About Dr Emmanuel James San

sanemmanueljames@gmail.com +27 (0) 72 529 0848


Dr San is a bioinformatics data science postdoctoral researcher at the CERI-KRISP. He completed his PhD in Medicine, Majoring in Virology at the Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, South Africa. His PhD research focused on the analysis and visualization of complex viral genomic and associated epidemiological datasets to infer their introduction, evolution, transmission and spatio-temporal spread. He also possess in-depth experience characterizing bacterial communities using the 16S-rRNA marker gene and analysing host factors affecting the distribution of these communities. Prior to his doctoral studies, he received a BSc. In Computer Science and MSc. In Data Communication and Software Engineering at Makerere University. Dr. San’s research interests include Bioinformatics Software, Databases and Pipelines Development, Next Generation Sequence Data Management and Analysis (Genomic Epidemiology, Phylogenetics, Phylogeography, Transmission Clusters, Recombination, Epistasis, Drug Resistance, and Microbiome), and High Performance and Cloud Computing for Data Intensive Projects. Dr. San has over 30 publications, with many of them in the top scientific journals including Nature, Science and Lancet.


KRISP - KwaZulu-Natal Research and Innovation Sequencing Platform, UKZN, Durban, South Africa.

CERI - Centre for Epidemic Response and Innovation, Stellenbosch University, Stellenbosch, South Africa.


PhD in Medicine, Makerere University, 2021. Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, South Africa.

Master of Science in Data Communications and Software Engineering, Makerere University, 2016. Funded by the Forgarty International Center Scholarship.

Bachelor of Science in Computer Science, Makerere University, 2009


Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil.
Giovanetti M, Slavov SN, Fonseca V, Wilkinson E, Tegally H, Patané JSL, Viala VL, San EJ, Rodrigues ES, Santos EV, Aburjaile F, Xavier J, Fritsch H, Adelino TER, Pereira F, Leal A, Iani FCM, de Carvalho Pereira G, Vazquez C, Sanabria GME, Oliveira EC, Demarchi L, Croda J, Dos Santos Bezerra R, Paola Oliveira de Lima L, Martins AJ, Renata Dos Santos Barros C, Marqueze EC, de Souza Todao Bernardino J, Moretti DB, Brassaloti RA, de Lello Rocha Campos Cassano R, Mariani PDSC, Kitajima JP, Santos B, Proto-Siqueira R, Cantarelli VV, Tosta S, Nardy VB, Reboredo de Oliveira da Silva L, Gómez MKA, Lima JG, Ribeiro AA, Guimarães NR, Watanabe LT, Barbosa Da Silva L, da Silva Ferreira R, da Penha MPF, Ortega MJ, de la Fuente AG, Villalba S, Torales J, Gamarra ML, Aquino C, Figueredo GPM, Fava WS, Motta-Castro ARC, Venturini J, do Vale Leone de Oliveira SM, Gonçalves CCM, do Carmo Debur Rossa M, Becker GN, Giacomini MP, Marques NQ, Riediger IN, Raboni S, Mattoso G, Cataneo AD, Zanluca C, Duarte Dos Santos CN, Assato PA, Allan da Silva da Costa F, Poleti MD, Lesbon JCC, Mattos EC, Banho CA, Sacchetto L, Moraes MM, Grotto RMT, Souza-Neto JA, Nogueira ML, Fukumasu H, Coutinho LL, Calado RT, Neto RM, Bispo de Filippis AM, Venancio da Cunha R, Freitas C, Peterka CRL, de Fátima Rangel Fernandes C, Navegantes W, do Carmo Said RF, Campelo de A E Melo CF, Almiron M, Lourenço J, de Oliveira T, Holmes EC, Haddad R, Sampaio SC, Elias MC, Kashima S, Junior de Alcantara LC, Covas DT, Nature Microbiology (2022), doi: 10.1038/s41564-022-01191-z:.

