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Tegally, H.; San, J. E.; Cotten, M.; Moir, M.; Tegomoh, B.; Mboowa, G.; Martin, D. P.; Baxter, C.; Lambisia, A. W.; Diallo, A.; Amoako, D. G.; Diagne, M. M.; Sisay, A.; Zekri, A. N.; Gueye, A. S.; Sangare, A. K.; Ouedraogo, A. S.; Sow, A.; Musa, A. O.; Sesay, A. K.; Abias, A. G.; Elzagheid, A. I.; Lagare, A.; Kemi, A. S.; Abar, A. E.; Johnson, A. A.; Fowotade, A.; Oluwapelumi, A. O.; Amuri, A. A.; Juru, A.; Kandeil, A.; Mostafa, A.; Rebai, A.; Sayed, A.; Kazeem, A.; Balde, A.; Christoffels, A.; Trotter, A. J.; Campbell, A.; Keita, A. K.; Kone, A.; Bouzid, A.; Souissi, A.; Agweyu, A.; Naguib, A.; Gutierrez, A. V.; Nkeshimana, A.; Page, A. J.; Yadouleton, A.; Vinze, A.; Happi, A. N.; Chouikha, A.; Iranzadeh, A.; Maharaj, A.; Batchi-Bouyou, A. L.; Ismail, A.; Sylverken, A. A.; Goba, A.; Femi, A.; Sijuwola, A. E.; Marycelin, B.; Salako, B. L.; Oderinde, B. S.; Bolajoko, B.; Diarra, B.; Herring, B. L.; Tsofa, B.; Lekana-Douki, B.; Mvula, B.; Njanpop-Lafourcade, B. M.; Marondera, B. T.; Khaireh, B. A.; Kouriba, B.; Adu, B.; Pool, B.; McInnis, B.; Brook, C.; Williamson, C.; Nduwimana, C.; Anscombe, C.; Pratt, C. B.; Scheepers, C.; Akoua-Koffi, C. G.; Agoti, C. N.; Mapanguy, C. M.; Loucoubar, C.; Onwuamah, C. K.; Ihekweazu, C.; Malaka, C. N.; Peyrefitte, C.; Grace, C.; Omoruyi, C. E.; Rafaï, C. D.; Morang'a, C. M.; Erameh, C.; Lule, D. B.; Bridges, D. J.; Mukadi-Bamuleka, D.; Park, D.; Rasmussen, D. A.; Baker, D.; Nokes, D. J.; Ssemwanga, D.; Tshiabuila, D.; Amuzu, D. S. Y.; Goedhals, D.; Grant, D. S.; Omuoyo, D. O.; Maruapula, D.; Wanjohi, D. W.; Foster-Nyarko, E.; Lusamaki, E. K.; Simulundu, E.; Ong'era, E. M.; Ngabana, E. N.; Abworo, E. O.; Otieno, E.; Shumba, E.; Barasa, E.; Ahmed, E. B.; Ahmed, E. A.; Lokilo, E.; Mukantwari, E.; Philomena, E.; Belarbi, E.; Simon-Loriere, E.; Anoh, E. A.; Manuel, E.; Leendertz, F.; Taweh, F. M.; Wasfi, F.; Abdelmoula, F.; Takawira, F. T.; Derrar, F.; Ajogbasile, F. V.; Treurnicht, F.; Onikepe, F.; Ntoumi, F.; Muyembe, F. M.; Ragomzingba, F. E. Z.; Dratibi, F. A.; Iyanu, F. A.; Mbunsu, G. K.; Thilliez, G.; Kay, G. L.; Akpede, G. O.; van Zyl, G. U.; Awandare, G. A.; Kpeli, G. S.; Schubert, G.; Maphalala, G. P.; Ranaivoson, H. C.; Omunakwe, H. E.; Onywera, H.; Abe, H.; Karray, H.; Nansumba, H.; Triki, H.; Kadjo, H. A. A.; Elgahzaly, H.; Gumbo, H.; Mathieu, H.; Kavunga-Membo, H.; Smeti, I.; Olawoye, I. B.; Adetifa, I. M. O.; Odia, I.; Ben Boubaker, I. B.; Mohammad, I. A.; Ssewanyana, I.; Wurie, I.; Konstantinus, I. S.; Halatoko, J. W. A.; Ayei, J.; Sonoo, J.; Makangara, J. C.; Tamfum, J. M.; Heraud, J. M.; Shaffer, J. G.; Giandhari, J.; Musyoki, J.; Nkurunziza, J.; Uwanibe, J. N.; Bhiman, J. N.; Yasuda, J.; Morais, J.; Kiconco, J.; Sandi, J. D.; Huddleston, J.; Odoom, J. K.; Morobe, J. M.; Gyapong, J. O.; Kayiwa, J. T.; Okolie, J. C.; Xavier, J. S.; Gyamfi, J.; Wamala, J. F.; Bonney, J. H. K.; Nyandwi, J.; Everatt, J.; Nakaseegu, J.; Ngoi, J. M.; Namulondo, J.; Oguzie, J. U.; Andeko, J. C.; Lutwama, J. J.; Mogga, J. J. H.; O'Grady, J.; Siddle, K. J.; Victoir, K.; Adeyemi, K. T.; Tumedi, K. A.; Carvalho, K. S.; Mohammed, K. S.; Dellagi, K.; Musonda, K. G.; Duedu, K. O.; Fki-Berrajah, L.; Singh, L.; Kepler, L. M.; Biscornet, L.; de