SPOTLIGHT

KRISP NEWS

Excess deaths increase but we are ‘still in the dark’

There have been 17090 more deaths in the country than there were in previous years during the same period. But the official number of Covid-19 deaths is about 6000. There is a significant departure from the historical trends, even under these abnormal circumstances.

South Africa 59% excess deaths imply hidden Covid-19 toll

South Africa witnessed some 17000 extra deaths from natural causes or 59% more than would normally be expected between early May and mid-July, scientists said, suggesting many more people are dying of Covid-19 than shown in official figures.

South Africa joins 'Big 5' COVID-19 countries

South Africa has joined the United States, Brazil, India, and Russia as the countries with the most recorded COVID-19 cases. On Saturday, Health Minister Dr Zweli Mkhize announced the country has 350,879 confirmed COVID-19 cases.

Experts question ‘underreported’ virus deaths in South Africa

The official number of deaths linked to Covid-19 in South Africa doesn’t reflect the true scale of the crisis, with provinces that have been hit hardest by the outbreak showing a surge in fatalities, health experts say.

South Africa Data May Underreport Virus Deaths, Experts Say

The official number of deaths linked to Covid-19 in South Africa doesn’t reflect the true scale of the crisis, with provinces that have been hit hardest by the outbreak showing a surge in fatalities, health experts say.

Initial COVID-19 Infections In CT Came From Europe, Researchers Find

CAPE TOWN - Genome sequencing, by colleagues at Stellenbosch University and the Network for Genomic Surveillance, was used to trace most of the very first COVID-19 cases reported in the Western Cape back to Europe.

Scientists found who may have triggered the coronavirus crisis in Cape Town

There were multiple — possibly hundreds — of introductions of the novel coronavirus virus to Cape Town from foreign travellers and return citizens, scientists found.

KRISP SCIENTIFIC PUBLICATIONS

Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation During a Pandemic.
Pillay S, Giandhari J, Tegally H, Wilkinson E, Chimukangara B, Lessells R, Mattison S, Moosa Y, Gazy I, Fish M, Singh L, Khanyile KS, Fonseca V, Giovanetti M, Alcantara LCJ, de Oliveira T, bioRxiv pre-print (2020), doi: https://doi.org/10.1101/2020.06.10.144212:.

Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report.
Giandhari J, Pillay S, Wilkinson E, Tegally H, Sinayskiy I, Schuld M, Lourenço J, Chimukangara B, Lessells R, Moosa Y, Gazy I, Fish M, Singh L, Khanyile KS, Fonseca V, Giovanetti M, Alcantara LCJ, Petruccione F, de Oliveira T, medRxiv pre-print (2020), doi: https://doi.org/10.1101/2020.05.29.20116376:.

Protocol: Leveraging a demographic and health surveillance system for Covid-19 Surveillance in rural KwaZulu-Natal.
Siedner MJ, Harling G, Derache A, Smit T, Khoza T, Gunda R, Mngomezulu T, Gareta D, Majozi N, Ehlers E, Dreyer J, Nxumalo S, Dayi N, Ording-Jesperson G, Ngwenya N, Wong E, Iwuji C, Shahmanesh M, Seeley J, de Oliveira T, Ndung'u T, Hanekom W, Herbst K, Wellcome Open Research (2020), 5:109:.

The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing.
Xavier J, Giovanetti M, Adelino T, Fonseca V, da Costa AVB, Ribeiro AA, Felicio KN, Duarte CG, Silva MVF, Salgado A, Lima MT, de Jesus D, Fabri A, Zoboli CFS, Santos TGS, Iani F,de Filippis AMB, de Siqueira AMNT, de Abreu AL, de Azevedo V, Ramalho DBR, de Albuquerque CFC, de Oliveira T, Holmes EC, Lourenco J, Alcantara CLJ, Oliveira MAA, medRxiv pre-print (2020), :.

Pervasive and non-random recombination in near full-length HIV genomes from Uganda.
Grant HE, Hodcroft EB, Ssemwanga D, Kitayimbwa JM, Yebra G, Gomez LRE, Frampton D, Gall A, Kellam P, de Oliveira T, Bbosa N, Nsubuga RN, Kibengo F, Kwan TH, Lycett S, Kao R, Robertson DL, Ratmann O, Fraser C, Pillay D, Kaleebu P, Leigh-Brown AJ, Virus Evolution (2020), veaa004, https://doi.org/10.1093/ve/veaa004:.

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable.
Mavian C, Pond SK, Marini S, Magalis BR, Vandamme A-M, Dellicour S, Scarpino SV, Houldcroft C, Villabona-Arenas J, Paisie TK, Trovão NS, Boucher C, Zhang Y, Scheuermann RH, Gascuel O, Lam TTY, Suchard MA, Abecasis A, Wilkinson E, de Oliveira T, Bento AI, Schmidt HA, Martin D, Hadfield J, Faria N, Grubaugh ND, Neher RA, Baele G, Lemey P, Stadler T, Albert J, Crandall KA, Leitner T, Stamatakis A, Prosperi M, Salemi M, Proceedings of the National Academy of Sciences (PNAS) (2020), doi:10.1073/pnas.2007295117:.

Priorities among HIV-positive individuals for tuberculosis preventive therapies.
Kim HY, Hanrahan CF, Dowdy DW, Martinson NA, Golub JE, Bridges JFP, Int J Tuberc Lung Dis (2020), 24(4):396-402. doi: 10.5588/ijtld.18.0740:.

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Curation and Analysis of Data in Africa by Africans: Network for Genomic Surveillance in South Africa (NGS-SA)
By: San Emmanuel James and Jennifer Giandhari

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