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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.

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.

4.
South African Medical Journal ; 111(6):570-574, 2021.
Article in English | MEDLINE | ID: covidwho-1353346

ABSTRACT

BACKGROUND: The COVID-19 pandemic has disrupted cancer diagnostic services. A decline in the number of new cancers being diagnosed over a relatively short term implies a delay in diagnosis and subsequent treatment. This delay is expected to have a negative effect on cancerrelated morbidity and mortality. The impact of the pandemic on the number of new cancer diagnoses in our setting is unknown. OBJECTIVES: To assess the impact of COVID-19 on the number of new cancers diagnosed at our institution in the first 3 months following the implementation of lockdown restrictions, by focusing on common non-cutaneous cancers. METHODS: A retrospective laboratory-based audit was performed at a large anatomical pathology laboratory in Western Cape Province, South Africa. The numbers of new diagnoses for six common cancers (breast, prostate, cervix, large bowel, oesophagus and stomach) from 1 April 2020 to 30 June 2020 were compared with the corresponding period in 2019. RESULTS: Histopathological diagnoses for the six cancers combined decreased by 193 (-36.3%), from 532 new cases in the 2019 study period to 339 in the corresponding period in 2020. Substantial declines were seen for prostate (-58.2%), oesophageal (-44.1%), breast (-32.9%), gastric (-32.6%) and colorectal cancer (-29.2%). The smallest decline was seen in cervical cancer (-7%). New breast cancers diagnosed by cytopathology declined by 61.1%. CONCLUSIONS: The first wave of the COVID-19 pandemic and the associated response resulted in a substantial decline in the number of new cancer diagnoses, implying a delay in diagnosis. Cancer-related morbidity and mortality is expected to rise as a result, with the greatest increase in mortality expected from breast and colorectal cancer.

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