Hepatitis C virus infection and primary hepatic large B-cell lymphoma: a non-fortuitous association. Case report and review of literature

We report a case of hepatitis C virus infection in association with primary hepatic large B-cell non-Hodgkin's lymphoma. Primary hepatic non-Hodgkin's lymphoma is a rare disease. Association of hepatitis C virus infection with primary hepatic B-cell non-hodgkin's lymphoma is probably not fortuitous. Indeed, in case of primary hepatic non-hodgkin's lymphoma' patients are often hepatitis C virus positive. Moreover, several studies have reported a high prevalence of chronic hepatitis C virus infection among patients with B-cell non-Hodgkin's lymphoma whatever the localization of the lymphoma. A recent study found a high rate of remission of a splenic form of lymphoma after treatment of hepatitis C virus infection. Our case report confirms the hypothesis of a key role of hepatitis C virus in the pathogenesis of various forms of B-cell lymphoproliferative disorders and in particular in primary hepatic lymphoma.     

Haplotype tagging reveals parallel formation of hybrid races in two butterfly species

Genetic variation segregates as linked sets of variants or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. Yet, genomic data often omit haplotype information due to constraints in sequencing technologies. Here, we present “haplotagging,” a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing color patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species, the geographic clines for the major wing-pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the center of the hybrid zone. We propose that shared warning signaling (Müllerian mimicry) may couple the cline shifts seen in both species and facilitate the parallel coemergence of a novel hybrid morph in both comimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations.

Understanding how changes in DNA sequence affect traits and shape the evolution of populations and species has been a defining goal in genetics and evolution (1–3). DNA is naturally organized in the genome as long molecules consisting of linked chromosome segments. Linkage is a core concept in genetics: in genetic mapping, geneticists map causal variants not by tracking the actual mutation but through many otherwise neutral and unremarkable linked variants. Likewise, the detection of selection relies on observing hitchhiking of linked variants rather than seeing the mutation itself. This recognition makes it all the more paradoxical that haplotype information is routinely omitted from most genomic studies as a technical compromise. Lacking haplotype information not only complicates analysis and ancestry reconstruction but also precludes detection of allele-specific expression (4) and chromosome rearrangements and reduces power to detect selective sweeps, even entirely missing them when multiple haplotypes sweep together (5). Instead of sequencing genomes as haplotypes, short-read sequencing produces 150-bp reads. Until long-read platforms become sufficiently accurate and affordable, this lack of haplotype context will continue to impact mapping and genomic studies, particularly those in nonmodel organisms.One way to simplify haplotype reconstruction and inference from sequencing data is to avoid discarding haplotype information in the first place. A promising emerging technique is linked-read (LR) sequencing (6–9), which preserves long-range information via molecular barcoding of long DNA molecules before sequencing. Individual short reads can then be linked via a shared barcode to reconstruct the original haplotype. However, existing options all suffer from high cost, poor scalability, and/or require custom sequencing primers or settings that have thus far prevented them from being applied as the default sequencing platform (SI Appendix, Tables S1 and S2). If LR sequencing could become scalable and affordable, it would significantly advance genetics by enabling the “haplotyping” of entire populations (i.e., the sequencing and systematic discovery of genomic variants as haplotypes in hundreds or even thousands of samples in model and nonmodel organisms alike).Here, we describe a solution called “haplotagging,” a simple and rapid protocol for LR sequencing. Importantly, haplotagging maintains full compatibility with standard Illumina sequencing and can easily scale to large populations with no extra costs. We demonstrate this in three steps. First, we show that direct haplotyping using haplotagging is robust in single human and mouse samples with known haplotypes (“phases”). Next, we show the feasibility of population haplotyping in 245 mice, even with very low-coverage LR sequencing. Finally, we apply haplotagging to investigate the emergence of a hybrid morph in a hybrid zone system in Ecuador featuring 670 individuals of two species of Heliconius butterflies.     

From the Cover: COVID-19 lockdown induces disease-mitigating structural changes in mobility networks

In the wake of the COVID-19 pandemic many countries implemented containment measures to reduce disease transmission. Studies using digital data sources show that the mobility of individuals was effectively reduced in multiple countries. However, it remains unclear whether these reductions caused deeper structural changes in mobility networks and how such changes may affect dynamic processes on the network. Here we use movement data of mobile phone users to show that mobility in Germany has not only been reduced considerably: Lockdown measures caused substantial and long-lasting structural changes in the mobility network. We find that long-distance travel was reduced disproportionately strongly. The trimming of long-range network connectivity leads to a more local, clustered network and a moderation of the “small-world” effect. We demonstrate that these structural changes have a considerable effect on epidemic spreading processes by “flattening” the epidemic curve and delaying the spread to geographically distant regions.

