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1.
Reference Module in Biomedical Sciences ; 2021.
Article in English | PMC | ID: covidwho-1321255

ABSTRACT

Human population growth, globalization, and climate change may pose a sustained risk of emerging infections of pandemic potential. Fortunately, technological development provides tools to identify and monitor emerging epidemics. The rapid full genome characterization of the SARS coronavirus-2 (SARS-CoV-2), responsible for coronavirus infectious disease 2019 (COVID-19), and free sharing of sequence information, enabled a rapid global response. This included diagnostics, epidemiological monitoring, nonmedical interventions, and vaccine development, limiting the pandemic impact. An early and efficient response to global health threats will continue to rely on the development, refinement, and utilization of novel technologies to detect and monitor emerging infectious diseases.

2.
Clin Infect Dis ; 2022 Jul 06.
Article in English | MEDLINE | ID: covidwho-1978217

ABSTRACT

A 22-year-old female with uncontrolled advanced HIV infection was persistently infected with SARS-CoV-2 beta variant for 9 months, the virus accumulating >20 additional mutations. Antiretroviral therapy suppressed HIV and cleared SARS-CoV-2 within 6-9 weeks. Increased vigilance is warranted to benefit affected individuals and prevent the emergence of novel SARS-CoV-2 variants.

3.
Afr J Emerg Med ; 12(3): 177-182, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-1803367

ABSTRACT

Background: Identification of SARS-CoV-2 infected individuals is imperative to prevent hospital transmission, but symptom-based screening may fail to identify asymptomatic/mildly symptomatic infectious children and their caregivers. Methods: A COVID-19 period prevalence study was conducted between 13 and 26 August 2020 at Tygerberg Hospital, testing all children and their accompanying asymptomatic caregivers after initial symptom screening. One nasopharyngeal swab was submitted for SARS-CoV-2 using real-time reverse-transcription polymerase chain reaction (rRT-PCR). An additional Respiratory Viral 16-multiplex rRT-PCR test was simultaneously done in children presenting with symptoms compatible with possible SARS-CoV-2 infection. Results: SARS-Co-V 2 RT-PCR tests from 196 children and 116 caregivers were included in the analysis. The SARS-CoV-2 period prevalence in children was 5.6% (11/196) versus 15.5% (18/116) in asymptomatic caregivers (p<0.01). Presenting symptoms did not correlate with SARS-CoV-2 test positivity; children without typical symptoms of SARS-CoV-2 were more likely to be positive than those with typical symptoms (10.2% [10/99] vs 1% [1/97]; p<0.01). Children with typical symptoms (97/196; 49.5%) mainly presented with acute respiratory (68/97; 70.1%), fever (17/97; 17.5%), or gastro-intestinal complaints (12/97; 12.4%); Human Rhinovirus (23/81; 28.4%) and Respiratory Syncytial Virus (18/81; 22.2%) were frequently identified in this group. Children-caregiver pairs' SARS-CoV-2 tests were discordant in 83.3%; 15/18 infected caregivers' children tested negative. Symptom-based COVID-19 screening alone would have missed 90% of the positive children and 100% of asymptomatic but positive caregivers. Conclusion: Given the poor correlation between SARS-CoV-2 symptoms and RT-PCR test positivity, universal testing of children and their accompanying caregivers should be considered for emergency and inpatient paediatric admissions during high COVID-19 community transmission periods. Universal PPE and optimising ventilation is likely the most effective way to control transmission of respiratory viral infections, including SARS-CoV-2, where universal testing is not feasible. In these settings, repeated point prevalence studies may be useful to inform local testing and cohorting strategies.

