scholarly journals Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report

Author(s):  
Jennifer Giandhari ◽  
Sureshnee Pillay ◽  
Eduan Wilkinson ◽  
Houriiyah Tegally ◽  
Ilya Sinayskiy ◽  
...  

BackgroundThe emergence of a novel coronavirus, SARS-CoV-2, in December 2019, progressed to become a world pandemic in a few months and reached South Africa at the beginning of March. To investigate introduction and understand the early transmission dynamics of the virus, we formed the South African Network for Genomics Surveillance of COVID (SANGS_COVID), a network of ten government and university laboratories. Here, we present the first results of this effort, which is a molecular epidemiological study of the first twenty-one SARS-CoV-2 whole genomes sampled in the first port of entry, KwaZulu-Natal (KZN), during the first month of the epidemic. By combining this with calculations of the effective reproduction number (R), we aim to shed light on the patterns of infections that define the epidemic in South Africa.MethodsR was calculated using positive cases and deaths from reports provided by the four major provinces. Molecular epidemiology investigation involved sequencing viral genomes from patients in KZN using ARCTIC protocols and assembling whole genomes using meticulous alignment methods. Phylogenetic analysis was performed using maximum likelihood (ML) and Bayesian trees, lineage classification and molecular clock calculations.FindingsThe epidemic in South Africa has been very heterogeneous. Two of the largest provinces, Gauteng, home of the two large metropolis Johannesburg and Pretoria, and KwaZulu-Natal, home of the third largest city in the country Durban, had a slow growth rate on the number of detected cases. Whereas, Western Cape, home of Cape Town, and the Eastern Cape provinces the epidemic is spreading fast. Our estimates of transmission potential for South Africa suggest a decreasing transmission potential towards R=1 since the first cases and deaths have been reported. However, between 06 May and 18 May 2020, we estimate that R was on average 1.39 (1.04–2.15, 95% CI). We also demonstrate that early transmission in KZN, and most probably in all main regions of SA, was associated with multiple international introductions and dominated by lineages B1 and B. The study also provides evidence for locally acquired infections in a hospital in Durban within the first month of the epidemic, which inflated early mortality in KZN.InterpretationThis first report of SANGS_COVID consortium focuses on understanding the epidemic heterogeneity and introduction of SARS-CoV-2 strains in the first month of the epidemic in South Africa. The early introduction of SARS-CoV-2 in KZN included caused a localized outbreak in a hospital, provides potential explanations for the initially high death rates in the province. The current high rate of transmission of COVID-19 in the Western Cape and Eastern Cape highlights the crucial need to strength local genomic surveillance in South Africa.FundingUKZN Flagship Program entitled: Afrocentric Precision Approach to Control Health Epidemic, by a research Flagship grant from the South African Medical Research Council (MRC-RFA-UFSP-01- 2013/UKZN HIVEPI, by the the Technology Innovation Agency and the the Department of Science and Innovation and by National Human Genome Re- search Institute of the National Institutes of Health under Award Number U24HG006941. H3ABioNet is an initiative of the Human Health and Heredity in Africa Consortium (H3Africa).Research in context Evidence before this studyWe searched PubMed, BioRxiv and MedRxiv for reports on epidemiology and phylogenetic analysis using whole genome sequencing (WGS) of SARS-CoV-2. We used the following keywords: SARS-CoV-2, COVID-19, 2019-nCoV or novel coronavirus and transmission genomics, epidemiology, phylogenetic or reproduction number. Our search identified an important lack of molecular epidemiology studies in the southern hemisphere, with only a few reports from Latin America and one in Africa. In other early transmission reports on SARS-CoV-2 infections in Africa, authors focused on transmission dynamics, but molecular and phylogenetic methods were missing.Added value of this studyWith a growing sampling bias in the study of transmission genomics of the SARS-CoV-2 pandemic, it is important for us to report high-quality whole genome sequencing (WGS) of local SARS-CoV-2 samples and in-depth phylogenetic analyses of the first month of infection in South-Africa. In our molecular epidemiological investigation, we identify the early transmission routes of the infection in the KZN and report thirteen distinct introductions from many locations and a cluster of localized transmission linked to a healthcare setting that caused most of the initial deaths in South Africa. Furthermore, we formed a national consortium in South Africa, funded by the Department of Science and Innovation and the South African Medical Research Council, to capacitate ten local laboratories to produce and analyse SARS-CoV-2 data in near real time.Implications of all the available evidenceThe COVID-19 pandemic is progressing around the world and in Africa. Early transmission genomics and dynamics of SARS-CoV-2 throw light on the early stages of the epidemic in a given region. This facilitates the investigation of localized outbreaks and serves to inform public health responses in South Africa.

