ABSTRACT
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.
Subject(s)
COVID-19ABSTRACT
Coronavirus disease 2019 (COVID-19) and associated social responses may uniquely affect people living with HIV (PLHIV). SARS-CoV-2 antibody testing and a cross-sectional survey on COVID-19's socio-behavioral impacts were conducted among a large PLHIV cohort in Hanoi, Vietnam. We examined anonymous antibody test results for 1243 PLHIV (99.8%) from whom plasma was obtained and completed surveys were collected in June/July 2020, just after the end of the first COVID-19 outbreak and nationwide lockdown. Three participants (0.2%) tested positive for anti-SARS-CoV-2 IgG antibodies. HIV treatment was generally maintained without antiretroviral therapy interruption, but COVID-19 had substantial impacts on economic security and risky health behaviors among PLHIV, which may have amplified psychological stress. These findings highlight the need for continuous monitoring of COVID-19's impacts on PLHIV and for efforts to mitigate these impacts.