SARS-CoV-2 sequencing with cloud-based analysis illustrates expedient co-ordinated surveillance of viral genomic epidemiology across six continents (preprint)

Viral sequencing has been critical in the COVID-19 pandemic response, but sequencing and bioinformatics capacity remain inconsistent. To examine the utility of a cloud-based sequencing analysis platform for SARS-CoV-2 sequencing, we conducted a cross-sectional study incorporating seven countries in July 2022. Sites submitted sequential SARS-CoV-2 sequences over two weeks to the Global Pathogen Analysis Service (GPAS). The GPAS bioinformatics cloud platform performs sequence assembly plus lineage and related sample identification. Users can share information with collaborators while retaining data ownership. Seven sites contributed sequencing reads from 5,346 clinical samples, of which 4,799/5,346 (89.8%) had a lineage identified. Omicron lineages dominated, with the vast majority being BA.5, BA.4 and BA.2, commensurate with contemporary genomic epidemiological observations. Phylogenetic analysis demonstrated low within-lineage diversity, and highly similar sequences present in globally disparate sites. A cloud-based analysis platform like GPAS addresses bioinformatics bottlenecks and facilitates collaboration in pathogen surveillance, enhancing epidemic and pandemic preparedness.

Baseline Marine Litter Surveys along Vietnam Coasts Using Citizen Science Approach

Marine litter is a significant threat to the marine environment, human health, and the economy. In this study, beach litter surveys along Vietnamese coasts were conducted in a local context to quantify and characterize marine litter using the modified GESAMP marine litter monitoring guideline. A total of 21,754 items weighing 136,820.2 g was recorded across 14 surveys from September 2020 to January 2021. Plastic was the most abundant type of litter by both quantity (20,744 items) and weight (100,371.2 g). Fishing gear 1 (fishing plastic rope, net pieces, fishing lures and lines, hard plastic floats) and soft plastic fragments were the most frequently observed items (17.65% and 17.24%, respectively). This study not only demonstrates the abundance and composition of marine litter in Vietnam, it also provides valuable information for the implementation of appropriate preventive measures, such as the redesign of collection, reuse, and recycling programs, and informs policy and priorities, with a focus on action and investment in Vietnam. Moreover, insights from this study indicate that citizen science is a useful approach for collecting data on marine litter in Vietnam.