Zootaxa ◽  
2019 ◽  
Vol 4577 (2) ◽  
pp. 361
Author(s):  
JIŘÍ JANÁK

A revision of the south African genus Neopimus Özdikmen, Demir & Türkeş, 2008 is presented. Based on revision of the type and additional material, three species are recognised. The genus Neopimus is redescribed and all species are described or redescribed and illustrated, two of them for the first time: Neopimus capensis Janák, sp. nov., from Eastern Cape Province, South Africa and N. zulu Janák, sp. nov., from KwaZulu-Natal Province, South Africa. The distribution of the genus is mapped and a key of species is presented. 


Zootaxa ◽  
2006 ◽  
Vol 1277 (1) ◽  
pp. 39 ◽  
Author(s):  
DAVID A. BARRACLOUGH

The South African Nemestrinidae are reviewed. Regional family characteristics, biology and the importance of long-proboscid species in pollination biology are discussed. Long-proboscid species (proboscis 15 mm or longer) are important pollinators in most provinces, but particularly in the Western Cape; all have specialised pollination interactions with long-tubed flower species. Five pollination guilds centered on long-proboscid species are briefly discussed.        A detailed, annotated key to the six genera is presented; in it particular attention is given to the problematic distinction between Prosoeca Schiner and Stenobasipteron Lichtwardt. A checklist of all described species considered to have a South African provenance is provided. A total of 43 described species is recorded in the following genera: Moegistorhynchus Macquart (4 species); Prosoeca (35 species); Stenobasipteron (1 species); Atriadops Wandolleck (1 species); Nycterimyia Lichtwardt (1 species); Trichopsidea Westwood (1 species).        Moegistorhynchus is restricted to the west coast (Western Cape, Northern Cape). Three of its species have a remarkably elongate proboscis, the best known and most widespread being M. longirostris (Wiedemann, 1819). Its proboscis reaches 90 to 100 mm in length in some specimens, this being the longest proboscis of all known Diptera. Two new species have been identified in the fauna.        Prosoeca dominates the fauna, and is the only genus likely to be represented in all nine provinces. It appears to occur in all habitats except closed-canopy forest. Prosoeca major Bezzi, 1924 is newly synonymised with P. robusta Bezzi, 1924. The likely South African provenance of P. nigripes (Macquart, 1840) is confirmed. Nemestrina obscura Westwood, 1835, previously referred to Prosoeca, is considered not to be an Afrotropical species. Prosoeca rhodesiensis Bequaert, 1925a, is recorded from South Africa for the first time.        Although Stenobasipteron is restricted to only one named South African species, namely S. wiedemanni Lichtwardt, 1910 from the Eastern Cape and KwaZulu-Natal, several undescribed species occur in Mpumalanga and Limpopo. Stenobasipteron wiedemanni occurs in closed-canopy forest, but species from Mpumalanga may occur in other habitats such as grassland and savanna.        There are at least two species of Atriadops, one almost certainly being A. vespertilio (Loew, 1858). The genus is recorded from the Western Cape, Eastern Cape, KwaZulu-Natal, Gauteng and Mpumalanga. A taxonomic revision is recommended. Nycterimyia is represented by one species only, namely N. capensis Bezzi, 1924 from KwaZulu-Natal and Limpopo. Trichopsidea is represented by one species, T. costata (Loew, 1858), recorded from North West, Gauteng and Limpopo.


