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1.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-322348

ABSTRACT

In regions lacking genomic data, analysis of sequences from the early stages of an outbreak can provide important insights into the diversity of pathogens present. Following the detection of the first imported case of COVID-19 in the Northern sector of Ghana on 13th March 2020, we have now molecularly characterized and phylogenetically analysed sequences including three (3) complete genomes of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) isolated from nine (9) patients observed in Ghana. Eight (8) of these patients reported with a recent history of foreign travel and one (1) with no history of foreign travel. We performed high throughput sequencing for 9 samples following the determination of high concentration of viral RNA. In addition, we estimated the potential impact that long distance transportation of samples to testing centres may have on sequencing outcomes. Here, two samples that were closest in terms of viral RNA concentration but transported from sites which are over 400km apart were assessed. All sequences were compared to previous sequences from Ghana and representative sequences from regions where our patients had previously travelled. Complete genomes were obtained for three (3) sequences and with another near complete genome with a coverage of 95.6%. Sequences with coverage in excess of 80% were found to belong to three lineages namely A, B.1 and B.2. Our sequences clustered in two different clades with the majority falling within a clade composed of sequences from sub-Saharan Africa. Less RNA fragmentation was seen in sample KATH23 which was collected 9km compared with sample TTH6 which was collected and transported over a distance of 400km to the testing site. The clustering of several sequences from sub-Saharan Africa suggests regional circulation of the viruses in the subregion. Importantly, there may be the need to decentralize testing sites and build more capacity across Africa to boost the sequencing output of the subregion.

2.
Ghana Med J ; 54(4 Suppl): 71-76, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-1436197

ABSTRACT

Across the globe, the outbreak of the COVID-19 pandemic is causing distress with governments doing everything in their power to contain the spread of the novel coronavirus (SARS-CoV-2) to prevent morbidity and mortality. Actions are being implemented to keep health care systems from being overstretched and to curb the outbreak. Any policy responses aimed at slowing down the spread of the virus and mitigating its immediate effects on health care systems require a firm basis of information about the absolute number of currently infected people, growth rates, and locations/hotspots of infections. The only way to obtain this base of information is by conducting numerous tests in a targeted way. Currently, in Ghana, there is a centralized testing approach, that takes 4-5 days for samples to be shipped and tested at central reference laboratories with results communicated to the district, regional and national stakeholders. This delay in diagnosis increases the risk of ongoing transmission in communities and vulnerable institutions. We have validated, evaluated and deployed an innovative diagnostic tool on a mobile laboratory platform to accelerate the COVID-19 testing. A preliminary result of 74 samples from COVID-19 suspected cases has a positivity rate of 12% with a turn-around time of fewer than 3 hours from sample taking to reporting of results, significantly reducing the waiting time from days to hours, enabling expedient response by the health system for contact tracing to reduce transmission and additionally improving case management. FUNDING: Test kits were provided by AngloGold Ashanti Obuasi Mine (AngloGold Ashanti Health Foundation). The American Leprosy Mission donated the PCR machine, and the mobile laboratory van was funded by the Embassy of the Kingdom of the Netherlands (EKN). AAS, YAA was supported by (PANDORA-ID-NET RIA2016E-1609) and ROP supported by EDCTP Senior Fellowship (TMA2016SF), both funded by the European and Developing Countries Clinical Trials Partnership (EDCTP2) programme which is supported under Horizon 2020, the European Union.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , Mobile Health Units , Population Surveillance , SARS-CoV-2/isolation & purification , Adolescent , Adult , Contact Tracing , Disease Transmission, Infectious/prevention & control , Early Diagnosis , Female , Humans , Infection Control/methods , Male , Middle Aged , SARS-CoV-2/genetics , Time Factors , Young Adult
3.
PLoS Negl Trop Dis ; 15(4): e0009335, 2021 04.
Article in English | MEDLINE | ID: covidwho-1201598

ABSTRACT

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.


Subject(s)
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
4.
PLoS One ; 16(4): e0249069, 2021.
Article in English | MEDLINE | ID: covidwho-1181194

ABSTRACT

BACKGROUND: The novel coronavirus disease (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), continues to remain a global challenge. There is emerging evidence of SARS-CoV-2 virus found in the blood of patients from China and some developed countries. However, there is inadequate data reported in Ghana and other parts of Africa, where blood transfusion service heavily relies on voluntary and replacement blood donors. This study aimed to investigate whether plasma of infected individuals could pose significant transfusion transmitted risk of COVID-19 in Ghanaian populations. METHODS: This cross-sectional retrospective study was conducted at the Kumasi Centre for Collaborative Research into Tropical Medicine (KCCR), KNUST, Ghana. Study subjects comprised contacts of COVID-19 individuals, those with classical symptoms of COVID-19 and individuals who had recovered based on the new Ghana discharge criteria. Whole blood, sputum or deep coughed saliva samples were collected and transported to KCCR for SARS-CoV-2 testing. Viral nucleic acid was extracted from sputum/nasopharyngeal samples using Da An Gene column based kit and from plasma using LBP nucleic acid extraction kit. Real-Time PCR was performed specifically targeting the ORF1ab and Nucleocapsid (N) genomic regions of the virus. RESULTS: A total of 97 individuals were recruited into the study, with more than half being males (58; 59.7%). The mean age of all subjects was 33 years (SD = 7.7) with minimum being 22 years and maximum 56 years. Majority (76; 78.4%) of all the subjects were asymptomatic, and among the few symptomatic subjects, cough (10; 10.3%) was the most predominant symptom. Of the 97 sputum samples tested, 79 (81.4%) were positive for SARS-CoV-2. We identified SARS-CoV-2 viral RNA in the plasma of 1 (1.03%) subject who had clinically recovered. CONCLUSION: This study reports the identification of SARS-CoV-2 viral RNA in a convalescent individual in Ghana. Due to the low prevalence observed and the marginal cycling thresholds associated, the risk of transfusion transmission of SARS-CoV-2 is negligible. Well-powered studies and advanced diagnostics to determine infectious viremia is recommended to further evaluate the potential risk of hematogenous transmission among recovered patients.


