Mother-to-Child HIV Transmission Bottleneck Selects for Consensus Virus with Lower Gag-Protease-Driven Replication Capacity.

In the large majority of cases, HIV infection is established by a single variant, and understanding the characteristics of successfully transmitted variants is relevant to prevention strategies. Few studies have investigated the viral determinants of mother-to-child transmission. To determine the impact of Gag-protease-driven viral replication capacity on mother-to-child transmission, the replication capacities of 148 recombinant viruses encoding plasma-derived Gag-protease from 53 nontransmitter mothers, 48 transmitter mothers, and 47 infected infants were assayed in an HIV-1-inducible green fluorescent protein reporter cell line. All study participants were infected with HIV-1 subtype C. There was no significant difference in replication capacities between the nontransmitter (n = 53) and transmitter (n = 44) mothers (P = 0.48). Infant-derived Gag-protease NL4-3 recombinant viruses (n = 41) were found to have a significantly lower Gag-protease-driven replication capacity than that of viruses derived from the mothers (P < 0.0001 by a paired t test). High percent similarities to consensus subtype C Gag, p17, p24, and protease sequences were also found in the infants (n = 28) in comparison to their mothers (P = 0.07, P = 0.002, P = 0.03, and P = 0.02, respectively, as determined by a paired t test). These data suggest that of the viral quasispecies found in mothers, the HIV mother-to-child transmission bottleneck favors the transmission of consensus-like viruses with lower viral replication capacities.IMPORTANCE Understanding the characteristics of successfully transmitted HIV variants has important implications for preventative interventions. Little is known about the viral determinants of HIV mother-to-child transmission (MTCT). We addressed the role of viral replication capacity driven by Gag, a major structural protein that is a significant determinant of overall viral replicative ability and an important target of the host immune response, in the MTCT bottleneck. This study advances our understanding of the genetic bottleneck in MTCT by revealing that viruses transmitted to infants have a lower replicative ability as well as a higher similarity to the population consensus (in this case HIV subtype C) than those of their mothers. Furthermore, the observation that "consensus-like" virus sequences correspond to lower in vitro replication abilities yet appear to be preferentially transmitted suggests that viral characteristics favoring transmission are decoupled from those that enhance replicative capacity.

Discordant Impact of HLA on Viral Replicative Capacity and Disease Progression in Pediatric and Adult HIV Infection.

HLA class I polymorphism has a major influence on adult HIV disease progression. An important mechanism mediating this effect is the impact on viral replicative capacity (VRC) of the escape mutations selected in response to HLA-restricted CD8+ T-cell responses. Factors that contribute to slow progression in pediatric HIV infection are less well understood. We here investigate the relationship between VRC and disease progression in pediatric infection, and the effect of HLA on VRC and on disease outcome in adult and pediatric infection. Studying a South African cohort of >350 ART-naïve, HIV-infected children and their mothers, we first observed that pediatric disease progression is significantly correlated with VRC. As expected, VRCs in mother-child pairs were strongly correlated (p = 0.004). The impact of the protective HLA alleles, HLA-B*57, HLA-B*58:01 and HLA-B*81:01, resulted in significantly lower VRCs in adults (p<0.0001), but not in children. Similarly, in adults, but not in children, VRCs were significantly higher in subjects expressing the disease-susceptible alleles HLA-B*18:01/45:01/58:02 (p = 0.007). Irrespective of the subject, VRCs were strongly correlated with the number of Gag CD8+ T-cell escape mutants driven by HLA-B*57/58:01/81:01 present in each virus (p = 0.0002). In contrast to the impact of VRC common to progression in adults and children, the HLA effects on disease outcome, that are substantial in adults, are small and statistically insignificant in infected children. These data further highlight the important role that VRC plays both in adult and pediatric progression, and demonstrate that HLA-independent factors, yet to be fully defined, are predominantly responsible for pediatric non-progression.

LiLA: lipid lung-based ATLAS built through a comprehensive workflow designed for an accurate lipid annotation.

Accurate lipid annotation is crucial for understanding the role of lipids in health and disease and identifying therapeutic targets. However, annotating the wide variety of lipid species in biological samples remains challenging in untargeted lipidomic studies. In this work, we present a lipid annotation workflow based on LC-MS and MS/MS strategies, the combination of four bioinformatic tools, and a decision tree to support the accurate annotation and semi-quantification of the lipid species present in lung tissue from control mice. The proposed workflow allowed us to generate a lipid lung-based ATLAS (LiLA), which was then employed to unveil the lipidomic signatures of the Mycobacterium tuberculosis infection at two different time points for a deeper understanding of the disease progression. This workflow, combined with manual inspection strategies of MS/MS data, can enhance the annotation process for lipidomic studies and guide the generation of sample-specific lipidome maps. LiLA serves as a freely available data resource that can be employed in future studies to address lipidomic alterations in mice lung tissue.

Impact of HLA-B*81-associated mutations in HIV-1 Gag on viral replication capacity.

HIV-1 attenuation resulting from immune escape mutations selected in Gag may contribute to slower disease progression in HIV-1-infected individuals expressing certain HLA class I alleles. We previously showed that the protective allele HLA-B*81 and the HLA-B*81-selected Gag T186S mutation are strongly associated with a lower viral replication capacity of recombinant viruses encoding Gag-protease derived from individuals chronically infected with HIV-1 subtype C. In the present study, we directly tested the effect of this mutation on viral replication capacity. In addition, we investigated potential compensatory effects of various polymorphisms, including other HLA-B*81-associated mutations that significantly covary with the T186S mutation. Mutations were introduced into a reference subtype B backbone and into patient-derived subtype C sequences in subtype B and C backbones by site-directed mutagenesis. The exponential-phase growth of mutant and wild-type viruses was assayed by flow cytometry of a green fluorescent protein reporter T cell line or by measurement of HIV-1 reverse transcriptase activity in culture supernatants. Engineering of the T186S mutation alone into all patient-derived subtype C sequences failed to yield replication-competent viruses, while in the subtype B sequence, the T186S mutation resulted in impaired replication capacity. Only the T186S mutation in combination with the T190I mutation yielded replication-competent viruses for all virus backbones tested; however, these constructs replicated slower than the wild type, suggesting that only partial compensation is mediated by the T190I mutation. Constructs encoding the T186S mutation in combination with other putative compensatory mutations were attenuated or defective. These results suggest that the T186S mutation is deleterious to HIV-1 subtype C replication and likely requires complex compensatory pathways, which may contribute to the clinical benefit associated with HLA-B*81.

