Bett, Bernard K.

Juma, John

Limbaso, Konongoi

Oyola, Samuel O.

Sang, R.

CGSpace

Genomic characterization of Rift Valley Fever Virus and co-circulating zoonotic pathogens from human samples from selected sites in Kenya Konongoi Limbaso1,2, John Juma1, Rosemary Sang2, Bernard Bett1 , Samuel Oyola1.1. International Livestock Research Institute (ILRI), Nairobi, Kenya.2. Kenya Medical Research Institute (KEMRI), Nairobi, Kenya.ContactS.konongoi@cgiar.org Box 30709 Nairobi, KenyaBackgroundHuman Rift Valley Fever (RVF) infections in Kenya and in the East African region at large  are being detected more frequently over wide geographical areas. Areas of concern:➢ Occurrence in new areas and at times not necessarily associated with heavy rains.➢ Human infections on the increase in the last decade.➢ What virus lineage/lineages are responsible?No. of RVF Outbreaks 1912-2010, M Baba et al., 2016Virus monitoring is critical➢ Limited Genetic diversity data - epidemic and inter epidemic.➢ Most studies/scientific outputs associated with outbreak periods.➢ RVF activity shown to occur during IEP in endemic countries (Sumaye et al., 2013). ➢ Concern that virus activity and evolution can occur below the threshold of detection methods by public health or animal health authorities during inter epidemic periods (Bird et al., 2008).➢ Virus may go undetected due to minimum surveillance in hosts and vectors.Methods Clean-up,sequence  assembly and  analysis(Geneious software)Reassortment Analysis, Genotyping, phylogenetic analysisApproach➢ 1,787 human serum samples identified in repository 1997-2021 with accompanying clinical information➢ 200 inoculations performed in KEMRI BSL3Isiolo 2020 CPE Day 3 Negative control –Vero cells Nyandarua 2019 – CPE day 13Diverse CPE types observed Anticipated results and conclusionOutputs from this study will be pivotal inunderstanding RVF epidemiology, evolution, andpathogen co-circulation in the country and region.Identification of co-circulating pathogens is a steptowards better understanding and response andupdate any existing baselines of zoonotic pathogenactivity in a region.Future activities➢ Generate libraries and full genome sequences of all the  PCR RVF positive isolates.➢ Attempt to characterize the non RVF positive isolates using a metagenomics approach.➢ Continue with pathogen isolation attempts in cell culture.Preliminary FindingsReal Time PCR➢ 70 CPE positive potential isolates harvested➢ RNA extracted (Qiagen)➢ RVF real time PCR performed using the altona RVF kits➢ 25 RVF positive isolates detected.sample_name before_trim after_trim mapped pct_mapped pct_N_bases pct_covered_bases longest_no_N_run qc_passKEM-BR 1495184 474814 20357 4.29 0.37 99.63 6381 TRUEKEM-ND 598576 177778 13521 7.61 0.37 99.63 6381 TRUE250618 618832 192024 26340 13.72 0.30 99.70 6386 TRUE500618 2179348 559776 9870 1.76 0.31 99.69 6385 TRUEHA-HAR 13341438 3839408 1429 0.04 8.53 91.47 1060 TRUEKEM-JC 495888 150560 7043 4.68 0.50 99.50 6373 TRUEK2 4284186 1295680 90222 6.96 0.28 99.72 6387 TRUEsample_name before_trim after_trim mapped pct_mapped pct_N_bases pct_covered_bases longest_no_N_run qc_passKEM-JC 495888 150560 1730 1.15 1.21 98.79 3839 TRUE500618 2179348 559776 7174 1.28 0.57 99.43 3864 TRUEKEM-BR 1495184 474812 6790 1.43 0.62 99.38 3862 TRUE250618 618832 192024 26674 13.89 0.26 99.74 3875 TRUEK2 4284186 1295680 62675 4.84 0.28 99.72 3874 TRUEKEM-ND 598576 177778 7457 4.19 0.77 99.23 3856 TRUEsample_name before_trim after_trim mapped pct_mapped pct_N_bases pct_covered_bases longest_no_N_run qc_passKEM-BR 1495184 474812 9507 2.0 4.32 95.68 838 TRUE250618 618832 192024 12545 6.53 2.37 97.63 847 TRUEKEM-JC 495888 150560 3628 2.41 4.97 95.03 832 TRUE500618 2179348 559780 10055 1.8 4.32 95.68 836 TRUEKEM-ND 598576 177778 4601 2.59 3.31 96.69 829 TRUEHA-HAR 13341438 3839402 1094 0.03 8.93 91.07 819 TRUEK2 4284186 1295678 124590 9.62 3.08 96.92 848 TRUESequencing>95% genome recovery from 7 human isolatesReferences➢R. D. Sumaye,E.Geubbels, E.Mbeyela, andD.Berkvens, “Interepidemic transmission of rift valley fever in livestock in the Kilombero river valley,Tanzania: a cross-sectional survey,” PLoS Neglected Tropical Diseases, vol. 7, no. 8,Article ID e2356, 2013.➢Bird BH, Githinji JW, Macharia JM, Kasiiti JL, Muriithi RM, Gacheru SG, et al. Multiple virus lineages sharing common recent ancestry were associated with a large Rift Valley fever outbreak among livestock in Kenya during 2006–2007. J Virol. 2008; 82:11152–66. doi:10.1128/JVI.01519-08This document is licensed for use under a Creative Commons Attribution 4.0 International Licence. October 2021

Genomic characterization of Rift Valley fever virus and co-circulating zoonotic pathogens from human samples from selected sites in Kenya

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Genomic characterization of Rift Valley fever virus and co-circulating zoonotic pathogens from human samples from selected sites in Kenya

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