Positive selection underlies repeated knockout of ORF8 in SARS-CoV-2 evolution.

Knockout of the ORF8 protein has repeatedly spread through the global viral population during SARS-CoV-2 evolution. Here we use both regional and global pathogen sequencing to explore the selection pressures underlying its loss. In Washington State, we identified transmission clusters with ORF8 knockout throughout SARS-CoV-2 evolution, not just on novel, high fitness viral backbones. Indeed, ORF8 is truncated more frequently and knockouts circulate for longer than for any other gene. Using a global phylogeny, we find evidence of positive selection to explain this phenomenon: nonsense mutations resulting in shortened protein products occur more frequently and are associated with faster clade growth rates than synonymous mutations in ORF8. Loss of ORF8 is also associated with reduced clinical severity, highlighting the diverse clinical impacts of SARS-CoV-2 evolution.

Genomic prediction of hybrid performance for agronomic traits in sorghum.

Hybrid breeding in sorghum [Sorghum bicolor (L.) Moench] utilizes the cytoplasmic-nuclear male sterility (CMS) system for seed production and subsequently harnesses heterosis. Since the cost of developing and evaluating inbred and hybrid lines in the CMS system is costly and time-consuming, genomic prediction of parental lines and hybrids is based on genetic data genotype. We generated 602 hybrids by crossing two female (A) lines with 301 diverse and elite male (R) lines from the sorghum association panel and collected phenotypic data for agronomic traits over two years. We genotyped the inbred parents using whole genome resequencing and used 2,687,342 high quality (minor allele frequency > 2%) single nucleotide polymorphisms for genomic prediction. For grain yield, the experimental hybrids exhibited an average mid-parent heterosis of 40%. Genomic best linear unbiased prediction (GBLUP) for hybrid performance yielded an average prediction accuracy of 0.76-0.93 under the prediction scenario where both parental lines in validation sets were included in the training sets (T2). However, when only female tester was shared between training and validation sets (T1F), prediction accuracies declined by 12-90%, with plant height showing the greatest decline. Mean accuracies for predicting the general combining ability of male parents ranged from 0.33 to 0.62 for all traits. Our results showed hybrid performance for agronomic traits can be predicted with high accuracy, and optimizing genomic relationship is essential for optimal training population design for genomic selection in sorghum breeding.

Dissecting the Genetic Architecture of Carbon Partitioning in Sorghum Using Multiscale Phenotypes.

Carbon partitioning in plants may be viewed as a dynamic process composed of the many interactions between sources and sinks. The accumulation and distribution of fixed carbon is not dictated simply by the sink strength and number but is dependent upon the source, pathways, and interactions of the system. As such, the study of carbon partitioning through perturbations to the system or through focus on individual traits may fail to produce actionable developments or a comprehensive understanding of the mechanisms underlying this complex process. Using the recently published sorghum carbon-partitioning panel, we collected both macroscale phenotypic characteristics such as plant height, above-ground biomass, and dry weight along with microscale compositional traits to deconvolute the carbon-partitioning pathways in this multipurpose crop. Multivariate analyses of traits resulted in the identification of numerous loci associated with several distinct carbon-partitioning traits, which putatively regulate sugar content, manganese homeostasis, and nitrate transportation. Using a multivariate adaptive shrinkage approach, we identified several loci associated with multiple traits suggesting that pleiotropic and/or interactive effects may positively influence multiple carbon-partitioning traits, or these overlaps may represent molecular switches mediating basal carbon allocating or partitioning networks. Conversely, we also identify a carbon tradeoff where reduced lignin content is associated with increased sugar content. The results presented here support previous studies demonstrating the convoluted nature of carbon partitioning in sorghum and emphasize the importance of taking a holistic approach to the study of carbon partitioning by utilizing multiscale phenotypes.

Leveraging gains from African Center for Integrated Laboratory Training to combat HIV epidemic in sub-Saharan Africa.

