Near-complete genome of SARS-CoV-2 Delta variant of concern identified in a symptomatic dog (Canis lupus familiaris) in Botswana

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.

Low CD4+ T-lymphocyte values in human immunodeficiency virus-negative adults in Botswana

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.

Comparison between c-ELISA and CFT in detecting antibodies to Mycoplasma mycoides mycoides biotype SC in cattle affected by CBPP in Botswana

Contagious bovine pleuropneumonia (CBPP), caused by Mycoplasma mycoides mycoides biotype small colony (SC) (MmmSC) appears to be making a serious comeback in Africa after successful control programs in many parts of the continent during the 1960s and 1970s. Botswana, a country that has been free from the disease for more than 50 years, was affected in 1995. An eradication policy was adopted by the Government of Botswana in which 320,000 cattle in the affected district of Ngamiland, Northwestern Botswana were slaughtered. This was followed by a restocking exercise in which 70,000 cattle were sent to the outbreak areas as replacement stock. It became necessary to carry out serosurveillance in order to ensure that the disease did not reenter Botswana and to ensure that the replacement stock remained free from the disease. The specificity and sensitivity of the complement fixation test (CFT) in Botswana was assessed in 82 cattle affected by the disease and held in a double fenced quarantine camp. The newly developed competitive ELISA was made available to the National Veterinary Laboratory (NVL) through the FAO/IAEA Joint Division in Vienna, Austria. Using postmortem lesions as the gold standard and a 2 x 2 contingency table, the two tests were compared in terms of their sensitivity and specificity in detecting antibodies to MmmSC. The CFT was found to be slightly more sensitive than the c-ELISA, and this could be related to the stage of the disease. A long-term study comparing the progression of the disease with the two tests is, therefore, essential.

An outbreak of contagious bovine pleuropneumonia in Ngamiland district of north-western Botswana

An outbreak of contagious bovine pleuropneumonia (CBPP) was detected in Botswana in 1995 after more than half a century of freedom from the disease. Lung tissues, pleural fluids, nasal swabs and serum samples were examined in laboratories in Botswana, South Africa and Namibia and the findings were confirmed in Italy. The disease was confirmed as CBPP from the gross and histopathological changes in the lungs of affected animals and by the culture of the agent of CBPP, Mycoplasma mycoides subspecies mycoides, small colony variant (MmmSC). These findings were supported by the demonstration of specific complement-fixing antibodies and the production of polymerase chain reaction products of MmmSC.