During the first phase of the coronavirus disease 2019 (COVID-19) pandemic, countries around the world implemented a host of containment policies aimed at mitigating the spread of the disease (1–4). Many policies restricted human mobility, intending to reduce close-proximity contacts, the major driver of the disease’s spread (5). In Germany, these policies included border closures, travel bans, and restrictions of public activity (school and business closures), paired with appeals by the government to avoid trips voluntarily whenever possible (6). We refer to these policies as “lockdown” measures for brevity.Based on various digital data sources such as mobile phone data or social media data, several studies show that mobility significantly changed during lockdowns (7). Most studies focused on general mobility trends and confirmed an overall reduction in mobility in various countries (8–12). Other research focused on the relation between mobility and disease transmission: For instance, it has been argued that mobility reduction is likely instrumental in reducing the effective reproduction number in many countries (13–17), in agreement with theoretical models and simulations, which have shown that containment can effectively slow down disease transmission (18–20).However, it remains an open question whether the mobility restrictions promoted deeper structural changes in mobility networks and how these changes impact epidemic spreading mediated by these networks. Recently, Galeazzi et al. (21) found increased geographical fragmentation of the mobility network. A thorough understanding of how structural mobility network changes impact epidemic spreading is needed to correctly assess the consequences of mobility restrictions not only for the current COVID-19 pandemic, but also for similar scenarios in the future.Here, we analyze structural changes in mobility patterns in Germany during the COVID-19 pandemic. We analyze movements recorded from mobile phones of 43.6 million individuals in Germany. Beyond a general reduction in mobility, we find considerable structural changes in the mobility network. Due to the reduction of long-distance travel, the network becomes more local and lattice-like. Most importantly, we find a changed scaling relation between path lengths and geographic distance: During lockdown, the effective distance (and arrival time in spreading processes) to a destination continually grows with geographic distance. This shows a marked reduction of the “small-world” characteristic, where geographic distance is usually of lesser importance in determining path lengths (22, 23). Using simulations of a commuter-based susceptible-infected-removed (SIR) model, we demonstrate that these changes have considerable practical implications as they suppress (or “flatten”) the curve of an epidemic remarkably and delay the disease’s arrival between distant regions.     

Plasmodium vivax Pre-Erythrocytic-Stage Antigen Discovery: Exploiting Naturally Acquired Humoral Responses

Abstract. The development of pre-erythrocytic Plasmodium vivax vaccines is hindered by the lack of in vitro culture systems or experimental rodent models. To help bypass these roadblocks, we exploited the fact that naturally exposed Fy- individuals who lack the Duffy blood antigen (Fy) receptor are less likely to develop blood-stage infections; therefore, they preferentially develop immune responses to pre-erythrocytic-stage parasites, whereas Fy+ individuals experience both liver- and blood-stage infections and develop immune responses to both pre-erythrocytic and erythrocytic parasites. We screened 60 endemic sera from P. vivax-exposed Fy+ or Fy- donors against a protein microarray containing 91 P. vivax proteins with P. falciparum orthologs that were up-regulated in sporozoites. Antibodies against 10 P. vivax antigens were identified in sera from P. vivax-exposed individuals but not unexposed controls. This technology has promising implications in the discovery of potential vaccine candidates against P. vivax malaria.     

Clinical diagnosis of hyposalivation in hospitalized patients

Objective

The aim of this study was to evaluate the effectiveness of clinical criteria for the diagnosis of hyposalivation in hospitalized patients.

Material and Methods

A clinical study was carried out on 145 subjects (48 males; 97 females; aged 20 to 90 years). Each subject was clinically examined, in the morning and in the afternoon, along 1 day. A focused anamnesis allowed identifying symptoms of hyposalivation, like xerostomia complaints (considered as a reference symptom), chewing difficulty, dysphagia and increased frequency of liquid intake. Afterwards, dryness of the mucosa of the cheecks and floor of the mouth, as well as salivary secretion during parotid gland stimulation were assessed during oral examination.

Results

Results obtained with Chi-square tests showed that 71 patients (48.9%) presented xerostomia complaints, with a significant correlation with all hyposalivation symptoms (p<0.05). Furthermore, xerostomia was also significantly correlated with all data obtained during oral examination in both periods of evaluation (p<0.05).

Conclusion

Clinical diagnosis of hyposalivation in hospitalized patients is feasible and can provide an immediate and appropriate therapy avoiding further problems and improving their quality of life.