BACKGROUND: In sub-Saharan Africa, there is dearth of trained laboratorians and strengthened laboratory systems to provide adequate and quality laboratory services for enhanced HIV control. In response to this challenge, in 2007, the African Centre for Integrated Laboratory Training (ACILT) was established in South Africa with a mission to train staffs from countries with high burdens of diseases in skills needed to strengthen sustainable laboratory systems. This study was undertaken to assess the transference of newly gained knowledge and skills to other laboratory staff, and to identify enabling and obstructive factors to their implementation. METHODS: We used Kirkpatrick model to determine training effectiveness by assessing the transference of newly gained knowledge and skills to participant's work environment, along with measuring enabling and obstructive factors. In addition to regular course evaluations at ACILT (pre and post training), in 2015 we sent e-questionnaires to 867 participants in 43 countries for course participation between 2008 and 2014. Diagnostics courses included Viral Load, and systems strengthening included strategic planning and Biosafety and Biosecurity. SAS v9.44 and Excel were used to analyze retrospective de-identified data collected at six months pre and post-training. RESULTS: Of the 867 participants, 203 (23.4%) responded and reported average improvements in accuracy and timeliness in Viral Load programs and to systems strengthening. For Viral Load testing, frequency of corrective action for unsatisfactory proficiency scores improved from 57 to 91%, testing error rates reduced from 12.9% to 4.9%; 88% responders contributed to the first national strategic plan development and 91% developed strategies to mitigate biosafety risks in their institutions. Key enabling factors were team and management support, and key obstructive factors included insufficient resources and staff's resistance to change. CONCLUSIONS: Training at ACILT had a documented positive impact on strengthening the laboratory capacity and laboratory workforce and substantial cost savings. ACILT's investment produced a multiplier effect whereby national laboratory systems, personnel and leadership reaped training benefits. This laboratory training centre with a global clientele contributed to improve existing laboratory services, systems and networks for the HIV epidemic and is now being leveraged for COVID-19 testing that has infected 41,332,899 people globally.

Lebanon's experience in surveillance of communicable diseases during a mass gathering: Sixth Francophone Games, 2009.

In 2009, Lebanon hosted the 6th Francophone Games. Pandemic A(H1N1)2009 virus presented significant health threat at the time. A surveillance strategy was implemented for the timely detection and management of epidemiological events and outbreaks, in particular for A(H1N1)2009 virus cases. Data were collected and managed daily and feedback was generated through daily bulletins. A total of 299 medical consultations were reported, 29% of which related to infectious diseases. There were 10 cases reported as acute respiratory infections; all tested negative for A(H1N1)2009 virus within 24 hours. Twenty-three cases of gastroenteritis were reported, for which 11 stool cultures were negative. While pandemic A(H1N1)2009 did not interfere with the Games, it was essential to strengthen surveillance and to have timely epidemiological information. This was achieved through preparedness, a multi-disciplinary approach, timely management and coordination.

Lebanon's experience in surveillance of communicable diseases during a mass gathering: Sixth Francophone Games, 2009

In 2009, Lebanon hosted the 6th Francophone Games. Pandemic A[H1N1]2009 virus presented significant health threat at the time. A surveillance strategy was implemented for the timely detection and management of epidemiological events and outbreaks, in particular for A[H1N1]2009 virus cases. Data were collected and managed daily and feedback was generated through daily bulletins. A total of 299 medical consultations were reported, 29% of which related to infectious diseases. There were 10 cases reported as acute respiratory infections; all tested negative for A[H1N1]2009 virus within 24 hours. Twenty-three cases of gastroenteritis were reported, for which 11 stool cultures were negative. While pandemic A[H1N1]2009 did not interfere with the Games, it was essential to strengthen surveillance and to have timely epidemiological information. This was achieved through preparedness, a multi-disciplinary approach, timely management and coordination