2021 ◽  
Author(s):  
Wendy Sykes ◽  
Laurette Mhlanga ◽  
Ronel Swanevelder ◽  
Tanya Nadia Glatt ◽  
Eduard Grebe ◽  
...  

Abstract Background: Population-level estimates of prevalence of anti-SARS-CoV-2 antibody positivity (seroprevalence) is a crucial epidemiological indicator for tracking the Covid-19 epidemic. Such data are in short supply, both internationally and in South Africa. The South African blood services (the South African National Blood Service, SANBS and the Western Cape Blood Service, WCBS) are coordinating a nationally representative survey of blood donors, which it is hoped can become a cost-effective surveillance method with validity for community-level seroprevalence estimation.Methods: Leveraging existing arrangements, SANBS human research ethics committee permission was obtained to test blood donations collected on predefined days (7th, 10th ,12th ,15th ,20th ,23th and 25th January) for anti-SARS-CoV-2 antibodies, using the Roche Elecsys Anti-SARS-CoV-2 assay on the cobas e411 platform currently available in the blood services’ donation testing laboratories. Using standard methods, prevalence analysis was done by province, age and race, allowing age to be regarded as either a continuous or categorical variable. Testing was performed in the Eastern Cape (EC), Free State (FS), KwaZulu Natal (ZN) and Northern Cape (NC) provinces.Results: We report on data from 4858 donors - 1457 in EC; 463 in NC; 831 in FS and 2107 in ZN. Prevalence varied substantially across race groups and between provinces, with seroprevalence among Black donors consistently several times higher than among White donors, and the other main population groups (Coloured and Asian) not consistently represented in all provinces. There is no clear evidence that seroprevalence among donors varies by age. Weighted net estimates of prevalence (in the core age range 15-69) by province (compared with official clinically-confirmed COVID-19 case rates in mid-January 2021) are: EC-63%(2.8%), NC-32%(2.2%), FS-46%(2.4%), and ZN-52%(2.4%).Conclusions: Our study demonstrates substantial differences in dissemination of SARS-CoV-2 infection between different race groups, most likely explained by historically based differences in socio-economic status and housing conditions. As has been seen in other areas, even such high seroprevalence does not guarantee population-level immunity against new outbreaks – probably due to viral evolution and waning of antibody neutralization. Despite its limitations, notably a ‘healthy donor’ effect, it seems plausible that these estimates are reasonably generalisable to actual population level anti-SARS-CoV-2 seroprevalence, but should be further verified.


2020 ◽  
Vol 72 (1-3) ◽  
Author(s):  
Lungisani Moyo

ABSTRACT This paper used qualitative methodology to explore the South African government communication and land expropriation without compensation and its effects on food security using Alice town located in the Eastern Cape Province South Africa as its case study. This was done to allow the participants to give their perceptions on the role of government communication on land expropriation without compensation and its effects on South African food security. In this paper, a total population of 30 comprising of 26 small scale farmers in rural Alice and 4 employees from the Department of Agriculture (Alice), Eastern Cape, South Africa were interviewed to get their perception and views on government communications and land expropriation without compensation and its effects on South African food security. The findings of this paper revealed that the agricultural sector plays a vital role in the South African economy hence there is a great need to speed up transformation in the sector.