Subject(s)
Blood Transfusion , COVID-19/pathology , Adult , COVID-19/transmission , COVID-19/virology , Cross-Sectional Studies , Female , Humans , Male , Middle Aged , RNA, Viral/blood , Real-Time Polymerase Chain Reaction , Retrospective Studies , Risk , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Saliva/virology , Sputum/virology , Young Adult
5.
Arch Virol ; 166(5): 1385-1393, 2021 May.
Article in English | MEDLINE | ID: covidwho-1135167

ABSTRACT

Following the detection of the first imported case of COVID-19 in the northern sector of Ghana, we molecularly characterized and phylogenetically analysed sequences, including three complete genome sequences, of severe acute respiratory syndrome coronavirus 2 obtained from nine patients in Ghana. We performed high-throughput sequencing on nine samples that were found to have a high concentration of viral RNA. We also assessed the potential impact that long-distance transport of samples to testing centres may have on sequencing results. Here, two samples that were similar in terms of viral RNA concentration but were transported from sites that are over 400 km apart were analyzed. All sequences were compared to previous sequences from Ghana and representative sequences from regions where our patients had previously travelled. Three complete genome sequences and another nearly complete genome sequence with 95.6% coverage were obtained. Sequences with coverage in excess of 80% were found to belong to three lineages, namely A, B.1 and B.2. Our sequences clustered in two different clades, with the majority falling within a clade composed of sequences from sub-Saharan Africa. Less RNA fragmentation was seen in sample KATH23, which was collected 9 km from the testing site, than in sample TTH6, which was collected and transported over a distance of 400 km to the testing site. The clustering of several sequences from sub-Saharan Africa suggests regional circulation of the viruses in the subregion. Importantly, there may be a need to decentralize testing sites and build more capacity across Africa to boost the sequencing output of the subregion.


Subject(s)
COVID-19/transmission , SARS-CoV-2/classification , Whole Genome Sequencing/methods , Female , Genome, Viral , Ghana , Humans , Male , Nasopharynx/virology , Oropharynx/virology , Phylogeny , SARS-CoV-2/genetics , Sequence Analysis, RNA
6.
PLoS One ; 15(12): e0243711, 2020.
Article in English | MEDLINE | ID: covidwho-968555

ABSTRACT

BACKGROUND: Global cases of COVID-19 continue to rise, causing havoc to several economies. So far, Ghana has recorded 48,643 confirmed cases with 320 associated deaths. Although summaries of data are usually provided by the Ministry of Health, detailed epidemiological profile of cases are limited. This study sought to describe the socio-demographic features, pattern of COVID-19 spread and the viral load dynamics among subjects residing in northern, middle and part of the southern belt of Ghana. METHODS: This was a cross-sectional retrospective study that reviewed records of samples collected from February to July, 2020. Respiratory specimens such as sputum, deep-cough saliva and nasopharyngeal swabs were collected from suspected COVID-19 subjects in 12 regions of Ghana for laboratory analysis and confirmation by real-time reverse transcription polymerase chain reaction (RT-PCR). RESULTS: A total of 72,434 samples were collected during the review period, with majority of the sampled individuals being females (37,464; 51.9%). The prevalence of SARS-CoV-2 identified in the study population was 13.2% [95%CI: 12.9, 13.4). Males were mostly infected (4,897; 51.5%) compared to females. Individuals between the ages 21-30 years recorded the highest number of infections (3,144, 33.4%). Symptomatic subjects had higher viral loads (1479.7 copies/µl; IQR = 40.6-178919) than asymptomatic subjects (49.9; IQR = 5.5-3641.6). There was significant association between gender or age and infection with SARS-CoV-2 (p<0.05). Among all the suspected clinical presentations, anosmia was the strongest predictor of SARS-CoV-2 infection (Adj. OR (95%CI): 24.39 (20.18, 29.49). We observed an average reproductive number of 1.36 with a minimum of 1.28 and maximum of 1.43. The virus trajectory shows a gradual reduction of the virus reproductive number. CONCLUSION: This study has described the epidemiological profile of COVID-19 cases in northern, middle and part of the southern belt of Ghana, with males and younger individuals at greater risk of contracting the disease. Health professionals should be conscious of individuals presenting with anosmia since this was seen as the strongest predictor of virus infection.


Subject(s)
COVID-19/epidemiology , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/diagnosis , COVID-19 Nucleic Acid Testing , Child , Cross-Sectional Studies , Female , Ghana/epidemiology , Humans , Male , Middle Aged , Retrospective Studies , Risk Factors , SARS-CoV-2/isolation & purification , Young Adult
7.
BMC Vet Res ; 16(1): 405, 2020 Oct 27.
Article in English | MEDLINE | ID: covidwho-895005

ABSTRACT

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.


Subject(s)
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
8.
Vet Microbiol ; 241: 108544, 2020 Feb.
Article in English | MEDLINE | ID: covidwho-823170

ABSTRACT

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.


Subject(s)
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
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