Immune Reconstitution During the First Year of Antiretroviral Therapy of HIV-1-Infected Adults in Rural Burkina Faso

There are no data on the outcome of highly active antiretroviral therapy (HAART) in HIV-infected adults in rural Burkina Faso. We therefore assessed CD4+ T-cell counts and HIV-1 plasma viral load (VL), the proportion of naive T-cells (co-expressing CCR7 and CD45RA) and T-cell activation (expression of CD95 or CD38) in 61 previously untreated adult patients from Nouna, Burkina Faso, at baseline and 2 weeks, 1, 3, 6, 9 and 12 months after starting therapy. Median CD4+ T-cell counts increased from 174 (10th-90th percentile: 33-314) cells/µl at baseline to 300 (114- 505) cells/µl after 3 months and 360 (169-562) cells/µl after 12 months of HAART. Median VL decreased from 5.8 (4.6- 6.6) log10 copies/ml at baseline to 1.6 (1.6-2.3) log10 copies/ml after 12 months. Early CD4+ T-cell recovery was accompanied by a reduction of the expression levels of CD95 and CD38 on T-cells. Out of 42 patients with complete virological follow-up under HAART, 19 (45%) achieved concordant good immunological (gain of ≥100 CD4+ T-cells/µl above baseline) and virological (undetectable VL) responses after 12 months of treatment (intention-to-treat analysis). Neither a decreased expression of the T-cell activation markers CD38 and CD95, nor an increase in the percentage of naive T-cells reliably predicted good virological treatment responses in patients with good CD4+ T-cell reconstitution. Repeated measurement of CD4+ T-cell counts during HAART remains the most important parameter for immunologic monitoring. Substitution of repeated VL testing by determination of T-cell activation levels (e.g., CD38 expression on CD8+ T-cells) should be applied with caution

Entangled co-evolutionary history of Hyaloperonospora arabidopsidis and its host Arabidopsis thaliana

Hyaloperonospora arabidopsidis (Har) is an obligate biotrophic pathogen that causes downy mildew on Arabidopsis thaliana (Ath). Molecular biology of Arabidopsis-downy mildew interaction has revealed several key players in plant immunity and pathogen virulence. Despite these advances, how genetic diversity in Har maps onto genetic diversity of Ath through their presumably shared co-evolutionary history remains completely unknown. Here we report the first range-wide collection of Har (over collection sites in 16 European countries) that was whole genome-sequenced along with the host Ath individuals. Har population structure analysis in the spatial framework reveals presence of three ancestral lineages. Demographic inference using sequentially Markovian coalescence (SMC)-based and site-frequency spectrum (SFS)-based approaches on the ancestral lineages of both the Har and Ath demonstrates almost contemporaneous population splits and migration events in this highly co-evolved pathosystem. We used parameters from demographic inference to perform forward simulations to compare with the observed patterns of genetic diversity in Har and Ath. Our results show that many known and putative Har effector loci have undergone episodes of balancing selection through negative-frequency dependent selection (NFDS). Further, signatures of NFDS-dependent balancing selection on cognate Ath immune receptors of known Har effectors strongly suggests entangled co-evolutionary history of Har-Athpathosystem

Birth, Death, and Persistence in NLR Diversity in the Arabidopsis Immune System

Plant pathogens have a major impact in both natural and agricultural ecosystems, inducing widespread disease, reduced fitness, and mortality. Genes encoding nucleotide-binding leucine-rich repeat (NLR) proteins are the major class of disease resistance (R) genes in plants, and encode receptors that directly or indirectly detect the molecular signals of pathogens and activate defense response. NLR genes are among the most variable in plant genomes, exhibiting tremendous diversity in sequence and structure. This structural diversity makes NLRs difficult to study but with long read sequencing we can directly sequence complex gene clusters. Here, we assembled the genomes of 18 diverse lines of Arabidopsis thaliana using the PacBio HIFI sequencing technology. We performed comprehensive genome annotation integrating full-length transcript data generated with Iso-Seq, pan-TEome (transposable elements) annotation, CG-methylation, segmental duplications, and recombination to investigate the processes that lead to the birth, death and maintenance of NLR diversity across the species. We found that TEs play a major role in generating structural diversity and that pseudogenization is a major force in moderating the genomic load of active NLRs. We also unravel hidden NLR diversity generated through isoform variation. Our findings give a better understanding of the different strategies used by plants to compete in the defensive arms race against pathogens

Pangenomic context reveals the extent of intraspecific plant NLR evolution

Nucleotide-binding leucine-rich repeat (NLR) proteins are a major component of the plant immune system, which directly or indirectly detect molecular signals of pathogen invasion. Despite their critical role, the processes by which NLR genes diversify remain poorly characterised due to the extraordinary sequence, structural, and regulatory variability of NLRs, even among closely related individuals. To understand the evolution of NLR diversity in Arabidopsis thaliana, we leverage graph-based methods to define pangenomic NLR neighbourhoods in 17 genetically diverse genomes. We integrate full-length transcript and transposable element information to exhaustively annotate all intact and degraded NLRs, enabling exploration of the processes that underpin the birth, death and maintenance of NLR diversity within a species. Our main finding is that many uncorrelated mutational processes create NLR diversity, and that there is no single metric that captures on its own the true extent of NLR structural and sequence variation. This immense diversity in plant immune system diversification allows populations to survive the constant onslaught of pathogens, not unlike vertebrate adaptive immunity, where variation is also generated by a variety of complementary mechanisms, albeit at the level of individuals

The Coevolutionary race between Hyaloperonospora Arabidopsidis and Arabidopsis Thaliana at a Transcontinental Scale

Plants and their pathogens are locked in a perpetual coevolutionary battle for survival. We present a transcontinental investigation of coevolution in the Hyaloperonospora arabidopsidis – Arabidopsis thaliana pathosystem. We generate whole genome sequences of over 400 host-pathogen pairs from natural infections collected throughout both the native eurasian range and the human-commensal colonisation of North America, as well as new near- complete long-read genome assemblies with evidence-based annotation. We investigate the demographic history of both host and pathogen, examine coevolution both generally and of individual gene pairs, and describe variation in the genetic networks of interacting host and pathogen genes. Our results show that the negative-frequency dependent selection on both the pathogen and host genomes leads to the presence of balanced polymorphisms in the wild pathosystem, in contrast to the directional selection generally experienced by pathogens of crop pathosystems