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1.
medrxiv; 2022.
Preprint in English | medRxiv | ID: ppzbmed-10.1101.2022.11.22.22282629

ABSTRACT

In many regions of the world, the Alpha, Beta and Gamma SARS-CoV-2 Variants of Concern (VOCs) co-circulated during 2020-21 and fueled waves of infections. During 2021, these variants were almost completely displaced by the Delta variant, causing a third wave of infections worldwide. This phenomenon of global viral lineage displacement was observed again in late 2021, when the Omicron variant disseminated globally. In this study, we use phylogenetic and phylogeographic methods to reconstruct the dispersal patterns of SARS-CoV-2 VOCs worldwide. We find that the source-sink dynamics of SARS-CoV-2 varied substantially by VOC, and identify countries that acted as global hubs of variant dissemination, while other countries became regional contributors to the export of specific variants. We demonstrate a declining role of presumed origin countries of VOCs to their global dispersal: we estimate that India contributed <15% of all global exports of Delta to other countries and South Africa <1-2% of all global Omicron exports globally. We further estimate that >80 countries had received introductions of Omicron BA.1 100 days after its inferred date of emergence, compared to just over 25 countries for the Alpha variant. This increased speed of global dissemination was associated with a rebound in air travel volume prior to Omicron emergence in addition to the higher transmissibility of Omicron relative to Alpha. Our study highlights the importance of global and regional hubs in VOC dispersal, and the speed at which highly transmissible variants disseminate through these hubs, even before their detection and characterization through genomic surveillance.

2.
medrxiv; 2022.
Preprint in English | medRxiv | ID: ppzbmed-10.1101.2022.05.01.22274406

ABSTRACT

South Africa's fourth COVID-19 wave was driven predominantly by three lineages (BA.1, BA.2 and BA.3) of the SARS-CoV-2 Omicron variant of concern. We have now identified two new lineages, BA.4 and BA.5. The spike proteins of BA.4 and BA.5 are identical, and comparable to BA.2 except for the addition of 69-70del, L452R, F486V and the wild type amino acid at Q493. The 69-70 deletion in spike allows these lineages to be identified by the proxy marker of S-gene target failure with the TaqPath COVID-19 qPCR assay. BA.4 and BA.5 have rapidly replaced BA.2, reaching more than 50% of sequenced cases in South Africa from the first week of April 2022 onwards. Using a multinomial logistic regression model, we estimate growth advantages for BA.4 and BA.5 of 0.08 (95% CI: 0.07 - 0.09) and 0.12 (95% CI: 0.09 - 0.15) per day respectively over BA.2 in South Africa.