4.
Tegally, Houriiyah, San, James, Cotten, Matthew, Tegomoh, Bryan, Mboowa, Gerald, Martin, Darren, Baxter, Cheryl, Moir, Monika, Lambisia, Arnold, Diallo, Amadou, Amoako, Daniel, Diagne, Moussa, Sisay, Abay, Zekri, Abdel-Rahman, Barakat, Abdelhamid, Gueye, Abdou Salam, Sangare, Abdoul, Ouedraogo, Abdoul-Salam, Sow, Abdourahmane, Musa, Abdualmoniem, Sesay, Abdul, Lagare, Adamou, Kemi, Adedotun-Sulaiman, Abar, Aden Elmi, Johnson, Adeniji, Fowotade, Adeola, Olubusuyi, Adewumi, Oluwapelumi, Adeyemi, Amuri, Adrienne, Juru, Agnes, Ramadan, Ahmad Mabrouk, Kandeil, Ahmed, Mostafa, Ahmed, Rebai, Ahmed, Sayed, Ahmed, Kazeem, Akano, Balde, Aladje, Christoffels, Alan, Trotter, Alexander, Campbell, Allan, Keita, Alpha Kabinet, Kone, Amadou, Bouzid, Amal, Souissi, Amal, Agweyu, Ambrose, Gutierrez, Ana, Page, Andrew, Yadouleton, Anges, Vinze, Anika, Happi, Anise, Chouikha, Anissa, Iranzadeh, Arash, Maharaj, Arisha, Batchi-Bouyou, Armel Landry, Ismail, Arshad, Sylverken, Augustina, Goba, Augustine, Femi, Ayoade, Sijuwola, Ayotunde Elijah, Ibrahimi, Azeddine, Marycelin, Baba, Salako, Babatunde Lawal, Oderinde, Bamidele, Bolajoko, Bankole, Dhaala, Beatrice, Herring, Belinda, Tsofa, Benjamin, Mvula, Bernard, Njanpop-Lafourcade, Berthe-Marie, Marondera, Blessing, Khaireh, Bouh Abdi, Kouriba, Bourema, Adu, Bright, Pool, Brigitte, McInnis, Bronwyn, Brook, Cara, Williamson, Carolyn, Anscombe, Catherine, Pratt, Catherine, Scheepers, Cathrine, Akoua-Koffi, Chantal, Agoti, Charles, Loucoubar, Cheikh, Onwuamah, Chika Kingsley, Ihekweazu, Chikwe, Malaka, Christian Noël, Peyrefitte, Christophe, Omoruyi, Chukwuma Ewean, Rafaï, Clotaire Donatien, Morang’a, Collins, Nokes, James, Lule, Daniel Bugembe, Bridges, Daniel, Mukadi-Bamuleka, Daniel, Park, Danny, Baker, David, Doolabh, Deelan, Ssemwanga, Deogratius, Tshiabuila, Derek, Bassirou, Diarra, Amuzu, Dominic S. Y.; Goedhals, Dominique, Grant, Donald, Omuoyo, Donwilliams, Maruapula, Dorcas, Wanjohi, Dorcas Waruguru, Foster-Nyarko, Ebenezer, Lusamaki, Eddy, Simulundu, Edgar, Ong’era, Edidah, Ngabana, Edith, Abworo, Edward, Otieno, Edward, Shumba, Edwin, Barasa, Edwine, Ahmed, El Bara, Kampira, Elizabeth, Fahime, Elmostafa El, Lokilo, Emmanuel, Mukantwari, Enatha, Cyril, Erameh, Philomena, Eromon, Belarbi, Essia, Simon-Loriere, Etienne, Anoh, Etilé, Leendertz, Fabian, Taweh, Fahn, Wasfi, Fares, Abdelmoula, Fatma, Takawira, Faustinos, Derrar, Fawzi, Ajogbasile, Fehintola, Treurnicht, Florette, Onikepe, Folarin, Ntoumi, Francine, Muyembe, Francisca, Ngiambudulu, Francisco, Zongo Ragomzingba, Frank Edgard, Dratibi, Fred Athanasius, Iyanu, Fred-Akintunwa, Mbunsu, Gabriel, Thilliez, Gaetan, Kay, Gemma, Akpede, George, George, Uwem, van Zyl, Gert, Awandare, Gordon, Schubert, Grit, Maphalala, Gugu, Ranaivoson, Hafaliana, Lemriss, Hajar, Omunakwe, Hannah, Onywera, Harris, Abe, Haruka, Karray, Hela, Nansumba, Hellen, Triki, Henda, Adje Kadjo, Herve Albéric, Elgahzaly, Hesham, Gumbo, Hlanai, mathieu, Hota, Kavunga-Membo, Hugo, Smeti, Ibtihel, Olawoye, Idowu, Adetifa, Ifedayo, Odia, Ikponmwosa, Boubaker, Ilhem Boutiba-Ben, Ssewanyana, Isaac, Wurie, Isatta, Konstantinus, Iyaloo, Afiwa Halatoko, Jacqueline Wemboo, Ayei, James, Sonoo, Janaki, Lekana-Douki, Jean Bernard, Makangara, Jean-Claude, Tamfum, Jean-Jacques, Heraud, Jean-Michel, Shaffer, Jeffrey, Giandhari, Jennifer, Musyoki, Jennifer, Uwanibe, Jessica, Bhiman, Jinal, Yasuda, Jiro, Morais, Joana, Mends, Joana, Kiconco, Jocelyn, Sandi, John Demby, Huddleston, John, Odoom, John Kofi, Morobe, John, Gyapong, John, Kayiwa, John, Okolie, Johnson, Xavier, Joicymara Santos, Gyamfi, Jones, Kofi Bonney, Joseph Humphrey, Nyandwi, Joseph, Everatt, Josie, Farah, Jouali, Nakaseegu, Joweria, Ngoi, Joyce, Namulondo, Joyce, Oguzie, Judith, Andeko, Julia, Lutwama, Julius, O’Grady, Justin, Siddle, Katherine, Victoir, Kathleen, Adeyemi, Kayode, Tumedi, Kefentse, Carvalho, Kevin Sanders, Mohammed, Khadija Said, Musonda, Kunda, Duedu, Kwabena, Belyamani, Lahcen, Fki-Berrajah, Lamia, Singh, Lavanya, Biscornet, Leon, Le.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-334191

