Genomic evaluation of Coffea arabica and its wild relative Coffea racemosa in Mozambique: settling resilience keys for the Coffee crop in the context of climate change

Climate change is negatively affecting the coffee value chain, with a direct effect on approximately 100 million people from 80 countries. This has been attributed to the high vulnerability of the two-mainstream species, Coffea arabica and Coffea canephora, to extreme weather events, with notable uneven increases in market prices. Taking into account the narrow genetic plasticity of the commercial coffee cultivars, wild-relatives and underutilized Coffea species are valuable genetic resources. In this work, we have assessed the occurrence of Coffea species in to understand the degree of genetic relationships between Coffea species in the country, as well as the patterns of genetic diversity, differentiation, and genetic structure. Only one wild species was found, C. racemosa, which showed a high level of genetic separation with C. arabica, based on plastid, as well as SSR and SNP analysis. C. arabica presented low levels of diversity likely related to their autogamous nature, while the allogamous C. racemosa presented higher levels of diversity and heterozygosity. The analysis of the functional pathways based on SNPs suggests that the stress signaling pathways are more robust in this species. This novel approach shows that it is vital to introduce more resilient species and increase genomic diversity in climate-smart practices.This researchwas funded by by Camões, Instituto da Cooperação e da Língua (CICL), Agência Brasileira de Cooperação (ABC), and ParqueNacional da Gorongosa (PNG), under the Triangular Project TriCafé (GorongosaCoffee), and by Fundação para a Ciência e a Tecnologia, I.P. (FCT)info:eu-repo/semantics/publishedVersio

Bimodal distribution and set point HBV DNA viral loads in chronic infection:retrospective analysis of cohorts from the UK and South Africa

CITATION: Downs, L. O. 2020. Bimodal distribution and set point HBV DNA viral loads in chronic infection : retrospective analysis of cohorts from the UK and South Africa. Wellcome Open Research, 14(5):113, doi: 10.12688/wellcomeopenres.15941.2.The original publication is available at: https://pubmed.ncbi.nlm.nih.govENGLISH ABSTRACT: Hepatitis B virus (HBV) viral load (VL) is used as a biomarker to assess risk of disease progression, and to determine eligibility for treatment. While there is a well recognised association between VL and the expression of the viral e-antigen protein, the distributions of VL at a population level are not well described. We here present cross-sectional, observational HBV VL data from two large population cohorts in the UK and in South Africa, demonstrating a consistent bimodal distribution. The right skewed distribution and low median viral loads are different from the left-skew and higher viraemia in seen in HIV and hepatitis C virus (HCV) cohorts in the same settings. Using longitudinal data, we present evidence for a stable 'set-point' VL in peripheral blood during chronic HBV infection. These results are important to underpin improved understanding of HBV biology, to inform approaches to viral sequencing, and to plan public health interventions.Publisher's versio

Bimodal distribution and set point HBV DNA viral loads in chronic infection:retrospective analysis of cohorts from the UK and South Africa

CITATION: Downs, L. O. 2020. Bimodal distribution and set point HBV DNA viral loads in chronic infection : retrospective analysis of cohorts from the UK and South Africa. Wellcome Open Research, 14(5):113, doi: 10.12688/wellcomeopenres.15941.2.The original publication is available at: https://pubmed.ncbi.nlm.nih.govENGLISH ABSTRACT: Hepatitis B virus (HBV) viral load (VL) is used as a biomarker to assess risk of disease progression, and to determine eligibility for treatment. While there is a well recognised association between VL and the expression of the viral e-antigen protein, the distributions of VL at a population level are not well described. We here present cross-sectional, observational HBV VL data from two large population cohorts in the UK and in South Africa, demonstrating a consistent bimodal distribution. The right skewed distribution and low median viral loads are different from the left-skew and higher viraemia in seen in HIV and hepatitis C virus (HCV) cohorts in the same settings. Using longitudinal data, we present evidence for a stable 'set-point' VL in peripheral blood during chronic HBV infection. These results are important to underpin improved understanding of HBV biology, to inform approaches to viral sequencing, and to plan public health interventions.Publisher's versio

Hepatitis B virus infection as a neglected tropical disease

PCM is funded by a Wellcome Trust Intermediate Fellowship Grant (ref 110110/Z/15/Z).Publisher PDFPeer reviewe

Hepatitis B virus infection as a neglected tropical disease

PCM is funded by a Wellcome Trust Intermediate Fellowship Grant (ref 110110/Z/15/Z).Publisher PDFPeer reviewe

Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa

Three lineages (BA.1, BA.2 and BA.3) of the SARS-CoV-2 Omicron variant of concern predominantly drove South Africa's fourth COVID-19 wave. We have now identified two new lineages, BA.4 and BA.5, responsible for a fifth wave of infections. The spike proteins of BA.4 and BA.5 are identical, and comparable to BA.2 except for the addition of 69-70del (present in the Alpha variant and the BA.1 lineage), L452R (present in the Delta variant), F486V and the wild type amino acid at Q493.The two lineages only differ outside of the spike region. The 69-70 deletion in spike allows these lineages to be identified by the proxy marker of S-gene target failure, on the background of variants not possessing this feature . BA.4 and BA.5 have rapidly replaced BA.2, reaching more than 50% of sequenced cases in South Africa by the first week of April 2022. Using a multinomial logistic regression model, we estimate growth advantages for BA.4 and BA.5 of 0.08 (95% CI: 0.08 - 0.09) and 0.10 (95% CI: 0.09 - 0.11) per day respectively over BA.2 in South Africa. The continued discovery of genetically diverse Omicron lineages points to the hypothesis that a discrete reservoir, such as human chronic infections and/or animal hosts, is potentially contributing to further evolution and dispersal of the virus

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in southern Africa has been characterised by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, whilst the second and third waves were driven by the Beta and Delta variants, respectively1-3. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng Province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, predicted to influence antibody neutralization and spike function4. Here, we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity

Gradual emergence followed by exponential spread of the SARS-CoV-2 Omicron variant in Africa.

The geographic and evolutionary origins of the SARS-CoV-2 Omicron variant (BA.1), which was first detected mid-November 2021 in Southern Africa, remain unknown. We tested 13,097 COVID-19 patients sampled between mid-2021 to early 2022 from 22 African countries for BA.1 by real-time RT-PCR. By November-December 2021, BA.1 had replaced the Delta variant in all African sub-regions following a South-North gradient, with a peak Rt of 4.1. Polymerase chain reaction and near-full genome sequencing data revealed genetically diverse Omicron ancestors already existed across Africa by August 2021. Mutations, altering viral tropism, replication and immune escape, gradually accumulated in the spike gene. Omicron ancestors were therefore present in several African countries months before Omicron dominated transmission. These data also indicate that travel bans are ineffective in the face of undetected and widespread infection