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PLoS Negl Trop Dis ; 15(4): e0009335, 2021 04.
Article in English | MEDLINE | ID: covidwho-1201598


Since late 2019, the coronavirus disease 2019 (COVID-19) outbreak, caused by SARS-CoV-2, has rapidly evolved to become a global pandemic. Each country was affected but with a varying number of infected cases and mortality rates. Africa was hit late by the pandemic but the number of cases rose sharply. In this study, we investigated 224 SARS-CoV-2 genome sequences from the Global Initiative on Sharing Avian Influenza Data (GISAID) in the early part of the outbreak, of which 69 were from Africa. We analyzed a total of 550 mutations by comparing them with the reference SARS-CoV-2 sequence from Wuhan. We classified the mutations observed based on country and region, and afterwards analyzed common and unique mutations on the African continent as a whole. Correlation analyses showed that the duo variants ORF1ab/RdRp 4715L and S protein 614G variants, which are strongly linked to fatality rate, were not significantly and positively correlated with fatality rates (r = -0.03757, P = 0.5331 and r = -0.2876, P = 0.6389, respectively), although increased number of cases correlated with number of deaths (r = 0.997, P = 0.0002). Furthermore, most cases in Africa were mainly imported from American and European countries, except one isolate with no mutation and was similar to the original isolate from Wuhan. Moreover, unique mutations specific to countries were identified in the early phase of the outbreak but these mutations were not regional-specific. There were common mutations in all isolates across the continent as well as similar isolate-specific mutations in different regions. Our findings suggest that mutation is rapid in SARS-CoV-2 in Africa and although these mutations spread across the continent, the duo variants could not possibly be the sole cause of COVID-19 deaths in Africa in the early phase of the outbreak.

COVID-19/virology , SARS-CoV-2/genetics , Africa/epidemiology , COVID-19/epidemiology , Disease Outbreaks , Europe/epidemiology , Genome, Viral , Genomics , Humans , Mutation , Pandemics , Phylogeny , Polyproteins , SARS-CoV-2/classification , Spike Glycoprotein, Coronavirus/genetics , Viral Proteins/genetics
BMC Vet Res ; 16(1): 405, 2020 Oct 27.
Article in English | MEDLINE | ID: covidwho-895005


BACKGROUND: Apart from the huge worldwide economic losses often occasioned by bovine coronavirus (BCoV) to the livestock industry, particularly with respect to cattle rearing, continuous surveillance of the virus in cattle and small ruminants is essential in monitoring variations in the virus that could enhance host switching. In this study, we collected rectal swabs from a total of 1,498 cattle, sheep and goats. BCoV detection was based on reverse transcriptase polymerase chain reaction. Sanger sequencing of the partial RNA-dependent RNA polymerase (RdRp) region for postive samples were done and nucleotide sequences were compared with homologous sequences from the GenBank. RESULTS: The study reports a BCoV prevalence of 0.3%, consisting of 4 positive cases; 3 goats and 1 cattle. Less than 10% of all the animals sampled showed clinical signs such as diarrhea and respiratory distress except for high temperature which occurred in > 1000 of the animals. However, none of the 4 BCoV positive animals manifested any clinical signs of the infection at the time of sample collection. Bayesian majority-rule cladogram comparing partial and full length BCoV RdRp genes obtained in the study to data from the GenBank revealed that the sequences obtained from this study formed one large monophyletic group with those from different species and countries. The goat sequences were similar to each other and clustered within the same clade. No major variations were thus observed between our isolates and those from elsewhere. CONCLUSIONS: Given that Ghana predominantly practices the extensive and semi-intensive systems of animal rearing, our study highlights the potential for spillover of BCoV to small ruminants in settings with mixed husbandry and limited separation between species.

Cattle Diseases/virology , Coronavirus Infections/veterinary , Coronavirus, Bovine/isolation & purification , Goat Diseases/virology , Sheep Diseases/virology , Animals , Base Sequence , Bayes Theorem , Cattle , Cattle Diseases/epidemiology , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Coronavirus, Bovine/genetics , Diarrhea/veterinary , Ghana/epidemiology , Goat Diseases/epidemiology , Goats , Phylogeny , Prevalence , RNA-Dependent RNA Polymerase/genetics , Respiratory Distress Syndrome/veterinary , Reverse Transcriptase Polymerase Chain Reaction/veterinary , Sheep , Sheep Diseases/epidemiology
Vet Microbiol ; 241: 108544, 2020 Feb.
Article in English | MEDLINE | ID: covidwho-823170


Cattle, goats and sheep are dominant livestock species in sub-Saharan Africa, with sometimes limited information on the prevalence of major infectious diseases. Restrictions due to notifiable epizootics complicate the exchange of samples in surveillance studies and suggest that laboratory capacities should be established domestically. Bovine Coronavirus (BCoV) causes mainly enteric disease in cattle. Spillover to small ruminants is possible. Here we established BCoV serology based on a recombinant immunofluorescence assay for cattle, goats and sheep, and studied the seroprevalence of BCoV in these species in four different locations in the Greater Accra, Volta, Upper East, and Northern provinces of Ghana. The whole sampling and testing was organized and conducted by a veterinary school in Kumasi, Ashanti Region of Ghana. Among sampled sheep (n = 102), goats (n = 66), and cattle (n = 1495), the seroprevalence rates were 25.8 %, 43.1 % and 55.8 %. For cattle, seroprevalence was significantly higher on larger farms (82.2 % vs 17.8 %, comparing farms with >50 or <50 animals; p = 0.027). Highest prevalence was seen in the Northern province with dry climate, but no significant trend following the north-south gradient of sampling sites was detected. Our study identifies a considerable seroprevalence for BCoV in Ghana and provides further support for the spillover of BCoV to small ruminants in settings with mixed husbandry and limited separation between species.

Cattle Diseases/epidemiology , Coronavirus Infections/veterinary , Coronavirus, Bovine/immunology , Goat Diseases/epidemiology , Sheep Diseases/epidemiology , Age Distribution , Animals , Cattle , Cattle Diseases/immunology , Cattle Diseases/transmission , Cattle Diseases/virology , Cluster Analysis , Coronavirus Infections/epidemiology , Coronavirus Infections/immunology , Coronavirus Infections/transmission , Cross-Sectional Studies , Female , Ghana/epidemiology , Goat Diseases/immunology , Goat Diseases/transmission , Goat Diseases/virology , Goats , Lactation , Male , Multivariate Analysis , Risk Factors , Seroepidemiologic Studies , Sex Distribution , Sheep , Sheep Diseases/immunology , Sheep Diseases/transmission , Sheep Diseases/virology