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. One-Sentence Summary Expanding Africa SARS-CoV-2 sequencing capacity in a fast evolving pandemic.

6.
SSRN;
Preprint in English | SSRN | ID: ppcovidwho-326191

ABSTRACT

A 22-year-old female with uncontrolled advanced HIV infection was persistently infected with SARS-CoV-2 beta variant for 9 months, the virus accumulating >20 additional mutations. Antiretroviral therapy suppressed HIV and cleared SARS-CoV-2 within 6-9 weeks. Increased vigilance is warranted to benefit affected individuals and prevent the emergence of novel SARS-CoV-2 variants.

7.
2021.
Preprint in English | Other preprints | ID: ppcovidwho-296139

ABSTRACT

The Beta variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in South Africa in late 2020 and rapidly became the dominant variant, causing over 95% of infections in the country during and after the second epidemic wave. Here we show rapid replacement of the Beta variant by the Delta variant, a highly transmissible variant of concern (VOC) that emerged in India and subsequently spread around the world. The Delta variant was imported to South Africa primarily from India, spread rapidly in large monophyletic clusters to all provinces, and became dominant within three months of introduction. This was associated with a resurgence in community transmission, leading to a third wave which was associated with a high number of deaths. We estimated a growth advantage for the Delta variant in South Africa of 0.089 (95% confidence interval [CI] 0.084-0.093) per day which corresponds to a transmission advantage of 46% (95% CI 44-48) compared to the Beta variant. These data provide additional support for the increased transmissibility of the Delta variant relative to other VOC and highlight how dynamic shifts in the distribution of variants contribute to the ongoing public health threat.