3.
Houriiyah Tegally; James E. San; Matthew Cotten; Bryan Tegomoh; Gerald Mboowa; Darren P. Martin; Cheryl Baxter; Monika Moir; Arnold Lambisia; Amadou Diallo; Daniel G. Amoako; Moussa M. Diagne; Abay Sisay; Abdel-Rahman N. Zekri; Abdelhamid Barakat; Abdou Salam Gueye; Abdoul K. Sangare; Abdoul-Salam Ouedraogo; Abdourahmane SOW; Abdualmoniem O. Musa; Abdul K. Sesay; Adamou LAGARE; Adedotun-Sulaiman Kemi; Aden Elmi Abar; Adeniji A. Johnson; Adeola Fowotade; Adewumi M. Olubusuyi; Adeyemi O. Oluwapelumi; Adrienne A. Amuri; Agnes Juru; Ahmad Mabrouk Ramadan; Ahmed Kandeil; Ahmed Mostafa; Ahmed Rebai; Ahmed Sayed; Akano Kazeem; Aladje Balde; Alan Christoffels; Alexander J. Trotter; Allan Campbell; Alpha Kabinet KEITA; Amadou Kone; Amal Bouzid; Amal Souissi; Ambrose Agweyu; Ana V. Gutierrez; Andrew J. Page; Anges Yadouleton; Anika Vinze; Anise N. Happi; Anissa Chouikha; Arash Iranzadeh; Arisha Maharaj; Armel Landry Batchi-Bouyou; Arshad Ismail; Augustina Sylverken; Augustine Goba; Ayoade Femi; Ayotunde Elijah Sijuwola; Azeddine Ibrahimi; Baba Marycelin; Babatunde Lawal Salako; Bamidele S. Oderinde; Bankole Bolajoko; Beatrice Dhaala; Belinda L. Herring; Benjamin Tsofa; Bernard Mvula; Berthe-Marie Njanpop-Lafourcade; Blessing T. Marondera; Bouh Abdi KHAIREH; Bourema Kouriba; Bright Adu; Brigitte Pool; Bronwyn McInnis; Cara Brook; Carolyn Williamson; Catherine Anscombe; Catherine B. Pratt; Cathrine Scheepers; Chantal G. Akoua-Koffi; Charles N. Agoti; Cheikh Loucoubar; Chika Kingsley Onwuamah; Chikwe Ihekweazu; Christian Noel MALAKA; Christophe Peyrefitte; Chukwuma Ewean Omoruyi; Clotaire Donatien Rafai; Collins M. Morang'a; D. James Nokes; Daniel Bugembe Lule; Daniel J. Bridges; Daniel Mukadi-Bamuleka; Danny Park; David Baker; Deelan Doolabh; Deogratius Ssemwanga; Derek Tshiabuila; Diarra Bassirou; Dominic S.Y. Amuzu; Dominique Goedhals; Donald S. Grant; Donwilliams O. Omuoyo; Dorcas Maruapula; Dorcas Waruguru Wanjohi; Ebenezer Foster-Nyarko; Eddy K. Lusamaki; Edgar Simulundu; Edidah M. Ong'era; Edith N. Ngabana; Edward O. Abworo; Edward Otieno; Edwin Shumba; Edwine Barasa; EL BARA AHMED; Elmostafa EL FAHIME; Emmanuel Lokilo; Enatha Mukantwari; Erameh Cyril; Eromon Philomena; Essia Belarbi; Etienne Simon-Loriere; Etile A. Anoh; Fabian Leendertz; Fahn M. Taweh; Fares Wasfi; Fatma Abdelmoula; Faustinos T. Takawira; Fawzi Derrar; Fehintola V Ajogbasile; Florette Treurnicht; Folarin Onikepe; Francine Ntoumi; Francisca M. Muyembe; FRANCISCO NGIAMBUDULU; Frank Edgard ZONGO Ragomzingba; Fred Athanasius DRATIBI; Fred-Akintunwa Iyanu; Gabriel K. Mbunsu; Gaetan Thilliez; Gemma L. Kay; George O. Akpede; George E Uwem; Gert van Zyl; Gordon A. Awandare; Grit Schubert; Gugu P. Maphalala; Hafaliana C. Ranaivoson; Hajar Lemriss; Hannah E Omunakwe; Harris Onywera; Haruka Abe; HELA KARRAY; Hellen Nansumba; Henda Triki; Herve Alberic ADJE KADJO; Hesham Elgahzaly; Hlanai Gumbo; HOTA mathieu; Hugo Kavunga-Membo; Ibtihel Smeti; Idowu B. Olawoye; Ifedayo Adetifa; Ikponmwosa Odia; Ilhem Boutiba-Ben Boubaker; Isaac Ssewanyana; Isatta Wurie; Iyaloo S Konstantinus; Jacqueline Wemboo Afiwa Halatoko; James Ayei; Janaki Sonoo; Jean Bernard LEKANA-DOUKI; Jean-Claude C. Makangara; Jean-Jacques M. Tamfum; Jean-Michel Heraud; Jeffrey G. Shaffer; Jennifer Giandhari; Jennifer Musyoki; Jessica N. Uwanibe; Jinal N. Bhiman; Jiro Yasuda; Joana Morais; Joana Q. Mends; Jocelyn Kiconco; John Demby Sandi; John Huddleston; John Kofi Odoom; John M. Morobe; John O. Gyapong; John T. Kayiwa; Johnson C. Okolie; Joicymara Santos Xavier; Jones Gyamfi; Joseph Humphrey Kofi Bonney; Joseph Nyandwi; Josie Everatt; Jouali Farah; Joweria Nakaseegu; Joyce M. Ngoi; Joyce Namulondo; Judith U. Oguzie; Julia C. Andeko; Julius J. Lutwama; Justin O'Grady; Katherine J Siddle; Kathleen Victoir; Kayode T. Adeyemi; Kefentse A. Tumedi; Kevin Sanders Carvalho; Khadija Said Mohammed; Kunda G. Musonda; Kwabena O. Duedu; Lahcen Belyamani; Lamia Fki-Berrajah; Lavanya Singh; Leon Biscornet; Leonardo de Oliveira