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• Immunocompromised patients may acquire different clades of SARS-CoV-2 infection. • Infection with different SARS-CoV-2 clades poses significant management challenges. • Prolonged secretion of SARS-CoV-2 occurs in immunocompromised patients. • The impact of rituximab and B cell-depleting agents requires definition. • The responses to COVID-19 vaccines need further study. Immunocompromised patients who have a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection pose many clinical and public health challenges. We describe the case of a hematopoietic stem cell transplantation patient with lymphoma who had a protracted illness requiring three consecutive hospital admissions. Whole genome sequencing confirmed two different SARS-CoV-2 clades. Clinical management issues and the unanswered questions arising from this case are discussed. [ABSTRACT FROM AUTHOR]

• Eight nations have contributed 79% of all SARS-CoV-2 isolates that have been sequenced. • Two-thirds of SARS-CoV-2 variants that have been found were reported by five nations. • The number of detected variants increases at the square root of sequencing effort. • International cooperation for SARS-CoV-2 sequencing is urgently needed. • Effective monitoring and prevention require a global pathogen sequencing mechanism. To assess the efforts deployed by different nations and territories in sequencing SARS-CoV-2 isolates, thus enabling detection of variants, known and novel, of concern. The sources of over one million full genome sequences of SARS-CoV-2 virus available in the COVID-19 virus Mutation Tracker (CovMT) were analyzed to determine the number of variants in the RBD region of the genome determining infectivity detected in the various nations and territories. The number of detected variants increased as the square root of sequencing effort by nations. Eight nations have contributed 79% of all SARS-CoV-2 isolates that have been sequenced, with two-thirds of all unique variants, adding to 1118 RBD variants, reported by five nations. The median number of sequenced isolates required to detect, on average, one novel RBD variant is 24.05, which is a threshold achieved by 70 nations. Many developing nations have not contributed any sequences due to lack of capacity. This poses a risk of dangerous virus variants in these under-sampled regions spreading globally before being detected. A collaborative program to sequence SARS-CoV-2 isolates, and other pathogens of concern, is needed to monitor, track, and control the pandemic. [Display omitted] [ABSTRACT FROM AUTHOR]

Mangroves are unique, and endangered, coastal ecosystems that play a vital role in the tropical and subtropical environments. A comprehensive description of the microbial communities in these ecosystems is currently lacking, and additional studies are required to have a complete understanding of the functioning and resilience of mangroves worldwide. In this work, we carried out a metagenomic study by comparing the microbial community of mangrove sediment with the rhizosphere microbiome of Avicennia marina , in northern Red Sea mangroves, along the coast of Saudi Arabia. Our results revealed that rhizosphere samples presented similar profiles at the taxonomic and functional levels and differentiated from the microbiome of bulk soil controls. Overall, samples showed predominance by Proteobacteria, Bacteroidetes and Firmicutes, with high abundance of sulfate reducers and methanogens, although specific groups were selectively enriched in the rhizosphere. Functional analysis showed significant enrichment in ‘metabolism of aromatic compounds’, ‘mobile genetic elements’, ‘potassium metabolism’ and ‘pathways that utilize osmolytes’ in the rhizosphere microbiomes. To our knowledge, this is the first metagenomic study on the microbiome of mangroves in the Red Sea, and the first application of unbiased 454-pyrosequencing to study the rhizosphere microbiome associated with A. marina . Our results provide the first insights into the range of functions and microbial diversity in the rhizosphere and soil sediments of gray mangrove ( A. marina ) in the Red Sea. [ABSTRACT FROM AUTHOR]