Metagenomic analysis of plant viruses associated with papaya ringspot disease in Carica papaya L. in Kenya

Carica papaya L. is an important fruit crop grown by small- and large-scale farmers in Kenya for local and export markets. However, its production is constrained by papaya ringspot disease (PRSD). The disease is believed to be caused by papaya ringspot virus (PRSV). Previous attempts to detect PRSV in papaya plants showing PRSD symptoms, using enzyme-linked immunosorbent assay (ELISA) and reverse transcriptase-polymerase chain reaction (RT-PCR) procedures with primers specific to PRSV, have not yielded conclusive results. Therefore, the nature of viruses responsible for PRSD was elucidated in papaya leaves collected from 22 counties through Illumina MiSeq next-generation sequencing (NGS) and validated by RT-PCR and Sanger sequencing. Viruses were detected in 38 out of the 48 leaf samples sequenced. Sequence analysis revealed the presence of four viruses: a Potyvirus named Moroccan watermelon mosaic virus (MWMV) and three viruses belonging to the genus Carlavirus. The Carlaviruses include cowpea mild mottle virus (CpMMV) and two putative Carlaviruses —closely related but distinct from cucumber vein-clearing virus (CuVCV) with amino acid and nucleotide sequence identities of 75.7–78.1 and 63.6–67.6%, respectively, in the coat protein genes. In reference to typical symptoms observed in the infected plants, the two putative Carlaviruses were named papaya mottle-associated virus (PaMV) and papaya mild mottle-associated virus (PaMMV). Surprisingly, and in contrast to previous studies conducted in other parts of world, PRSV was not detected. The majority of the viruses were detected as single viral infections, while a few were found to be infecting alongside another virus (for example, MWMV and PaMV). Furthermore, the NGS and RT-PCR analysis identified MWMV as being strongly associated with ringspot symptoms in infected papaya fruits. This study has provided the first complete genome sequences of these viruses isolated from papaya in Kenya, together with primers for their detection—thus proving to be an important step towards the design of long-term, sustainable disease management strategies

Influence of Si in maize plants in Kenyan populations of Spodoptera frugiperda (Lepidoptera: Noctuidae)

The fall armyworm (FAW), Spodoptera frugiperda (Lepidoptera: Noctuidae), native to the Americas, was confirmed in West and Central Africa in 2016 and reported in almost all countries of sub-Saharan Africa in 2017, becoming thereafter one of the major constraints on the production of maize, the main staple food crop in the region. Cereals depend on silicon (Si)-based defences to fight off herbivores. Both FAW strains, namely rice and corn strains, have been found to be present in Kenya. The present study tested the influence of Si on larval survival and relative growth rate according to the FAW strain, using potted maize plants treated with 10 and 20 g of Si. The results showed that plants treated with Si disturbed the larval growth of FAW larvae only from the corn strain but not from the rice strain. Overall, the corn strain performed better on maize as compared to the rice strain regardless of Si treatment, explaining why it has become the most abundant strain in Africa

Influence of Si in maize plants in Kenyan populations of Spodoptera frugiperda (Lepidoptera: Noctuidae)

The fall armyworm (FAW), Spodoptera frugiperda (Lepidoptera: Noctuidae), native to the Americas, was confirmed in West and Central Africa in 2016 and reported in almost all countries of sub-Saharan Africa in 2017, becoming thereafter one of the major constraints on the production of maize, the main staple food crop in the region. Cereals depend on silicon (Si)-based defences to fight off herbivores. Both FAW strains, namely rice and corn strains, have been found to be present in Kenya. The present study tested the influence of Si on larval survival and relative growth rate according to the FAW strain, using potted maize plants treated with 10 and 20 g of Si. The results showed that plants treated with Si disturbed the larval growth of FAW larvae only from the corn strain but not from the rice strain. Overall, the corn strain performed better on maize as compared to the rice strain regardless of Si treatment, explaining why it has become the most abundant strain in Africa

Characteristics of soils in selected maize growing sites along altitudinal gradients in East African highlands