Martins; Lucious Chabuka; Luicer Olubayo; Lul Lojok Deng; Lynette Isabella Ochola-Oyier; Madisa Mine; Magalutcheemee Ramuth; Maha Mastouri; Mahmoud ElHefnawi; Maimouna Mbanne; Maitshwarelo I. Matsheka; Malebogo Kebabonye; Mamadou Diop; Mambu Momoh; Maria da Luz Lima Mendonca; Marietjie Venter; Marietou F Paye; Martin Faye; Martin M. Nyaga; Mathabo Mareka; Matoke-Muhia Damaris; Maureen W. Mburu; Maximillian Mpina; Claujens Chastel MFOUTOU MAPANGUY; Michael Owusu; Michael R. Wiley; Mirabeau Youtchou Tatfeng; Mitoha Ondo'o Ayekaba; Mohamed Abouelhoda; Mohamed Amine Beloufa; Mohamed G Seadawy; Mohamed K. Khalifa; Mohammed Koussai DELLAGI; Mooko Marethabile Matobo; Mouhamed Kane; Mouna Ouadghiri; Mounerou Salou; Mphaphi B. Mbulawa; Mudashiru Femi Saibu; Mulenga Mwenda; My V.T. Phan; Nabil Abid; Nadia Touil; Nadine Rujeni; Nalia Ismael; Ndeye Marieme Top; Ndongo Dia; Nedio Mabunda; Nei-yuan Hsiao; Nelson Borico Silochi; Ngonda Saasa; Nicholas Bbosa; Nickson Murunga; Nicksy Gumede; Nicole Wolter; Nikita Sitharam; Nnaemeka Ndodo; Nnennaya A. Ajayi; Noel Tordo; Nokuzola Mbhele; Norosoa H Razanajatovo; Nosamiefan Iguosadolo; Nwando Mba; Ojide C. Kingsley; Okogbenin Sylvanus; Okokhere Peter; Oladiji Femi; Olumade Testimony; Olusola Akinola Ogunsanya; Oluwatosin Fakayode; Onwe E. Ogah; Ousmane Faye; Pamela Smith-Lawrence; Pascale Ondoa; Patrice Combe; Patricia Nabisubi; Patrick Semanda; Paul E. Oluniyi; Paulo Arnaldo; Peter Kojo Quashie; Philip Bejon; Philippe Dussart; Phillip A. Bester; Placide K. Mbala; Pontiano Kaleebu; Priscilla Abechi; Rabeh El-Shesheny; Rageema Joseph; Ramy Karam Aziz; Rene Ghislain Essomba; Reuben Ayivor-Djanie; Richard Njouom; Richard O. Phillips; Richmond Gorman; Robert A. Kingsley; Rosemary Audu; Rosina A.A. Carr; Saad El Kabbaj; Saba Gargouri; Saber Masmoudi; Safietou Sankhe; Sahra Isse Mohamed; Salma MHALLA; Salome Hosch; Samar Kamal Kassim; Samar Metha; Sameh Trabelsi; Sanaa Lemriss; Sara Hassan Agwa; Sarah Wambui Mwangi; Seydou Doumbia; Sheila Makiala-Mandanda; Sherihane Aryeetey; Shymaa S. Ahmed; SIDI MOHAMED AHMED; Siham Elhamoumi; Sikhulile Moyo; Silvia Lutucuta; Simani Gaseitsiwe; Simbirie Jalloh; Soafy Andriamandimby; Sobajo Oguntope; Solene Grayo; Sonia Lekana-Douki; Sophie Prosolek; Soumeya Ouangraoua; Stephanie van Wyk; Stephen F. Schaffner; Stephen Kanyerezi; Steve AHUKA-MUNDEKE; Steven Rudder; Sureshnee Pillay; Susan Nabadda; Sylvie Behillil; Sylvie L. Budiaki; Sylvie van der Werf; Tapfumanei Mashe; Tarik Aanniz; Thabo Mohale; Thanh Le-Viet; Thirumalaisamy P. Velavan; Tobias Schindler; Tongai Maponga; Trevor Bedford; Ugochukwu J. Anyaneji; Ugwu Chinedu; Upasana Ramphal; Vincent Enouf; Vishvanath Nene; Vivianne Gorova; Wael H. Roshdy; Wasim Abdul Karim; William K. Ampofo; Wolfgang Preiser; Wonderful T. Choga; Yahaya ALI ALI AHMED; Yajna Ramphal; Yaw Bediako; Yeshnee Naidoo; Yvan Butera; Zaydah R. de Laurent; Ahmed E.O. Ouma; Anne von Gottberg; George Githinji; Matshidiso Moeti; Oyewale Tomori; Pardis C. Sabeti; Amadou A. Sall; Samuel O. Oyola; Yenew K. Tebeje; Sofonias K. Tessema; Tulio de Oliveira; Christian Happi; Richard Lessells; John Nkengasong; Eduan Wilkinson.
medrxiv; 2022.
Preprint in English | medRxiv | ID: ppzbmed-10.1101.2022.04.17.22273906

ABSTRACT

Investment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massive increase in the number of sequences, exceeding 100,000 genomes generated to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence within their own borders, coupled with a decrease in sequencing turnaround time. Findings from this genomic surveillance underscores the heterogeneous nature of the pandemic but we observe repeated dissemination of SARS-CoV-2 variants within the continent. Sustained investment for genomic surveillance in Africa is needed as the virus continues to evolve, particularly in the low vaccination landscape. These investments are very crucial for preparedness and response for future pathogen outbreaks.

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