes

Senior Lecturer / Associate Professor

Previous to joining LSTM, Kayla was a NIH career development fellow at the Harvard School of Public Health where she established a single cell program in Malawi exploring infant health dynamics. Prior to her fellowship at HSPH, Kayla was a postdoc at the Broad Institute where she co-led two genome-wide association studies of susceptibility to Ebola Virus Disease and Lassa fever as well as numerous projects exploring viral genetics, novel CRISPR diagnostics and single cell genomics. This work included setting up sequencing and genomics capabilities in Sierra Leone and Nigeria. During her postdoc she also helped establish sequencing capabilities and ‘omics’ projects in Sierra Leone, Liberia and Nigeria. Kayla carried out her PhD work at the Liverpool School of Tropical Medicine elucidating insecticide resistance in Malawi, Zambia and Mozambique using transcriptomics. Prior to Kayla’s postgraduate work she was a research assistant at the Harvard School of Public Health investigating malaria parasite phylogeny and drug resistance.

Kayla Barnes in genomics researcher based at the Malawi-Liverpool Wellcome Trust. Kayla’s lab focuses on two programs that bookend the dynamics of health in low-income countries. These include tracking viral pathogens and vaccines using wastewater and other surveillance tools and understanding, at the omics cell level, why vaccines underperform in LICs. Kayla has helped establish pathogen and single cell sequencing in Malawi.

Selected publications

  • Kotliar D*, Raju S, Tabrizi S*, Odia I*,....Grant DS*, Garry R*, Barnes KG*, Happi C*, Sabeti PC*. A genome-wide association study identifies host genetic variants associated with susceptibility to Lassa Fever. Nature Microbiology (2024) 10.1038/s41564-023-01589-3

    Santus L, García-Pérez R, Sopena-Rios M, Lin AE, Adams GC, Barnes KG, Siddle KJ, Wohl S, Reverter F, Rinn JL, Bennett RS, Hensley LE, Sabeti PC, Melé M. In vivo single-cell profiling of lncRNAs during Ebola virus infection. Nat Comm (2023)

    Barnes KG§, Levy JI, Gauld J, ……., Nyirenda T, Kawalazira G, Feasey N. Utility of river water as a low-cost surveillance tool for SARS-CoV-2 to predict trends in COVID-19 and identify variants of concern in Blantyre, Malawi. Nature Comm (2023) 10.1038.s41467-023-43047-y

    Anscombe C*, Lissaure S*, Thole H*, Rylance J, Dula D, Menyere M, Kutambe B, van der Veer C, Phiri T, Banda NO, Mndolo KS, Mponda K, Phiri C, Mallewa J, Nyirenda M, Katha G, Mwandumba H, Gordon SB, Jambo KC, Cornick J, Feasey N, Barnes KG*, Morton B*, Ashton PM*. A comparison of four epidemic waves of CVID-19 in Malawi; an observational cohort study. BMC ID (2022) doi.org/10.1186/s12879-022-07941-y

    Morton B*, Barnes KG*, Anscombe C, Jere KC, Kamng'ona R, ……., Mwandumba HC, Gordon SB, Cornick J*, Jambo KC*. Distinct clinical and immunological profiles of patients with evidence of SARS-CoV-2 infection in sub-Saharan Africa. Nat Comm, (2021) 10.1038/s41467-021-23267-w

    Kotliar D*, Lin AE*, Logue J, Hughes TK, Khoury KM, Raju SS, Wadsworth MH, Chen H, Kurtz JR, Dighero-Kemp B, Bjornson ZB, Mukherjee N, Sellers BA, Tran N, Bauer MB, Adams GC, Adams R, Rinn JL, Melé M, Nolan GP*, Barnes KG*, Hensley LE*, McIlwain DR*, Shalek EK*, Sabeti PC*, Bennett RC*. Single-cell profiling of Ebola virus infection in vivo reveals viral and host transcriptional dynamics. Cell. (2020) 10.1016/j.cell.2020.10.002

    Barnes KG*§, Lachenauer AE*, Nitido A, Siddiqui S, Gross R,… Sabeti PC. Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time. Nature Comm. (2020) 10.1038/s41467-020-17994-9

    Metsky, HC, Siddle, KJ, Gladden-Young, A… Barnes, KG… Matranga CB. Capturing sequence diversity in metagenomes with comprehensive and scalable probe design. Nat Biotechnol 37, 160–168 (2019) 10.1038/s41587-018-0006-x

    Okogbenin S, Okoeguale J, Akpede G, Colubri A, Barnes KG, Mehta S, et al. Retrospective Cohort Study of Lassa Fever in Pregnancy, Southern Nigeria. Emerg Infect Dis. (2019) 10.3201/eid2508.181299

    Myhrvold C*, Freije CA*, ….., Barnes KG, …., Zhang F, and Sabeti PC. Field-deployable viral diagnostics using CRISPR-Cas. Science. (2018) 10.1126/science.aas8836

    Siddle KJ*, Eromon P*, Barnes KG*§, Mehta S*, Oguzie JU*, Odia I*....MacInnis BL*, Sabeti PC*, Happi CT*§. Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018. NEJM. (2018) 10.1056/NEJMoa1804498

    Barnes KG*§, Kindrachuk J*, Lin AE*, Wohl S, Qu J, Tostenson SD, Dorman WR, Busby M, Siddle KJ, Luo CY, Matranga CB, Davey RT, Sabeti PC, and Chertow DS. Evidence of Ebola Virus Replication and High Concentration in Semen of a Patient During Recovery. Clin Infect Dis 2017 Oct 15. 10.1093/cid/cix518

    Barnes KG*, Weedall G*, Ndula M, Irving H, Mzilahowa T, Hemingway J, Wondji CS. Africa-wide selective sweep of pyrethroid genes correlates with scaling up of malaria control. Plos Genetics. (2017) 10.1371/pgen1006539

    Barnes KG, Irving H, Chiumia M, Mzilahowa T, Coleman M, Hemingway J, Wondji CS. Restriction to gene flow is linked to changes in the molecular basis of pyrethroid resistance in the malaria vector Anopheles funestus. PNAS. (2016) 10.1073/pnas.1615458114