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

Diogo Antônio Feijó e Romualdo Antônio de Seixas: regalistas e romanizados na formação do Estado nacional brasileiro (1820-1840)

Exportado OPUSMade available in DSpace on 2019-08-12T08:39:45Z (GMT). No. of bitstreams: 1 tesegabrielab_lio.pdf: 2223112 bytes, checksum: 1614f9b4263cada84288dadb40715dee (MD5) Previous issue date: 13Atentando para a histórica heterogeneidade da formação intelectual e da ação política dos representantes da hierarquia eclesiástica e de seus interlocutores, o presente trabalho privilegiará o estudo de duas tendências político-eclesiológicas que começaram a se esboçar noPrimeiro Reinado e intensificaram seus embates durante as Regências. Cada uma dessas tendências, na cena pública, teve suas lideranças nas figuras de dois importantes sacerdotes, protagonistas do processo aqui analisado, nomeadamente, o paulista Diogo Antônio Feijó,regente do Império brasileiro, e D. Romualdo Antônio de seixas, arcebispo da Bahia. Diogo Feijó e Romualdo Seixas produziram um vasto e multifacetado repertório intelectual e projetaram-se no cenário político coevo. No que se refere às balizas cronológicas da tese,consideram-se fundamentais as duas primeiras décadas da formação do Estado nacional brasileiro. Durante o referido período, assistiu-se à ascensão do clero regalista liderado por Feijó, juntamente com o grupo político liberal moderado e também ao dissenso no seio dessegrupo. Entre as duas alas formadas no interior dos moderados, divergências incontornáveis tornaram-se evidentes e alimentaram o Regresso conservador. Esse movimento contou com a liderança de Bernardo Pereira de Vasconcelos, tendo a seu lado D. Romualdo Seixas e outras personalidades ligadas ao clero contrarrevolucionário, ortodoxo e romanizado. O político mineiro e o sacerdote paraense estavam entre os protagonistas da ferrenha oposição empreendida, a partir do Legislativo, à regência de Diogo Antônio Feijó. Subsequente àsreformas do Ato Adicional de 1834, a ofensiva regressista foi fundamental para a consolidação do núcleo político Saquarema e para a gênese do Partido Conservador.Paying attention to the historical heterogeneity of intellectual formation and to the political action of the ecclesiastical hierarchys representatives and their partners, this work will privilege the study of two political and ecclesiological tendencies that began to draft in the First Kingdom and intensified their disputes during the Regencies. Each of these trends had priests at its leadership in the public sphere, namely, Regent Diogo Antônio Feijó, regent of the Brazilian Empire, and Archbishop Romualdo Antônio de Seixas. Feijó and Romualdo produced a vast intellectual repertoire and projected themselves on the coeval political scene. Concerning the chronological beacons of this work, the first two decades of the formation of the Brazilian national State are considered fundamental. That period witnessed the rise of the regalist clergyled by Feijó, along with the moderate liberal political group and also the dissension within this group. Between the two wings formed within the moderates, uncontrollable divergences became evident and nourished the conservative Regress. This movement had the leadership ofBernardo Pereira de Vasconcelos, having at his side D. Romualdo Seixas and other personalities linked to a counterrevolutionary, orthodox and Romanized clergy. Vasconcelos and Romualdo were among the protagonists of the fierce opposition undertaken to the regency of DiogoAntônio Feijó. Subsequent to the reforms of the Additional Act of 1834, the regressive offensive was fundamental to the creation of the Saquaremas political nucleus and to the genesis of the Conservative Party