2020 ◽  
Author(s):  
Neven Chetty ◽  
Bamise Adeleye ◽  
Abiola Olawale Ilori

BACKGROUND The impact of climate temperature on the counts (number of positive COVID-19 cases reported), recovery, and death rates of COVID-19 cases in South Africa's nine provinces was investigated. The data for confirmed cases of COVID-19 were collected for March 25 and June 30, 2020 (14 weeks) from South Africa's Government COVID-19 online resource, while the daily provincial climate temperatures were collected from the website of the South African Weather Service. Our result indicates that a higher or lower climate temperature does not prevent or delay the spread and death rates but shows significant positive impacts on the recovery rates of COVID-19 patients. Thus, it indicates that the climate temperature is unlikely to impose a strict limit on the spread of COVID-19. There is no correlation between the cases and death rates, an indicator that no particular temperature range is closely associated with a faster or slower death rate of COVID-19 patients. As evidence from our study, a warm climate temperature can only increase the recovery rate of COVID-19 patients, ultimately impacting the death and active case rates and freeing up resources quicker to enable health facilities to deal with those patients' climbing rates who need treatment. OBJECTIVE This study aims to investigate the impact of climate temperature variation on the counts, recovery, and death rates of COVID-19 cases in all South Africa's provinces. The findings were compared with those of countries with comparable climate temperature values. METHODS The data for confirmed cases of COVID-19 were collected for March 25 and June 30 (14 weeks) for South African provinces, including daily counts, death, and recovery rates. The dates were grouped into two, wherein weeks 1-5 represent the periods of total lockdown to contain the spread of COVID-19 in South Africa. Weeks 6-14 are periods where the lockdown was eased to various levels 4 and 3. The daily information of COVID-19 count, death, and recovery was obtained from South Africa's Government COVID-19 online resource (https://sacoronavirus.co.za). Daily provincial climate temperatures were collected from the website of the South African Weather Service (https://www.weathersa.co.za). The provinces of South Africa are Eastern Cape, Western Cape, Northern Cape, Limpopo, Northwest, Mpumalanga, Free State, KwaZulu-Natal, Western Cape, and Gauteng. Weekly consideration was given to the daily climate temperature (average minimum and maximum). The recorded values were considered, respectively, to be in the ratio of death-to-count (D/C) and recovery-to-count (R/C). Descriptive statistics were performed for all the data collected for this study. The analyses were performed using the Person’s bivariate correlation to analyze the association between climate temperature, death-to-count, and recovery-to-count ratios of COVID-19. RESULTS The results showed that higher climate temperatures aren't essential to avoid the COVID-19 from being spread. The present results conform to the reports that suggested that COVID-19 is unlike the seasonal flu, which does dissipate as the climate temperature rises [17]. Accordingly, the ratio of counts and death-to-count cannot be concluded to be influenced by variations in the climate temperatures within the study areas. CONCLUSIONS The study investigates the impact of climate temperature on the counts, recovery, and death rates of COVID-19 cases in all South Africa's provinces. The findings were compared with those of countries with comparable climate temperatures as South Africa. Our result indicates that a higher or lower climate temperature does not prevent or delay the spread and death rates but shows significant positive impacts on the recovery rates of COVID-19 patients. Warm climate temperatures seem not to restrict the spread of the COVID-19 as the count rate was substantial at every climate temperatures. Thus, it indicates that the climate temperature is unlikely to impose a strict limit on the spread of COVID-19. There is no correlation between the cases and death rates, an indicator that there is no particular temperature range of the climatic conditions closely associated with a faster or slower death rate of COVID-19 patients. However, other shortcomings in this study's process should not be ignored. Some other factors may have contributed to recovery rates, such as the South African government's timely intervention to announce a national lockout at the early stage of the outbreak, the availability of intensive medical care, and social distancing effects. Nevertheless, this study shows that a warm climate temperature can only help COVID-19 patients recover more quickly, thereby having huge impacts on the death and active case rates.


