Assessment of inter-laboratory differences in SARS-CoV-2 consensus genome assemblies between public health laboratories in Australia

Whole-genome sequencing of viral isolates is critical for informing transmission patterns and ongoing evolution of pathogens, especially during a pandemic. However, when genomes have low variability in the early stages of a pandemic, the impact of technical and/or sequencing errors increases. We quantitatively assessed inter-laboratory differences in consensus genome assemblies of 72 matched SARS-CoV-2-positive specimens sequenced at different laboratories in Sydney, Australia. Raw sequence data were assembled using two different bioinformatics pipelines in parallel, and resulting consensus genomes were compared to detect laboratory-specific differences. Matched genome sequences were predominantly concordant, with a median pairwise identity of 99.997%. Identified differences were predominantly driven by ambiguous site content. Ignoring these produced differences in only 2.3% (5/216) of pairwise comparisons, each differing by a single nucleotide. Matched samples were assigned the same Pango lineage in 98.2% (212/216) of pairwise comparisons, and were mostly assigned to the same phylogenetic clade. However, epidemiological inference based only on single nucleotide variant distances may lead to significant differences in the number of defined clusters if variant allele frequency thresholds for consensus genome generation differ between laboratories. These results underscore the need for a unified, best-practices approach to bioinformatics between laboratories working on a common outbreak problem.

Creating a Cursed and Sanctified Temple, 1965–1984

This chapter examines the transformation of the Kirtland Temple as a site of interest into a site of contagion, only then to be blessed along with the surrounding land as a place of promise. While the Kirtland Temple still remained an ambiguous site for many Church of Jesus Christ of Latter-day Saints pilgrims, Church of Jesus Christ of Latter-day Saints agents on the ground in Cleveland worked out a story that could explain Reorganized Church of Jesus Christ of Latter Day Saints' possession of the temple while still embracing it as a holy site. This resanctification of sacred space offers several insights into the study of sacred space that may be “useful to think with.” First, this case study illustrates the power of middling agents in creating and sustaining sacred spaces. Second, it illustrates that the creation and maintenance of sacred space may be one strategy that religious groups use to answer theodical questions, or questions about the presence of evil.

All the Memory in the World, All the Music in the World: Mediating Musical Patrimony in the Digital Age

In this article, I will examine the internet through the lens of consumption and waste studies. The internet will be conceived of as the place where the cultural waste of music – in the form of marginal artefacts and obsolete media (such as vinyl records, tapes, and ephemera) – can effectively be excavated, recirculated and re-mediated by means of systematic digitisation and uploading. The redemptive role of popular and spontaneous digital archives (such as the video platform YouTube or dedicated audio blogs) will be critically examined. Complementarily, I will underline the idea that the internet also encourages a paradoxical return of tangible artefacts, as the work of digital music collectors may prompt the actual reissue of previously lost music objects (a tendency that is exemplified in the UK by the work of British contemporary reissue record labels such as Trunk Records or Finders Keepers). The internet will be discussed as an ambiguous site of redemption, forming the basis for a nostalgic retro-consumption of music. As such, it will be conceived of as a site of memory and as a possible archive, though the ambiguity of such a term will be discussed. I will reflect upon the cultural meaning of digital archives that, as they are ceaselessly renewed, continue to erase themselves. Lastly, I will suggest that the forms of redemption that are enabled by the internet are strictly inseparable from the production of further layers of cultural waste. Departing from Straw's assertion that the internet ‘has strengthened the cultural weight of the past, increasing its intelligibility and accessibility’ (2007, 4), I will point out that the internet may accelerate the processes of cultural obsolescence and oblivion that it seeks to suspend.