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1.
Front Public Health ; 10: 919668, 2022.
Article in English | MEDLINE | ID: covidwho-1963645

ABSTRACT

Objectives: Coronavirus disease 2019 was declared a global pandemic in March 2020 with correct and early detection of cases using laboratory testing central to the response. Hence, the establishment of quality management systems and monitoring their implementation are critical. This study describes the experience of implementing the COVID-19 Laboratory Testing and Certification Program (CoLTeP) in Africa. Methods: Private and public laboratories conducting SARS-CoV-2 testing using polymerase chain reaction were enrolled and assessed for quality and safety using the CoLTeP checklists. Results: A total of 84 laboratories from 7 countries were assessed between April 2021 to December 2021 with 52% of these from the private sector. Among them, 64% attained 5 stars and were certified. Section 4 had the highest average score of 92% and the lowest of 78% in Section 3. Also, 82% of non-conformities (NCs) were related to sample collection, transportation, and risk assessments. Non-availability, inconsistency in performing, recording, instituting corrective actions for failed internal and external quality controls were among major NCs reported. Conclusions: Laboratories identified for SARS-CoV-2 testing by public and private institutions mostly met the requirements for quality and safe testing as measured by the CoLTeP checklist.


Subject(s)
COVID-19 Testing , COVID-19 , Certification , Africa , COVID-19/diagnosis , COVID-19/epidemiology , Clinical Laboratory Techniques , Humans , Laboratories , SARS-CoV-2
2.
Nat Med ; 2022 Jun 27.
Article in English | MEDLINE | ID: covidwho-1908212

ABSTRACT

Three lineages (BA.1, BA.2 and BA.3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern predominantly drove South Africa's fourth Coronavirus Disease 2019 (COVID-19) wave. We have now identified two new lineages, BA.4 and BA.5, responsible for a fifth wave of infections. The spike proteins of BA.4 and BA.5 are identical, and similar to BA.2 except for the addition of 69-70 deletion (present in the Alpha variant and the BA.1 lineage), L452R (present in the Delta variant), F486V and the wild-type amino acid at Q493. The two lineages differ only outside of the spike region. The 69-70 deletion in spike allows these lineages to be identified by the proxy marker of S-gene target failure, on the background of variants not possessing this feature. BA.4 and BA.5 have rapidly replaced BA.2, reaching more than 50% of sequenced cases in South Africa by the first week of April 2022. Using a multinomial logistic regression model, we estimated growth advantages for BA.4 and BA.5 of 0.08 (95% confidence interval (CI): 0.08-0.09) and 0.10 (95% CI: 0.09-0.11) per day, respectively, over BA.2 in South Africa. The continued discovery of genetically diverse Omicron lineages points to the hypothesis that a discrete reservoir, such as human chronic infections and/or animal hosts, is potentially contributing to further evolution and dispersal of the virus.

4.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-335264

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.

5.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-334417

ABSTRACT

We sought to investigate whether SARS-CoV-2 was present, and to perform full-length genomic sequencing, in a 5-year-old male crossbreed dog that presented with flu-like symptoms (including a dry hacking cough and mild dyspnea) and resided in a household with 3 adults that were diagnosed with SARS CoV-2 infection. Next generation sequencing based on MinION technology was performed on amplicons that were generated using a reverse transcriptase real-time polymerase chain reaction (RT-qPCR) of confirmed positive SARS-CoV-2 nasopharyngeal and buccal swabs, as well as a bronchoalveolar lavage with mean qCt value of 36 based on the Nucleocapsid gene. Descriptive comparisons to known sequences in Botswana and internationally were made using mutation profiling analysis and phylogenetic inferences based on maximum likelihood. Samples from the dog’s owners were not available. A near-full length SARS-CoV-2 genome (~90% coverage) was successfully genotyped and classified under clade 20 O and Pango-Lineage AY.43 (Pango v.4.0.6 PLEARN-v1.3;2022-04-21), which is a sub-lineage of the Delta variant of concern (VOC) (formerly called B.1.617.2, first detected in India). We did not identify novel mutations that may be used to distinguish SARS-CoV-2 isolates from the dog and humans. In addition to S region mutation profiling, we performed phylogenetic analysis using Delta sequences from Botswana (n=1303);expectedly, the sequence isolated from the dog was closely related to the Delta sequences, particularly the AY.43, AY.116, and B.1.617.2 sub-lineages that were reported in Botswana within the same time frame. This is the first documented report of human-associated SARS-CoV-2 infection in a dog in Botswana. Although the direction of transmission remains unknown, this study further affirms the need for monitoring pets during different COVID-19 waves for possible clinically relevant SARS-CoV-2 transmissions between species.