Hospitals early challenges and interventions combatting COVID-19 in the Eastern Mediterranean Region.

BACKGROUND: During rapidly evolving outbreaks, health services and essential medical care are interrupted as facilities have become overwhelmed responding to COVID-19. In the Eastern Mediterranean Region (EMR), more than half of countries are affected by emergencies, hospitals face complex challenges as they respond to humanitarian crises, maintain essential services, and fight the pandemic. While hospitals in the EMR have adapted to combat COVID-19, evidence-based and context-specific recommendations are needed to guide policymakers and hospital managers on best practices to strengthen hospitals' readiness, limit the impact of the pandemic, and create lasting hospital sector improvements towards recovery and resilience. AIM: Guided by the WHO/EMR's "Hospital readiness checklist for COVID-19", this study presents the experiences of EMR hospitals in combatting COVID-19 across the 22 EMR countries, including their challenges and interventions across the checklist domains, to inform improvements to pandemic preparedness, response, policy, and practice. METHODS: To collect in-depth and comprehensive information on hospital experiences, qualitative and descriptive quantitative data was collected between May-October 2020. To increase breadth of responses, this comprehensive qualitative study triangulated findings from a regional literature review with the findings of an open-ended online survey (n = 139), and virtual in-depth key informant interviews with 46 policymakers and hospital managers from 18 out of 22 EMR countries. Purposeful sampling supported by snowballing was used and continued until reaching data saturation, measures were taken to increase the trustworthiness of the results. Led by the checklist domains, qualitative data was thematically analyzed using MAXQDA. FINDINGS: Hospitals faced continuously changing challenges and needed to adapt to maintain operations and provide essential services. This thematic analysis revealed major themes for the challenges and interventions utilized by hospitals for each of hospital readiness domains: Preparedness, Leadership, Operational support, logistics, supply management, Communications and Information, Human Resources, Continuity of Essential Services and Surge Capacity, Rapid Identification and Diagnosis, Isolation and Case Management, and Infection, Prevention and Control. CONCLUSION: Hospitals are the backbone of COVID-19 response, and their resilience is essential for achieving universal health coverage. Multi-pronged (across each of the hospitals readiness domains) and multi-level policies are required to strengthen hospitals resilience and prepare health systems for future outbreaks and shocks.

A COVID-19 field hospital in a conference centre - The Cape Town, South Africa experience.

BACKGROUND: The coronavirus pandemic has put extreme pressure on health care services in South Africa. AIM: To describe the design, patients and outcomes of a field hospital during the first wave of the coronavirus disease 2019 (COVID-19) pandemic. SETTING: The Cape Town International Convention Centre was the first location in Cape Town to be commissioned as a field hospital that would serve as an intermediate care bed facility. METHODS: This was a retrospective descriptive study of patients admitted to this facility between 8th June 2020 and 14th August 2020 using deidentified data extracted from patient records. RESULTS: There were 1502 patients admitted, 56.4% female, with a mean age of 58.6 years (standard deviation [s.d.]: 14.2). The majority of patients (82.9%) had at least one comorbidity, whilst 15.4% had three or more. Nearly 80.0% (79.8%) of patients required oxygen and 63.5% received steroids, and only 5.7% of patients were required to be transferred for escalation of care. The mean length of stay was 6 days (s.d.: 4.8) with an overall mortality of 5.7%. CONCLUSION: This study highlights the role of a field hospital in providing surge capacity. Its use halved the predicted duration of stay at acute care hospitals, allowing them the capacity to manage more unstable and critical patients. Adaptability and responsivity as well as adequate referral platforms proved to be crucial. Daily communication with the whole health care service platform was a critical success factor. This study provides information to assist future health planning and strategy development in the current pandemic and future disease outbreaks.

Compromised Metabolic Reprogramming Is an Early Indicator of CD8+ T Cell Dysfunction during Chronic Mycobacterium tuberculosis Infection.

The immunometabolic mechanisms underlying suboptimal T cell immunity in tuberculosis remain undefined. Here, we examine how chronic Mycobacterium tuberculosis (Mtb) and M. bovis BCG infections rewire metabolic circuits and alter effector functions in lung CD8+ T cells. As Mtb infection progresses, mitochondrial metabolism deteriorates in CD8+ T cells, resulting in an increased dependency on glycolysis that potentiates inflammatory cytokine production. Over time, these cells develop bioenergetic deficiencies that reflect metabolic "quiescence." This bioenergetic signature coincides with increased mitochondrial dysfunction and inhibitory receptor expression and was not observed in BCG infection. Remarkably, the Mtb-triggered decline in T cell bioenergetics can be reinvigorated by metformin, giving rise to an Mtb-specific CD8+ T cell population with improved metabolism. These findings provide insights into Mtb pathogenesis whereby glycolytic reprogramming and compromised mitochondrial function contribute to the breakdown of CD8+ T cell immunity during chronic disease, highlighting opportunities to reinvigorate immunity with metabolically targeted pharmacologic agents.