Oliveira Martins, L.; Chabuka, L.; Olubayo, L.; Ojok, L. D.; Deng, L. L.; Ochola-Oyier, L. I.; Tyers, L.; Mine, M.; Ramuth, M.; Mastouri, M.; ElHefnawi, M.; Mbanne, M.; Matsheka, M. I.; Kebabonye, M.; Diop, M.; Momoh, M.; Lima Mendonça, M. D. L.; Venter, M.; Paye, M. F.; Faye, M.; Nyaga, M. M.; Mareka, M.; Damaris, M. M.; Mburu, M. W.; Mpina, M. G.; Owusu, M.; Wiley, M. R.; Tatfeng, M. Y.; Ayekaba, M. O.; Abouelhoda, M.; Beloufa, M. A.; Seadawy, M. G.; Khalifa, M. K.; Matobo, M. M.; Kane, M.; Salou, M.; Mbulawa, M. B.; Mwenda, M.; Allam, M.; Phan, M. V. T.; Abid, N.; Rujeni, N.; Abuzaid, N.; Ismael, N.; Elguindy, N.; Top, N. M.; Dia, N.; Mabunda, N.; Hsiao, N. Y.; Silochi, N. B.; Francisco, N. M.; Saasa, N.; Bbosa, N.; Murunga, N.; Gumede, N.; Wolter, N.; Sitharam, N.; Ndodo, N.; Ajayi, N. A.; Tordo, N.; Mbhele, N.; Razanajatovo, N. H.; Iguosadolo, N.; Mba, N.; Kingsley, O. C.; Sylvanus, O.; Femi, O.; Adewumi, O. M.; Testimony, O.; Ogunsanya, O. A.; Fakayode, O.; Ogah, O. E.; Oludayo, O. E.; Faye, O.; Smith-Lawrence, P.; Ondoa, P.; Combe, P.; Nabisubi, P.; Semanda, P.; Oluniyi, P. E.; Arnaldo, P.; Quashie, P. K.; Okokhere, P. O.; Bejon, P.; Dussart, P.; Bester, P. A.; Mbala, P. K.; Kaleebu, P.; Abechi, P.; El-Shesheny, R.; Joseph, R.; Aziz, R. K.; Essomba, R. G.; Ayivor-Djanie, R.; Njouom, R.; Phillips, R. O.; Gorman, R.; Kingsley, R. A.; Neto Rodrigues, Rmdesa, Audu, R. A.; Carr, R. A. A.; Gargouri, S.; Masmoudi, S.; Bootsma, S.; Sankhe, S.; Mohamed, S. I.; Femi, S.; Mhalla, S.; Hosch, S.; Kassim, S. K.; Metha, S.; Trabelsi, S.; Agwa, S. H.; Mwangi, S. W.; Doumbia, S.; Makiala-Mandanda, S.; Aryeetey, S.; Ahmed, S. S.; Ahmed, S. M.; Elhamoumi, S.; Moyo, S.; Lutucuta, S.; Gaseitsiwe, S.; Jalloh, S.; Andriamandimby, S. F.; Oguntope, S.; Grayo, S.; Lekana-Douki, S.; Prosolek, S.; Ouangraoua, S.; van Wyk, S.; Schaffner, S. F.; Kanyerezi, S.; Ahuka-Mundeke, S.; Rudder, S.; Pillay, S.; Nabadda, S.; Behillil, S.; Budiaki, S. L.; van der Werf, S.; Mashe, T.; Mohale, T.; Le-Viet, T.; Velavan, T. P.; Schindler, T.; Maponga, T. G.; Bedford, T.; Anyaneji, U. J.; Chinedu, U.; Ramphal, U.; George, U. E.; Enouf, V.; Nene, V.; Gorova, V.; Roshdy, W. H.; Karim, W. A.; Ampofo, W. K.; Preiser, W.; Choga, W. T.; Ahmed, Y. A.; Ramphal, Y.; Bediako, Y.; Naidoo, Y.; Butera, Y.; de Laurent, Z. R.; Ouma, A. E. O.; von Gottberg, A.; Githinji, G.; Moeti, M.; Tomori, O.; Sabeti, P. C.; Sall, A. A.; Oyola, S. O.; Tebeje, Y. K.; Tessema, S. K.; de Oliveira, T.; Happi, C.; Lessells, R.; Nkengasong, J.; Wilkinson, E..
Science ; : eabq5358, 2022.
Article in English | PubMed | ID: covidwho-2029459