En 2009, le Liban a accueilli la sixième édition des Jeux de la Francophonie. Le virus pandémique A[H1N1] 2009 représentait une menace sanitaire majeure à l'époque. Une stratégie de surveillance a été mise en place en vue d'une détection et d'une prise en charge rapides des événements épidémiologiques et des flambées, notamment de cas de virus A[H1N1]2009. Les données ont été collectées et gérées sur une base journalière, et une rétroinformation était générée au moyen de bulletins quotidiens. Un total de 299 consultations médicales a été rapporté, dont 29% en rapport avec des maladies infectieuses. Dix cas d'infections respiratoires aiguës ont été notifiés. Tous se sont révélés négatifs au test de recherche du virus A[H1N1] 2009 réalisé sous 24h. Vingt-trois cas de gastroentérite ont été signalés, pour lesquels 11 coprocultures se sont révélées négatives. Si la pandémie A[H1N1] 2009 n'a pas impacté les Jeux, il était essentiel de renforcer la surveillance et de mettre en place un système d'information épidémiologique rapide. Ces objectifs ont été atteints au moyen d'une préparation, d'une approche multidisciplinaire, ainsi que d'une prise en charge et d'une coordination rapides

Determinants of malaria diagnostic uptake in the retail sector: qualitative analysis from focus groups in Uganda.

BACKGROUND: In Uganda, as in most other malaria-endemic countries, presumptive treatment for malaria based on symptoms without a diagnostic blood test is still very common. While diagnostic testing in public sector facilities is increasing, many people in Uganda who suspect malaria visit private sector outlets to purchase medications. Increasing the availability and uptake of rapid diagnostic tests (RDTs) for malaria in private outlets could help increase diagnostic testing for malaria but raises questions about the patient demand for and valuation of testing that are less critical for public sector introduction. METHODS: In preparation for a behaviour change campaign to encourage and sustain the demand for RDTs in drug shops, eight focus group discussions with a total of 84 community members were conducted in six districts across Uganda's Eastern Region in November-December 2011. Focus groups explored incentives and barriers to seeking diagnosis for malaria, how people react to test results and why, and what can be done to increase the willingness to pay for RDTs. RESULTS: Overall, participants were very familiar with malaria diagnostic testing and understood its importance, yet when faced with limited financial resources, patients preferred to spend their money on medication and sought testing only when presumptive treatment proved ineffective. While side effects did seem to be a concern, participants did not mention other potential costs of taking unnecessary or ineffective medications, such as money wasted on excess drugs or delays in resolution of symptoms. Very few individuals were familiar with RDTs. CONCLUSION: In order to boost demand, these results suggest that private sector RDTs will have to be made convenient and affordable and that targeted behaviour change campaigns should strive to increase the perceived value of diagnosis.

Substitutions in the glycoprotein (GP) of the Candid#1 vaccine strain of Junin virus increase dependence on human transferrin receptor 1 for entry and destabilize the metastable conformation of GP.

Candid#1 (Cd1) is an attenuated vaccine strain of Junin virus, the causative agent of Argentine hemorrhagic fever. Although several substitutions are present in Cd1, their importance for attenuation has not been established. We functionally characterized the substitutions present in the Cd1 glycoprotein (GP) and identified F427I in the transmembrane domain of the GP2 subunit as reducing infectivity in a reconstituted viral system. We further showed that this phenotype derives from the destabilization of the GP metastable conformation. Lastly, we identified an increased dependence of Cd1 GP on human transferrin receptor type 1 (hTfR-1) for entry, which may affect the tropism of the attenuated strain in vivo.

Investigation of clade B New World arenavirus tropism by using chimeric GP1 proteins.

Clade B of the New World arenaviruses contains both pathogenic and nonpathogenic members, whose surface glycoproteins (GPs) are characterized by different abilities to use the human transferrin receptor type 1 (hTfR1) protein as a receptor. Using closely related pairs of pathogenic and nonpathogenic viruses, we investigated the determinants of the GP1 subunit that confer these different characteristics. We identified a central region (residues 85 to 221) in the Guanarito virus GP1 that was sufficient to interact with hTfR1, with residues 159 to 221 being essential. The recently solved structure of part of the Machupo virus GP1 suggests an explanation for these requirements.