MycoBank gearing up for new horizons.

MycoBank, a registration system for fungi established in 2004 to capture all taxonomic novelties, acts as a coordination hub between repositories such as Index Fungorum and Fungal Names. Since January 2013, registration of fungal names is a mandatory requirement for valid publication under the International Code of Nomenclature for algae, fungi and plants (ICN). This review explains the database innovations that have been implemented over the past few years, and discusses new features such as advanced queries, registration of typification events (MBT numbers for lecto, epi- and neotypes), the multi-lingual database interface, the nomenclature discussion forum, annotation system, and web services with links to third parties. MycoBank has also introduced novel identification services, linking DNA sequence data to numerous related databases to enable intelligent search queries. Although MycoBank fills an important void for taxon registration, challenges for the future remain to improve links between taxonomic names and DNA data, and to also introduce a formal system for naming fungi known from DNA sequence data only. To further improve the quality of MycoBank data, remote access will now allow registered mycologists to act as MycoBank curators, using Citrix software

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

Determining the optimal time to assess the reversibility of airway obstruction

Context: The optimal time to interpret bronchodilator reversibility remains controversial. This time may affect a positive diagnosis and manage asthma and chronic obstructive pulmonary disease (COPD). Aims: We sought to document the time when maximum respiratory function is reached after inhalation of salbutamol and to define the optimal time of bronchodilator response to assess the reversibility or non reversibility of airway obstruction. Subjects and Methods: This prospective analytical study was spread over 8 months and included 58 patients with asthma or COPD with airway obstruction. Spirometry was performed before and at 5, 10, 15, 20, and 30 min after salbutamol inhalation (200 mcg) administered through pressurized metered-dose inhalers and large volume spacer. Results: After salbutamol inhalation, the mean individual peak bronchodilation occurred at 20 min for the forced vital capacity and at 30 min for the forced expiratory volume in 1 s. The percentage of reversible patients in our sample was guideline dependent. It increased from 53% to 67.2% when using the American Thoracic Society/European Respiratory Society definition compared to using the Global Initiative for Chronic Obstructive Lung Disease. The maximum number of reversible patients was significantly different at 20 min compared to 5 and 10 min. Conclusions: Interpreting bronchodilator reversibility after 20 min was the ideal time to judge the reversibility or nonreversibility in obstructive ventilatory disorders in adults

Transformed dermatofibrosarcoma protuberans: A series of nine cases and literature review

The fibrosarcomatous variant of dermatofibrosarcoma protuberans (DFSP) represents an uncommon form of DFSP which has a higher risk of local recurrence and distant metastases than ordinary DFSP. The aim of our study is to investigate clinicopathologic characteristics, treatment modalities and prognostic factors of nine cases of transformed DFSP admitted in Salah Azaiez Institute between 2002 and 2009. They were five men and four women. Median age at diagnosis was 52 years (35–87 years). The lesions were located on the abdominal wall (three cases), the upper limb (two cases), the back (two cases), the lower limb (one case) and the chest wall (one case). Tumor size ranged from 25 mm to 150 mm. After diagnosis, six patients were treated by wide local excision with margins ⩾2 cm, two patients had local excision without defined margins and one patient had incomplete local excision. Three patients underwent radiotherapy because of either cramped or unknown limits. Local recurrence was diagnosed in 5 cases and distant metastasis occurred in one patient. Fibrosarcomatous DFSP exhibits more aggressive behavior than DFSP. Their similar clinical presentation requires histopathological differentiation for prognosis. Treatment is based on wide local excision, radiation and targeted therapy

MycoBank gearing up for new horizons.

MycoBank, a registration system for fungi established in 2004 to capture all taxonomic novelties, acts as a coordination hub between repositories such as Index Fungorum and Fungal Names. Since January 2013, registration of fungal names is a mandatory requirement for valid publication under the International Code of Nomenclature for algae, fungi and plants (ICN). This review explains the database innovations that have been implemented over the past few years, and discusses new features such as advanced queries, registration of typification events (MBT numbers for lecto, epi- and neotypes), the multi-lingual database interface, the nomenclature discussion forum, annotation system, and web services with links to third parties. MycoBank has also introduced novel identification services, linking DNA sequence data to numerous related databases to enable intelligent search queries. Although MycoBank fills an important void for taxon registration, challenges for the future remain to improve links between taxonomic names and DNA data, and to also introduce a formal system for naming fungi known from DNA sequence data only. To further improve the quality of MycoBank data, remote access will now allow registered mycologists to act as MycoBank curators, using Citrix software

MycoBank gearing up for new horizons

MycoBank, a registration system for fungi established in 2004 to capture all taxonomic novelties, acts as a coordination hub between repositories such as Index Fungorum and Fungal Names. Since January 2013, registration of fungal names is a mandatory requirement for valid publication under the International Code of Nomenclature for algae, fungi and plants (ICN). This review explains the database innovations that have been implemented over the past few years, and discusses new features such as advanced queries, registration of typification events (MBT numbers for lecto, epi- and neotypes), the multi-lingual database interface, the nomenclature discussion forum, annotation system, and web services with links to third parties. MycoBank has also introduced novel identification services, linking DNA sequence data to numerous related databases to enable intelligent search queries. Although MycoBank fills an important void for taxon registration, challenges for the future remain to improve links between taxonomic names and DNA data, and to also introduce a formal system for naming fungi known from DNA sequence data only. To further improve the quality of MycoBank data, remote access will now allow registered mycologists to act as MycoBank curators, using Citrix software