ABSTRACT

Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time and more regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and shed light on the distinct dispersal dynamics of Variants of Concern, particularly Alpha, Beta, Delta, and Omicron, on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve, while the continent faces many emerging and re-emerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

2.
Topics in Antiviral Medicine ; 30(1 SUPPL):10, 2022.
Article in English | EMBASE | ID: covidwho-1880370

ABSTRACT

Background: Botswana has a high prevalence of women living with HIV (WLHIV) and experienced a severe nationwide COVID-19 epidemic in 2021. We evaluated adverse birth outcomes among women routinely tested for COVID-19 by HIV status, during a period when few women had access to COVID-19 vaccination. Methods: The Tsepamo Study performs birth outcomes surveillance at government hospitals throughout Botswana. We analyzed data from 13 Tsepamo sites that performed routine COVID-19 screening at delivery with rapid antigen or PCR testing between Sept 1, 2020 and Sept 30, 2021 (start dates differed by site). This analysis includes singleton deliveries with known HIV status and a COVID-19 screening test between 14 days prior and 3 days after delivery. Outcomes included maternal death, preterm delivery (PTD), very preterm delivery (VPTD), small for gestational age (SGA), very small for gestational age (VSGA), stillbirth, and neonatal death. Differences in outcomes by COVID-19 and HIV status were assessed using log binomial regression adjusted for maternal age. Results: A total of 17,627 deliveries occurred at the included sites during COVID-19 screening, and 11,149 (63.3%) were screened for COVID-19;among 10,090 (99.7%) with a known HIV status, 530 (5.3%) COVID-19 tests were positive, including 141/2129 (6.6%) among WLHIV and 389/7961 (4.9%) among women without HIV (aRR 1.32, 95% CI 1.09, 1.60). Maternal deaths were reported in 19 (3.8%) women with COVID-19 and 11 (0.12%) women without COVID-19 (aRR 30.5, 95% CI 14.6, 63.7), and did not differ by HIV status. Adverse birth outcomes (any) were more common among infants born to women with COVID-19 (34.3% vs. 26.3%;aRR 1.32, 95% CI 1.16,1.49), including PTD (21.2% vs. 13.3%;aRR 1.60, 95% CI 1.34,1.90) and stillbirth (5.5% vs. 2.8%;aRR 1.89, 95% CI 1.30,2.75), and there was a trend for higher neonatal mortality (2.0% vs. 1.4%, aRR 1.5, 95% CI 0.79, 2.85). Most adverse birth outcomes were highest among infants exposed to both COVID-19 and HIV (Figure 1). Conclusion: Infants born to women with COVID-19 experienced more adverse birth outcomes than other infants, including a 2-fold risk for stillbirth. Those exposed to both COVID-19 and HIV had the highest risk for most adverse outcomes. Further research is warranted to understand the biological interaction between COVID-19, HIV infection, and adverse birth outcomes, and whether some associations were impacted by challenges in care delivery during the height of the COVID-19 epidemic in Botswana.

3.
Embase;
Preprint in English | EMBASE | ID: ppcovidwho-326897

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in southern Africa has been characterised by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, whilst the second and third waves were driven by the Beta and Delta variants respectively1–3. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng Province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, predicted to influence antibody neutralization and spike function4. Here, we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.

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