Author(s):  
James R. Barnacle ◽  
Oliver Johnson ◽  
Ian Couper

Background: Many European-trained doctors (ETDs) recruited to work in rural district hospitals in South Africa have insufficient generalist competencies for the range of practice required. Africa Health Placements recruits ETDs to work in rural hospitals in Africa. Many of these doctors feel inadequately prepared. The Stellenbosch University Ukwanda Centre for Rural Health is launching a Postgraduate Diploma in Rural Medicine to help prepare doctors for such work.Aim: To determine the competencies gap for ETDs working in rural district hospitals in South Africa to inform the curriculum of the PG Dip (Rural Medicine).Setting: Rural district hospitals in South Africa.Methods: Nine hospitals in the Eastern Cape, KwaZulu-Natal and Mpumalanga were purposefully selected by Africa Health Placements as receiving ETDs. An online survey was developed asking about the most important competencies and weaknesses for ETDs when working rurally. The clinical manager and any ETDs currently working in each hospital were invited to complete the survey.Results: Surveys were completed by 19 ETDs and five clinical managers. The top clinical competencies in relation to 10 specific domains were identified. The results also indicate broader competencies required, specific skills gaps, the strengths that ETDs bring to South Africa and how ETDs prepare themselves for working in this context.Conclusion: This study identifies the important competency gaps among ETDs and provides useful direction for the diploma and other future training initiatives. The diploma faculty must reflect on these findings and ensure the curriculum is aligned with these gaps.


Plant Disease ◽  
2010 ◽  
Vol 94 (4) ◽  
pp. 478-478 ◽  
Author(s):  
L. Mostert ◽  
W. Bester ◽  
T. Jensen ◽  
S. Coertze ◽  
A. van Hoorn ◽  
...  

Southern highbush blueberry plants (Vaccinium corymbosum interspecific hybrids) showing rust-like symptoms were observed in July 2006 in Porterville in the Western Cape (WC), South Africa. Diseased plants were also found in Villiersdorp and George in the WC in 2007. In 2008, symptoms were observed in George, and in 2009, in all the previous reported areas. Cvs. Bluecrisp, Emerald, Jewel, Sharpblue, and Star were infected. Reddish-to-brown spots appeared on the adaxial surface of leaves and developed into yellow-to-orange erumpent uredinia with pulverulent urediniospores. Uredinia were hypophyllous, dome shaped, 113 to 750 μm wide, and occasionally coalescing. Urediniospores were broadly obovate, sometimes ellipsoidal or pyriform, with yellowish orange content, and measured 19 to 27 × 12 to 20 μm (average 24 × 15 μm, n = 30). Spore walls were echinulate, hyaline, 1 to 1.5 μm thick, and with obscure germ pores. No telia or teliospores were observed. Voucher specimens were lodged in the South African National Fungus Collection in Pretoria (PREM 60245). The isolate was initially identified as Thekopsora minima P. Syd. & Syd., based primarily on the absence of conspicuous ostiolar cells characteristic of Naohidemyces spp. (3). Genomic DNA was extracted from urediniospores. Approximately 1,400 bp were amplified spanning the 5.8S, ITS2, and 28S large subunit of the ribosomal DNA (1). The sequence (GU355675) shared 96% (907 of 942 bp; GenBank AF522180) and 94% (1,014 of 1,047 bp; GenBank DQ354563) similarities in the 28S portion, respectively, to those of Naohidemyces vaccinii (Wint.) Sato, Katsuya et Y. Hiratsuka and Pucciniastrum geoppertianum (Kuehn) Kleb, two of the three known rust species of blueberry (2). Although no sequences of T. minima were available for direct comparison, phylogenetic analyses of the 28S region strongly supported the South African blueberry rust as congeneric with T. guttata (J. Schröt.) P. Syd. & Syd. (GenBank AF426231) and T. symphyti (Bubák) Berndt (GenBank AF26230) (data not shown). Four 6-month-old cv. Sharpblue plants were inoculated with a suspension (approximate final concentration of 1 × 105 spores per ml) of fresh urediniospores in a water solution with 0.05% Tween 20. After incubation at 20°C for 48 h under continuous fluorescent lighting, the plants were grown in a glasshouse (18/25°C night/day temperatures). Identical uredinia and symptoms developed approximately 3 weeks after inoculation on the inoculated plants, but not on two control plants of cv. Sharpblue sprayed with distilled water and kept at the same conditions. The alternate host hemlock (Tsuga spp.) is not endemic to South Africa and not sold as an ornamental plant according to a large conifer nursery. Hosts of T. minima include Gaylussacia baccata, G. frondosa, Lyonia neziki, Menziesia pilosa, Rhododendron canadense, R. canescens, R. lutescens R. ponticum, R. prunifolium, R. viscosum, V. angustifolium var. laevifolium, V. corumbosum, and V. erythrocarpon (3). Visual inspection of possible hosts in the gardens in close proximity of Vaccinium production areas did not show any rust symptoms. To our knowledge, this is the first report of T. minima on blueberries outside of Asia and the United States (2). References: (1) M. C. Aime. Mycoscience 47:112, 2006. (2) D. F. Farr and A. Y. Rossman. Fungal Databases. Systematic Botany and Mycology Laboratory. Online publication. USDA-ARS, 2009. (3) S. Sato et al. Trans. Mycol. Soc. Jpn. 34:47, 1993.