6.
Afr J Lab Med ; 11(1): 1571, 2022.
Article in English | MEDLINE | ID: covidwho-1786160

ABSTRACT

Background: The novel coronavirus disease 2019 (COVID-19), declared a pandemic by the World Health Organization (WHO) in March 2020, has taught us about the importance of epidemic preparedness. Objective: We analysed the pre-COVID-19 preparedness of sub-Saharan African countries and how this may have influenced the trajectory of COVID-19 cases. Methods: The WHO Joint External Evaluation (JEE) tool and the Global Health Security (GHS) Index were used to determine the epidemic preparedness of countries in the WHO African Region. The relationship between pre-COVID-19 preparedness and the reported number of cases per million people was evaluated over the first 120 days of the first reported case in each country, between February 2020 and September 2020. Results: The overall performance of the 42 countries was 40% in the 19 JEE core capacities and 32% in the six GHS Index indicators. At Day 1, the mean number of cases per million population was significantly higher among countries rated as 'prepared' in the JEE legislation, policy and finance (p = 0.03), ports of entry (p = 0.001), and international health regulation coordination, communication and advocacy (p = 0.03) categories. At Day 90, countries rated as 'prepared' in the national laboratory systems (p = 0.05) and real-time surveillance (p = 0.04) JEE categories had statistically significantly fewer cases per million population. Conclusion: This analysis highlights the importance of building capacity for pandemic preparedness in Africa. The WHO African Region was not adequately prepared for the COVID-19 pandemic as measured by the WHO JEE tool and the GHS Index.

7.
Nature ; 603(7902): 679-686, 2022 03.
Article in English | MEDLINE | ID: covidwho-1638766

ABSTRACT

The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, while the second and third waves were driven by the Beta (B.1.351) and Delta (B.1.617.2) 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, B.1.1.529) 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, which are 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.


Subject(s)
COVID-19/epidemiology , COVID-19/virology , Immune Evasion , SARS-CoV-2/isolation & purification , Antibodies, Neutralizing/immunology , Botswana/epidemiology , COVID-19/immunology , COVID-19/transmission , Humans , Models, Molecular , Mutation , Phylogeny , Recombination, Genetic , SARS-CoV-2/classification , SARS-CoV-2/immunology , South Africa/epidemiology , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/immunology
8.
Viruses ; 12(7), 2020.
Article in English | MEDLINE | ID: covidwho-662128

ABSTRACT

Hepatitis B virus (HBV) is the primary cause of liver-related malignancies worldwide, and there is no effective cure for chronic HBV infection (CHB) currently. Strong immunological responses induced by T cells are associated with HBV clearance during acute infection;however, the repertoire of epitopes (epi) presented by major histocompatibility complexes (MHCs) to elicit these responses in various African populations is not well understood. In silico approaches were used to map and investigate 15-mers HBV peptides restricted to 9 HLA class II alleles with high population coverage in Botswana. Sequences from 44 HBV genotype A and 48 genotype D surface genes (PreS/S) from Botswana were used. Of the 1819 epi bindings predicted, 20.2% were strong binders (SB), and none of the putative epi bind to all the 9 alleles suggesting that multi-epitope, genotype-based, population-based vaccines will be more effective against HBV infections as opposed to previously proposed broad potency epitope-vaccines which were assumed to work for all alleles. In total, there were 297 unique epi predicted from the 3 proteins and amongst, S regions had the highest number of epi (n = 186). Epitope-densities (Depi) between genotypes A and D were similar. A number of mutations that hindered HLA-peptide binding were observed. We also identified antigenic and genotype-specific peptides with characteristics that are well suited for the development of sensitive diagnostic kits. This study identified candidate peptides that can be used for developing multi-epitope vaccines and highly sensitive diagnostic kits against HBV infection in an African population. Our results suggest that viral variability may hinder HBV peptide-MHC binding, required to initiate a cascade of immunological responses against infection.

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