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1.
Nature ; 603(7902): 679-686, 2022 03.
Article in English | MEDLINE | ID: mdl-35042229

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
2.
Vet Med Sci ; 9(4): 1465-1472, 2023 07.
Article in English | MEDLINE | ID: mdl-37119524

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 from Gaborone, Botswana that presented overt clinical signs (flu-like symptoms, dry hacking cough and mild dyspnoea). It was only sampled a posteriori, because three adult owners were diagnosed with SARS-CoV-2 infection. Next-generation sequencing based on Oxford Nanopore Technology (ONT) 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 real cycle threshold (qCt) value of 36 based on the Nucleocapsid (N) gene. Descriptive comparisons to known sequences in Botswana and internationally were made using mutation profiling analysis and phylogenetic inferences. Human samples 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 sublineage 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 Spike (S) region mutation profiling, we performed phylogenetic analysis including 30 Delta sequences publicly available reference also isolated from dogs. In addition, we performed another exploratory analysis to investigate the phylogenetic relatedness of sequence isolated from dog with those from humans in Botswana (n = 1303) as of 31 March 2022 and of same sublineage. Expectedly, the sequence formed a cluster with Delta sublineages - AY.43, AY.116 and B.1.617.2 - circulating in 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.


Subject(s)
COVID-19 , Dog Diseases , Wolves , Humans , Male , Dogs , Animals , SARS-CoV-2/genetics , Botswana/epidemiology , COVID-19/veterinary , Phylogeny , Dog Diseases/diagnosis , Dog Diseases/epidemiology
3.
AIDS ; 19 Suppl 2: S19-24, 2005 May.
Article in English | MEDLINE | ID: mdl-15930837

ABSTRACT

OBJECTIVE: Antenatal clinic (ANC)-based surveillance through unlinked anonymous testing (UAT) for HIV without informed consent provides solid long-term trend data in resource-constrained countries with generalized epidemics. The rapid expansion of the prevention of mother-to-child transmission (PMTCT) and voluntary counseling and testing (VCT) programmes prompts the question regarding their utility for HIV surveillance and their potential to replace UAT-based ANC surveillance. METHODS: Four presentations on the use of PMTCT or VCT data for HIV surveillance were presented at a recent international conference. The main findings are presented in this paper, and the operational and epidemiological aspects of using PMTCT or VCT data for surveillance are considered. RESULTS: VCT data in Uganda confirm the falling trend in HIV prevalence observed in ANC surveillance. Thailand, a country with nationwide PMTCT coverage and a very high acceptance of HIV testing, has replaced UAT data in favor of PMTCT data for surveillance. Studies from Botswana and Kenya showed that PMTCT-based HIV prevalences was similar, but the quality and availability of the PMTCT data varied. CONCLUSION: The strength of UAT lies in the absence of selection bias and the availability of individual data. Conversely, the quantity of VCT and PMTCT programme testing data often exceed those in UAT, but may be subject to bias due to self-selection or test refusal. When using VCT or PMTCT data for surveillance, investigators must consider these caveats, as well as their varying data quality, accessibility, and availability of individual records.


Subject(s)
Counseling , HIV Infections/transmission , Infectious Disease Transmission, Vertical/prevention & control , Pregnancy Complications, Infectious/prevention & control , Adolescent , Adult , Africa/epidemiology , Age Distribution , Anonymous Testing , Female , HIV Infections/prevention & control , Humans , Pregnancy , Prenatal Diagnosis/methods , Prevalence , Thailand/epidemiology
4.
Antivir Chem Chemother ; 16(2): 103-15, 2005.
Article in English | MEDLINE | ID: mdl-15889533

ABSTRACT

Current HIV-1 antiretroviral (ARV) drug resistance knowledge is limited to HIV-1 subtype B (HIV-1B). We addressed whether unique genetic and phenotypic properties of HIV-1 subtype C (HIV-1C), southern Africa's most prevalent subtype, may foment earlier and/or distinct resistance mutations. Population-level HIV-1C genotypes were evaluated with respect to drug resistance prevalence before Botswana's public ARV treatment programme began. Viruses were genotyped from 11 representative districts of northern and southern Botswana, and consensus sequences from these 71 individuals and 51 previously reported sequences from HIV-positive blood donors were constructed. Phylogenetic analysis classified all 71 sequences but one, which exhibited pol gene mosaicism, as HIV-1C. The protease and reverse transcriptase coding region had no detectable known primary mutations associated with HIV-1B protease inhibitor (PI) drug resistance. Secondary mutations associated with PI drug resistance were found in all sequences. Several HIV-1C-specific polymorphic sites were found across the pol gene. Northern and southern Botswana viral sequences showed no significant differences from each other. Population genotyping shows that, without countrywide ARV treatment, HIV-1C-infected Batswana harbour virtually no primary mutations known to confer resistance to the three major HIV-1B ARV drug classes. Some secondary PI mutations and polymorphic sites in the protease enzyme necessitate continuous population monitoring, particularly after introduction of countrywide ARV treatment in Botswana. Although its PI resistance development rate and kinetics are not known, our data may suggest increased susceptibility and readiness of HIV-1C to develop resistance under drug pressure when the PI class of drugs is used.


Subject(s)
Anti-HIV Agents/pharmacology , Anti-HIV Agents/therapeutic use , Drug Resistance, Viral , HIV Infections/drug therapy , HIV-1/drug effects , Amino Acid Sequence , Botswana/epidemiology , Drug Resistance, Viral/genetics , Genotype , HIV Infections/epidemiology , HIV-1/genetics , Humans , Molecular Sequence Data , Mutation , Phylogeny , Polymorphism, Genetic
5.
Clin Diagn Lab Immunol ; 11(5): 930-5, 2004 Sep.
Article in English | MEDLINE | ID: mdl-15358655

ABSTRACT

CD4+-lymphocyte counts (LCs) play a crucial role in the management and monitoring of HIV infection. Variability in CD4+ LCs has been reported to occur as a result of measurement techniques and/or biological variations. We report on the CD4+ LCs of healthy human immunodeficiency virus (HIV)-seronegative adults in Botswana. Samples were obtained from HIV-seronegative blood donors. The median CD4+ LC was 726 cells/mm3 (for females, 782 cells/mm3; for males, 698 cells/mm3). The median CD8+ LC was 488 cells/mm3 (for females, 494 cells/mm3; for males, 485 cells/mm3). The median CD4+-to-CD8+ ratio was 1.57 (for females, 1.66; for males, 1.51). Our findings of low CD4+ LCs among HIV-negative adults in Botswana are significant and have important implications for the management of HIV disease in the population of this sub-Saharan African country.


Subject(s)
CD4-Positive T-Lymphocytes/cytology , HIV Seronegativity , Adult , Botswana/epidemiology , CD4 Lymphocyte Count , CD4-CD8 Ratio , Female , HIV Infections/diagnosis , Humans , Male , Reference Values , Sentinel Surveillance
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