8.
Nat Med ; 27(3): 440-446, 2021 03.
Article in English | MEDLINE | ID: covidwho-1319035

ABSTRACT

The first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in South Africa was identified on 5 March 2020, and by 26 March the country was in full lockdown (Oxford stringency index of 90)1. Despite the early response, by November 2020, over 785,000 people in South Africa were infected, which accounted for approximately 50% of all known African infections2. In this study, we analyzed 1,365 near whole genomes and report the identification of 16 new lineages of SARS-CoV-2 isolated between 6 March and 26 August 2020. Most of these lineages have unique mutations that have not been identified elsewhere. We also show that three lineages (B.1.1.54, B.1.1.56 and C.1) spread widely in South Africa during the first wave, comprising ~42% of all infections in the country at the time. The newly identified C lineage of SARS-CoV-2, C.1, which has 16 nucleotide mutations as compared with the original Wuhan sequence, including one amino acid change on the spike protein, D614G (ref. 3), was the most geographically widespread lineage in South Africa by the end of August 2020. An early South African-specific lineage, B.1.106, which was identified in April 2020 (ref. 4), became extinct after nosocomial outbreaks were controlled in KwaZulu-Natal Province. Our findings show that genomic surveillance can be implemented on a large scale in Africa to identify new lineages and inform measures to control the spread of SARS-CoV-2. Such genomic surveillance presented in this study has been shown to be crucial in the identification of the 501Y.V2 variant in South Africa in December 2020 (ref. 5).


Subject(s)
COVID-19/epidemiology , COVID-19/virology , SARS-CoV-2/genetics , Datasets as Topic , Genome, Viral , Humans , Molecular Typing , Mutation , Pandemics , Phylogeny , Phylogeography , Real-Time Polymerase Chain Reaction , SARS-CoV-2/classification , SARS-CoV-2/isolation & purification , Sequence Analysis, RNA , South Africa/epidemiology , Whole Genome Sequencing
9.
Viruses ; 13(6)2021 06 12.
Article in English | MEDLINE | ID: covidwho-1282640

ABSTRACT

There is a growing number of perinatally HIV-1-infected children worldwide who must maintain life-long ART. In early life, HIV-1 infection is established in an immunologically inexperienced environment in which maternal ART and immune dynamics during pregnancy play a role in reservoir establishment. Children that initiated early antiretroviral therapy (ART) and maintained long-term suppression of viremia have smaller and less diverse HIV reservoirs than adults, although their proviral landscape during ART is reported to be similar to that of adults. The ability of these early infected cells to persist long-term through clonal expansion poses a major barrier to finding a cure. Furthermore, the effects of life-long HIV persistence and ART are yet to be understood, but growing evidence suggests that these individuals are at an increased risk for developing non-AIDS-related comorbidities, which underscores the need for an HIV cure.


Subject(s)
Anti-Retroviral Agents/therapeutic use , Antiretroviral Therapy, Highly Active , Disease Reservoirs/virology , HIV Infections/virology , HIV-1/pathogenicity , Child , DNA, Viral/genetics , Female , HIV-1/genetics , Humans , Infectious Disease Transmission, Vertical , Pregnancy , Proviruses/genetics , Viral Load , Viremia/drug therapy
10.
Clin Infect Dis ; 72(12): e938-e944, 2021 06 15.
Article in English | MEDLINE | ID: covidwho-1269551

ABSTRACT

BACKGROUND: Children seem relatively protected from serious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-related disease, but little is known about children living in settings with high tuberculosis and human immunodeficiency virus (HIV) burden. This study reflects clinical data on South African children with SARS-CoV-2. METHODS: We collected clinical data of children aged <13 years with laboratory-confirmed SARS-CoV-2 presenting to Tygerberg Hospital, Cape Town, between 17 April and 24 July 2020. RESULTS: One hundred fifty-nine children (median age, 48.0 months [interquartile range {IQR}, 12.0-106.0 months]) were included. Hospitalized children (n = 62), with a median age of 13.5 months (IQR, 1.8-43.5 months) were younger than children not admitted (n = 97; median age, 81.0 months [IQR, 34.5-120.5 months]; P < .01.). Thirty-three of 159 (20.8%) children had preexisting medical conditions. Fifty-one of 62 (82.3%) hospitalized children were symptomatic; lower respiratory tract infection was diagnosed in 21 of 51 (41.2%) children, and in 11 of 16 (68.8%) children <3 months of age. Respiratory support was required in 25 of 51 (49.0%) children; 13 of these (52.0%) were <3 months of age. One child was HIV infected and 11 of 51 (21.2%) were HIV exposed but uninfected, and 7 of 51 (13.7%) children had a recent or new diagnosis of tuberculosis. CONCLUSIONS: Children <1 year of age hospitalized with SARS-CoV-2 in Cape Town frequently required respiratory support. Access to oxygen may be limited in some low- and middle-income countries, which could potentially drive morbidity and mortality. HIV infection was uncommon but a relationship between HIV exposure, tuberculosis, and SARS-CoV-2 should be explored.