International audienceMaize is the main staple crop in the East African Mountains. Understanding how the edaphic characteristics change along altitudinal gradients is important for maximizing maize production in East African Highlands, which are the key maize production areas in the region. This study evaluated and compared the levels of some macro and micro-elements (Al, Ca, Fe, K, Mg, Mn, Na and P) and other soil parameters (pH, organic carbon content, soil texture [i.e. % Sand, % Clay and % Silt], cation exchange capacity [CEC], electric conductivity [EC], and water holding capacity [HC]). Soil samples were taken from maize plots along three altitudinal gradients in East African highlands (namely Machakos Hills, Taita Hills and Mount Kilimanjaro) characterized by graded changes in climatic conditions. For all transects, pH, Ca, K and Mg decreased with the increase in altitude. In contrast, % Silt, organic carbon content, Al and water holding capacity (HC) increased with increasing altitude. The research provides information on the status of the physical–chemical characteristics of soils along three altitudinal ranges of East African Highlands and includes data available for further research

Pooled testing conserves SARS-CoV-2 laboratory resources and improves test turn-around time: Experience on the Kenyan Coast

Background: International recommendations for the control of the coronavirus disease 2019 (COVID-19) pandemic emphasize the central role of laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent, at scale. The availability of testing reagents, laboratory equipment and qualified staff are important bottlenecks to achieving this. Elsewhere, pooled testing (i.e. combining multiple samples in the same reaction) has been suggested to increase testing capacities in the pandemic period. Methods: We discuss our experience with SARS-CoV-2 pooled testing using real-time reverse transcription polymerase chain reaction (RT-PCR) on the Kenyan Coast. Results: In mid-May, 2020, our RT-PCR testing capacity for SARS-CoV-2 was improved by ~100% as a result of adoption of a six-sample pooled testing strategy. This was accompanied with a concomitant saving of ~50% of SARS-CoV-2 laboratory test kits at both the RNA extraction and RT-PCR stages. However, pooled testing came with a slight decline of test sensitivity. The RT-PCR cycle threshold value (ΔCt) was ~1.59 higher for samples tested in pools compared to samples tested singly. Conclusions: Pooled testing is a useful strategy to increase SARS-CoV-2 laboratory testing capacity especially in low-income settings

An optimization of four SARS-CoV-2 qRT-PCR assays in a Kenyan laboratory to support the national COVID-19 rapid response teams

Background: The COVID-19 pandemic relies on real-time polymerase chain reaction (qRT-PCR) for the detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), to facilitate roll-out of patient care and infection control measures. There are several qRT-PCR assays with little evidence on their comparability. We report alterations to the developers’ recommendations to sustain the testing capability in a resource-limited setting. Methods: We used a SARS-CoV-2 positive control RNA sample to generate several 10-fold dilution series that were used for optimization and comparison of the performance of the four qRT-PCR assays: i) Charité Berlin primer-probe set, ii) European Virus Archive – GLOBAL (EVAg) primer-probe set, iii) DAAN premixed commercial kit and iv) Beijing Genomics Institute (BGI) premixed commercial kit. We adjusted the manufacturer- and protocol-recommended reaction component volumes for these assays and assessed the impact on cycle threshold (Ct) values. Results: The Berlin and EVAg E gene and RdRp assays reported mean Ct values within range of each other across the different titrations and with less than 5% difference. The DAAN premixed kit produced comparable Ct values across the titrations, while the BGI kit improved in performance following a reduction of the reaction components. Conclusion: We achieved a 2.6-fold and 4-fold increase in the number of tests per kit for the commercial kits and the primer-probe sets, respectively. All the assays had optimal performance when the primers and probes were used at 0.375X, except for the Berlin N gene assay. The DAAN kit was a reliable assay for primary screening of SARS-CoV-2 whereas the BGI kit’s performance was dependent on the volumes and concentrations of both the reaction buffer and enzyme mix. Our recommendation for SARS-CoV-2 diagnostic testing in resource-limited settings is to optimize the assays available to establish the lowest volume and suitable concentration of reagents required to produce valid results