Viruses ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 2050
Author(s):  
Tanya Nadia Glatt ◽  
Caroline Hilton ◽  
Cynthia Nyoni ◽  
Avril Swarts ◽  
Ronel Swanevelder ◽  
...  

Background: COVID-19 convalescent plasma (CCP) has been considered internationally as a treatment option for COVID-19. CCP refers to plasma collected from donors who have recovered from and made antibodies to SARS-CoV-2. To date, convalescent plasma has not been collected in South Africa. As other investigational therapies and vaccination were not widely accessible, there was an urgent need to implement a CCP manufacture programme to service South Africans. Methods: The South African National Blood Service and the Western Cape Blood Service implemented a CCP programme that included CCP collection, processing, testing and storage. CCP units were tested for SARS-CoV-2 Spike ELISA and neutralising antibodies and routine blood transfusion parameters. CCP units from previously pregnant females were tested for anti-HLA and anti-HNA antibodies. Results: A total of 987 CCP units were collected from 243 donors, with a median of three donations per donor. Half of the CCP units had neutralising antibody titres of >1:160. One CCP unit was positive on the TPHA serology. All CCP units tested for anti-HLA antibodies were positive. Conclusion: Within three months of the first COVID-19 diagnosis in South Africa, a fully operational CCP programme was set up across South Africa. The infrastructure and skills implemented will likely benefit South Africans in this and future pandemics.


Zootaxa ◽  
2020 ◽  
Vol 4885 (4) ◽  
pp. 579-590
Author(s):  
ALLEN F. SANBORN ◽  
MARTIN H. VILLET

Ingcainyenzane irhiniensis n. gen., n. sp. and Ingcainyenzane nolukhanyoensis n. gen., n. sp. are described from Eastern Cape and Ingcainyenzane umgeniensis n. gen., n. sp. is described from KwaZulu-Natal, South Africa. Notes on its biology of the species and a key to species of the genus are also provided. 


2014 ◽  
Vol 10 (4) ◽  
pp. 490-503
Author(s):  
GS Horn

Original Equipment Manufacturers (OEMs) in South Africa are under pressure to meet the Black Economic Empowerment (BEE) policies and charters of the South African government by giving BEE suppliers additional opportunities to tender. However, many BEE suppliers, due to being historically disadvantaged, experience various problems which make it difficult for them to win tenders, including lack of finances, opportunities to tender and management and business skills, and problems with quality and capacity. This paper outlines these practical problems experienced by BEE suppliers, the effects of these problems on risk and complexity in the South African automotive industry and policies that address these problems and assist BEE suppliers to become A-rated suppliers. Data for the paper was obtained from interviews with: senior employees of the AIDC involved with supplier development training; middle managers of supplier quality and development departments at the three OEMs in the Eastern Cape Province; and BEE and small suppliers identified to undergo AIDC training. The findings of the study are that unless sufficient training is given to BEE and potential BEE suppliers, supply to OEMs will remain in the hands of existing established suppliers and very little transformation will occur within the automobile industry in South Africa.


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