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SARS-CoV-2 sequences can be reverse-transcribed and integrated into the genomes of virus-infected cells by a LINE1-mediated retrotransposition mechanism. Whole-genome sequencing (WGS) methods detected retrotransposed SARS-CoV-2 subgenomic sequences in virus-infected cells overexpressing LINE1, while an enrichment method (TagMap) identified retrotranspositions in cells that did not overexpress LINE1. LINE1 overexpression increased retrotranspositions about 1000-fold as compared to non-overexpressing cells. Nanopore WGS can directly recover retrotransposed viral and flanking host sequences, but its sensitivity depends on the depth of sequencing (a typical 20-fold sequencing depth would only examine 10 diploid cell equivalents). In contrast, TagMap enriches the host–virus junctions and can interrogate up to 20,000 cells and is able to detect rare viral retrotranspositions in LINE1 non-overexpressing cells. Although Nanopore WGS is 10–20-fold more sensitive per tested cell, TagMap can interrogate 1000–2000-fold more cells and, therefore, can identify infrequent retrotranspositions. When comparing SARS-CoV-2 infection and viral nucleocapsid mRNA transfection by TagMap, retrotransposed SARS-CoV-2 sequences were only detected in infected but not in transfected cells. Retrotransposition in virus-infected cells, in contrast to transfected cells, may be facilitated because virus infection, in contrast to viral RNA transfection, results in significantly higher viral RNA levels and stimulates LINE1 expression by causing cellular stress.

Change in sea levels, be they isostatic or eustatic, impact humans and the paleogeography they inhabit. In this paper we examine paleogeography at Iqaluktuuq, a section of the Ekalluk River, Victoria Island, Nunavut, between Tahiryuaq (Ferguson Lake) and Wellington Bay. The area’s isostatic rebound impacted the Ekalluk River’s development and the use of the area by two essential subsistence resources, Arctic char (Salvelinus alpinus) and caribou (Rangifer tarandus). This, in turn, impacted the choices of Pre-Dorset, Middle and Late Dorset, and Thule/Inuit people regarding site locations. A new relative sea-level curve developed using calibrated radiocarbon dates on marine shells and terrestrial material from archaeological sites is produced for Iqaluktuuq. Based on the data, large scale (1:50,000) paleogeography maps are presented for the period of human occupation of Iqaluktuuq, 3100 calibrated years Before Present (B.P. cal) to present, revealing how paleogeography impacts people’s settlement choices.