The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The Case of the Rouged Corpse: Shakespeare, Malone, and the Modern Subject

This report, or meditation, reflects on some highly selective features of the ongoing debate about the materiality of Shakespeare's texts (and by extension of any text), and the new challenges thrown down, often in a spirit of revolutionary fervor, to contest what had been thought of as received notions of scholarship, editorial practice, and even the pursuit of literary study itself.Over the last few years a series of articles (many of them in the journal 'Textual Practice) have debated the protocols, value, and implications of idealistic versus materialistic approaches to the play texts (and indeed the sonnets) that stemmed from Margreta de Grazia's 'Shakespeare Verbatim: The Reproduction of Authenticity and the 1790 Apparatus' (1991) and from de Grazia and Peter Stallybrass's later article "The Materiality of the Shakespearean Text," which appeared in 'Shakespeare Quarterly' in 1993.The whole question of editorial practice has become a topic of intense theoretical discussion - not only regarding editorial practice in relation to the texts of Shakespeare but also regarding early modern literature at large and, by a logical extension, editorial intervention in all texts

Historicizing Irony: The Case of Milton and the Restoration

In September 1660 Thomas Rugg, professional barber and amateur court and social observer, reader of newsbooks, pamphlets and broadsides, listener at street corners and coffee houses, noted in his 'Diurnal' of the years 1659-1661 the sudden craze for novelty tobacco boxes:"At this time great store of tobacco boxes was made, the outside of the box lide the late Kinge, the inside of the box lide the present King Charles the Second, and one the inside of the bottome the picture of Oliver Cromwell, leaninge to a post and gallow tree over his heade, and about his neck a haulter tied to the tree, and by him the pictuer of the devill, wide-mouthed."Rugg then explains these ironical juxtapositions-familiar as they arein the Restoration context- in a rather surprising way: his responseto the rise and fall of the princes of the earth is medieval or, onecould also say, 'Miltonic'. Instead of the customary sarcastic crowingover Cromwell's reversal he offers, in this cockpit of partisanship, a curiously detached formula that embraces the two Charles as well asCromwell in its moral orbit: "so that men in great power (right orwrong goten), are admired, but once fallen from that are the mostdispiseable men that are.

Crull, Jodocus

Crull, Jodocus (d. 1713/14), writer and translator, was a native of Hamburg who studied medicine at Leiden (MD, 1679) and thereafter settled in England. He was admitted MD of Cambridge by incorporation on 7 August 1681 and licentiate of the Royal College of Physicians on 22 December 1692. Although elected a fellow of the Royal Society on23 and admitted on 30 November 1681, his name was omitted from the annual lists, presumably from inability to pay the fees. Amongthe Sloane Manuscripts (no. 4041, fol. 288) is a letter from Crull canvassing votes at the election of a navy physician, but he apparently had little success in his profession and turned to translating and compiling for the booksellers. He resided in both London and the country: he is identified on the Royal College of Physicians list as a 'country' member, and his publication Denmark Vindicated (1694) is 'sent from a gentleman in the country, to hisfriend in London'

Early Modern English Lives: Autobiography and Self-Representation 1500-1660

In what has been commonly regarded as one of the earliest examples of 'modern' autobiographical writing in English - in the sense of a sustained life-narrative consciously designed with a beginning, middle, and end - Thomas Whythorne's manuscript, written about 1576 and discovered in 1955, 'lay[s] open unto you the most part of all my private affairs and secrets', and is structured along the 'ages of man' divisions. The full title of Whythorne's combined life story and collection of musical compositions is; 'A book of songs and sonetts, with longe discourses sett with them, of the chylds lypfe, together with A yoong mans lyfe, and entring into the old mans lyfe. devysed and written with A new Orthografye by Thomas Whythrony, gent'