Subject(s)
COVID-19 , HIV Infections , Child , Child, Preschool , HIV Infections/complications , HIV Infections/epidemiology , Hospitals , Humans , Infant , SARS-CoV-2 , South Africa/epidemiology
11.
Nature ; 592(7854): 438-443, 2021 04.
Article in English | MEDLINE | ID: covidwho-1164876

ABSTRACT

Continued uncontrolled transmission of SARS-CoV-2 in many parts of the world is creating conditions for substantial evolutionary changes to the virus1,2. Here we describe a newly arisen lineage of SARS-CoV-2 (designated 501Y.V2; also known as B.1.351 or 20H) that is defined by eight mutations in the spike protein, including three substitutions (K417N, E484K and N501Y) at residues in its receptor-binding domain that may have functional importance3-5. This lineage was identified in South Africa after the first wave of the epidemic in a severely affected metropolitan area (Nelson Mandela Bay) that is located on the coast of the Eastern Cape province. This lineage spread rapidly, and became dominant in Eastern Cape, Western Cape and KwaZulu-Natal provinces within weeks. Although the full import of the mutations is yet to be determined, the genomic data-which show rapid expansion and displacement of other lineages in several regions-suggest that this lineage is associated with a selection advantage that most plausibly results from increased transmissibility or immune escape6-8.


Subject(s)
COVID-19/virology , Mutation , Phylogeny , Phylogeography , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , COVID-19/epidemiology , COVID-19/immunology , COVID-19/transmission , DNA Mutational Analysis , Evolution, Molecular , Genetic Fitness , Humans , Immune Evasion , Models, Molecular , SARS-CoV-2/immunology , SARS-CoV-2/pathogenicity , Selection, Genetic , South Africa/epidemiology , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/metabolism , Time Factors
12.
Viruses ; 13(3)2021 03 22.
Article in English | MEDLINE | ID: covidwho-1154522

ABSTRACT

Cape Town was the first city in South Africa to experience the full impact of the coronavirus disease 2019 (COVID-19) pandemic. We acquired samples from all suspected cases and their contacts during the first month of the pandemic from Tygerberg Hospital. Nanopore sequencing generated SARS-CoV-2 whole genomes. Phylogenetic inference with maximum likelihood and Bayesian methods were used to determine lineages that seeded the local epidemic. Three patients were known to have travelled internationally and an outbreak was detected in a nearby supermarket. Sequencing of 50 samples produced 46 high-quality genomes. The sequences were classified as lineages: B, B.1, B.1.1.1, B.1.1.161, B.1.1.29, B.1.8, B.39, and B.40. All the sequences from persons under investigation (PUIs) in the supermarket outbreak (lineage B.1.8) fall within a clade from the Netherlands with good support (p > 0.9). In addition, a new mutation, 5209A>G, emerged within the Cape Town cluster. The molecular clock analysis suggests that this occurred around 13 March 2020 (95% confidence interval: 9-17 March). The phylogenetic reconstruction suggests at least nine early introductions of SARS-CoV-2 into Cape Town and an early localized transmission in a shopping environment. Genomic surveillance was successfully used to investigate and track the spread of early introductions of SARS-CoV-2 in Cape Town.


Subject(s)
COVID-19/epidemiology , SARS-CoV-2/physiology , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/virology , Disease Outbreaks , Female , Genome, Viral , Humans , Male , Middle Aged , Netherlands , Phylogeny , SARS-CoV-2/classification , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , South Africa/epidemiology , Travel , Whole Genome Sequencing , Young Adult
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