Benchmarking and Assessment of Eight De Novo Genome Assemblers on Viral Next-Generation Sequencing Data, Including the SARS-CoV-2

Phylogenetic Investigations of Dengue 2019-2021 Outbreak in Guadeloupe and Martinique Caribbean Islands

Dengue fever has been a public health problem in the Caribbean region since 1981, when it first reappeared in Cuba. In 1989, it was reported in Martinique and Guadeloupe (two French islands 200 km apart); since then, DENV has caused several epidemics locally. In 2019-2021, DENV-1, DENV-2, and DENV-3 were detected. Serotype distribution was differentiated, with DENV-2 and DENV-3 predominating in Guadeloupe and Martinique, respectively. Complete genome sequencing was carried out on 32 specimens, and phylogenic analysis identified the circulation of genotype V for DENV-1, cosmopolitan genotype for DENV-2, and genotype III for DENV-3. However, two distinct circulating groups were identified for DENV-1 and DENV-3, suggesting independent introductions. Overall, despite the context of the COVID-19 pandemic and the associated travel restrictions, these results confirm the active circulation of DENV and specific epidemiological features on each of the two islands. Such differences may be linked to the founder effect of the various introduction events, and to local factors such as the population immunity and the transmission capacity of the vectors. Further genomic and epidemiological characterization of DENV strains remains essential to understand how dengue spreads in each specific geographical context and to prevent future epidemics.

A practical approach to genome assembly and annotation of Basidiomycota using the example of Armillaria

Technological advancements in genome sequencing, assembly and annotation platforms and algorithms that resulted in several genomic studies have created an opportunity to further our understanding of the biology of phytopathogens, including Armillaria species. Most Armillaria species are facultative necrotrophs that cause root- and stem-rot, usually on woody plants, significantly impacting agriculture and forestry worldwide. Genome sequencing, assembly and annotation in terms of samples used and methods applied in Armillaria genome projects are evaluated in this review. Infographic guidelines and a database of resources to facilitate future Armillaria genome projects were developed. Knowledge gained from genomic studies of Armillaria species is summarized and prospects for further research are provided. This guide can be applied to other diploid and dikaryotic fungal genomics.

Challenges and Opportunities for Global Genomic Surveillance Strategies in the COVID-19 Era

Global SARS-CoV-2 genomic surveillance efforts have provided critical data on the ongoing evolution of the virus to inform best practices in clinical care and public health throughout the pandemic. Impactful genomic surveillance strategies generally follow a multi-disciplinary pipeline involving clinical sample collection, viral genotyping, metadata linkage, data reporting, and public health responses. Unfortunately, current limitations in each of these steps have compromised the overall effectiveness of these strategies. Biases from convenience-based sampling methods can obfuscate the true distribution of circulating variants. The lack of standardization in genotyping strategies and bioinformatic expertise can create bottlenecks in data processing and complicate interpretation. Limitations and inconsistencies in clinical and demographic data collection and sharing can slow the compilation and limit the utility of comprehensive datasets. This likewise can complicate data reporting, restricting the availability of timely data. Finally, gaps and delays in the implementation of genomic surveillance data in the public health sphere can prevent officials from formulating effective mitigation strategies to prevent outbreaks. In this review, we outline current SARS-CoV-2 global genomic surveillance methods and assess roadblocks at each step of the pipeline to identify potential solutions. Evaluating the current obstacles that impede effective surveillance can improve both global coordination efforts and pandemic preparedness for future outbreaks.