mycoCLAP, the database for characterized lignocellulose-active proteins of fungal origin: resource and text mining curation support

Enzymes active on components of lignocellulosic biomass are used for industrial applications ranging from food processing to biofuels production. These include a diverse array of glycoside hydrolases, carbohydrate esterases, polysaccharide lyases and oxidoreductases. Fungi are prolific producers of these enzymes, spurring fungal genome sequencing efforts to identify and catalogue the genes that encode them. To facilitate the functional annotation of these genes, biochemical data on over 800 fungal lignocellulose-degrading enzymes have been collected from the literature and organized into the searchable database, mycoCLAP (http://mycoclap.fungalgenomics.ca). First implemented in 2011, and updated as described here, mycoCLAP is capable of ranking search results according to closest biochemically characterized homologues: this improves the quality of the annotation, and significantly decreases the time required to annotate novel sequences. The database is freely available to the scientific community, as are the open source applications based on natural language processing developed to support the manual curation of mycoCLAP. Database URL: http://mycoclap.fungalgenomics.ca

Evaluation of the feasibility of a midwifery educator continuous professional development (CPD) programme in Kenya and Nigeria: a mixed methods study

Background: Midwifery education is under-invested in developing countries with limited opportunities for midwifery educators to improve/maintain their core professional competencies. To improve the quality of midwifery education and capacity for educators to update their competencies, a blended midwifery educator-specific continuous professional development (CPD) programme was designed with key stakeholders. This study evaluated the feasibility of this programme in Kenya and Nigeria. Methods: This was a mixed methods intervention study using a concurrent nested design. 120 randomly selected midwifery educators from 81 pre-service training institutions were recruited. Educators completed four self-directed online learning (SDL) modules and three-day practical training of the blended CPD programme on teaching methods (theory and clinical skills), assessments, effective feedback and digital innovations in teaching and learning. Pre- and post-training knowledge using multiple choice questions in SDL; confidence (on a 0–4 Likert scale) and practical skills in preparing a teaching a plan and microteaching (against a checklist) were measured. Differences in knowledge, confidence and skills were analysed. Participants’ reaction to the programme (relevance and satisfaction assessed on a 0–4 Likert scale, what they liked and challenges) were collected. Key informant interviews with nursing and midwifery councils and institutions’ managers were conducted. Thematic framework analysis was conducted for qualitative data. Results: 116 (96.7%) and 108 (90%) educators completed the SDL and practical components respectively. Mean knowledge scores in SDL modules improved from 52.4% (± 10.4) to 80.4% (± 8.1), preparing teaching plan median scores improved from 63.6% (IQR 45.5) to 81.8% (IQR 27.3), and confidence in applying selected pedagogy skills improved from 2.7 to 3.7, p 0.05). Qualitatively, educators found the programme educative, flexible, convenient, motivating, and interactive for learning. Internet connectivity, computer technology, costs and time constraints were potential challenges to completing the programme. Conclusion: The programme was feasible and effective in improving the knowledge and skills of educators for effective teaching/learning. For successful roll-out, policy framework for mandatory midwifery educator specific CPD programme is needed

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Identification and characterization of influenza A viruses in selected domestic animals in Kenya, 2010-2012

<div><p>Background</p><p>Influenza A virus subtypes in non-human hosts have not been characterized in Kenya. We carried out influenza surveillance in selected domestic animals and compared the virus isolates with isolates obtained in humans during the same period.</p><p>Methods</p><p>We collected nasal swabs from pigs, dogs and cats; oropharyngeal and cloacal swabs from poultry; and blood samples from all animals between 2010 and 2012. A standardized questionnaire was administered to farmers and traders. Swabs were tested for influenza A by rtRT-PCR, virus isolation and subtyping was done on all positive swabs. All sera were screened for influenza A antibodies by ELISA, and positives were evaluated by hemagglutination inhibition (HI). Full genome sequencing was done on four selected pig virus isolates.</p><p>Results</p><p>Among 3,798 sera tested by ELISA, influenza A seroprevalence was highest in pigs (15.9%; 172/1084), 1.2% (3/258) in ducks, 1.4% (1/72) in cats 0.6% (3/467) in dogs, 0.1% (2/1894) in chicken and 0% in geese and turkeys. HI testing of ELISA-positive pig sera showed that 71.5% had positive titers to A/California/04/2009(H1N1). Among 6,289 swabs tested by rRT-PCR, influenza A prevalence was highest in ducks [1.2%; 5/423] and 0% in cats and turkeys. Eight virus isolates were obtained from pig nasal swabs collected in 2011 and were determined to be A(H1N1)pdm09 on subtyping. On phylogenetic analysis, four hemagglutinin segments from pig isolates clustered together and were closely associated with human influenza viruses that circulated in Kenya in 2011.</p><p>Conclusion</p><p>Influenza A(H1N1)pdm09 isolated in pigs was genetically similar to contemporary human pandemic influenza virus isolates. This suggest that the virus was likely transmitted from humans to pigs, became established and circulated in Kenyan pig populations during the study period. Minimal influenza A prevalence was observed in the other animals studied.</p></div

Distribution of hemagglutination-inhibition (HI) titers and proportion positive of enzyme-linked immunosorbent assay (ELISA)-positive pig sera against three reference antigens for household and slaughterhouse sites, May 2010 –August 2012 (n = 172)^*.

<p>Distribution of hemagglutination-inhibition (HI) titers and proportion positive of enzyme-linked immunosorbent assay (ELISA)-positive pig sera against three reference antigens for household and slaughterhouse sites, May 2010 –August 2012 (n = 172)^{<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0192721#t003fn001" target="_blank">*</a>}.</p

Analysis of HA segment of Kenya swine isolates alongside other contemporary isolates.

<p>Branches highlighted in red referto Kenya swine isolates while those in blue are Kenya human isolates. A/California/04/2009 is used to root the phylogenetic tree.</p

Influenza A seroprevalence by ELISA among pigs sampled at the slaughter house, 2010–2012.

<p>Influenza A seroprevalence by ELISA among pigs sampled at the slaughter house, 2010–2012.</p

Prevalence of PCR positivity for influenza A in nasal, oropharyngeal and cloacal swabs, by species and site, Kenya, May 2010-August 2012.

<p>Prevalence of PCR positivity for influenza A in nasal, oropharyngeal and cloacal swabs, by species and site, Kenya, May 2010-August 2012.</p

Proportion of enrolled households (HH) owning different animal types by study site, Kenya, May 2010-August 2012.

<p>Proportion of enrolled households (HH) owning different animal types by study site, Kenya, May 2010-August 2012.</p

Map of Kenya counties showing the location of the study sites, Kibera in Nairobi, Ndumbui-ini slaughterhouse in Kiambu County and Asembo in Siaya County.

<p>Map of Kenya counties showing the location of the study sites, Kibera in Nairobi, Ndumbui-ini slaughterhouse in Kiambu County and Asembo in Siaya County.</p