Omicron infection enhances Delta antibody immunity in vaccinated persons.
Khan K, Karim F, Cele S, Reedoy K, San EJ, Lustig G, Tegally H, Rosenberg Y, Bernstein M, Jule Z, Ganga Y, Ngcobo N, Mazibuko M, Mthabela N, Mhlane Z, Mbatha N, Miya Y, Giandhari J, Ramphal Y, Naidoo T, Sivro A, Samsunder N, Kharsany A, Amoako D, Bhiman J, Manickchund N, Karim Q, Magula N, Abdool Karim SS, Gray G, Hanekom W, von Gottberg A, Milo R, Gosnell B, Lessells R, Moore P, de Olveira T, Moosa M-Y S, Sigal A, Nature (2022), https://doi.org/10.1038/s41586-022-04830-x:.

Replacement of the Gamma by the Delta variant in Brazil: Impact of lineage displacement on the ongoing pandemic.
Giovanetti M, Fonseca V, Wilkinson E, Tegally H, San EJ, Althaus CL, Xavier J, Nanev Slavov S, Viala VL, Ranieri Jerônimo Lima A, Ribeiro G, Souza-Neto JA, Fukumasu H, Lehmann Coutinho L, Venancio da Cunha R, Freitas C, Campelo de A E Melo CF, Navegantes de Araújo W, Do Carmo Said RF, Almiron M, de Oliveira T, Coccuzzo Sampaio S, Elias MC, Covas DT, Holmes EC, Lourenço J, Kashima S, de Alcantara LCJ, Virus Evolution (2022), doi: 10.1093/ve/veac024:.

Rapid Replacement of SARS-CoV-2 Variants by Delta and Subsequent Arrival of Omicron, Uganda, 2021.
Bbosa N, Ssemwanga D, Namagembe H, Kiiza R, Kiconco J, Kayiwa J, Lutalo T, Lutwama J, Ssekagiri A, Ssewanyana I, Nabadda S, Kyobe-Bbosa H, Giandhari J, Pillay S, Ramphal U, Ramphal Y, Naidoo Y, Tshiabuila D, Tegally H, San EJ, Wilkinson E, de Oliveira T, Kaleebu P, Emerg Infect Dis (2022), doi: 10.3201/eid2805.220121:.

The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages .
Martin DP, Weaver S, Tegally H, San EJ, Shank SD, Wilkinson E, Lucaci AG, Giandhari J, Naidoo S, Pillay Y, Singh L, Lessells RJ; NGS-SA; COVID-19 Genomics UK (COG-UK), Gupta RK, Wertheim JO, Nekturenko A, Murrell B, Harkins GW, Lemey P, MacLean OA, Robertson DL, de Oliveira T, Kosakovsky Pond SL. , Cell (2021), https://doi.org/10.1016/j.cell.2021.09.003:.

Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing. .
Singh L, Anyaneji UJ, Ndifon W, Turok N, Mattison SA, Lessells R, Sinayskiy I, San EJ, Tegally H, Barnett S, Lorimer T, Petruccione F, de Oliveira T. , Scientific Reports (2021), 11(1):17793. doi: 10.1038/s41598-021-96934-z:.

HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens..
Fischer W, Giorgi EE, Chakraborty S, Nguyen K, Bhattacharya T, Theiler J, Goloboff PA, Yoon H, Abfalterer W, Foley BT, Tegally H, San EJ, de Oliveira T, Network for Genomic Surveillance in South Africa (NGS-SA), Gnanakaran S, Korber B, Cell Host Microbe (2022), 29(7):1093-1110. doi: 10.1016/j.chom.2021.05.012:.

Sixteen novel lineages of SARS-CoV-2 in South Africa.
Tegally H, Wilkinson E, Lessells R, Giandhari J, Pillay S, Msomi N, Mlisana K, Bhiman J, Gottberg A, Walaza S, Fonseca V, Allam M, Ismail A, Engelbrecht S, Van Zyl G, Preiser W, Williamson C, Pettruccione F, Sigal A, Gazy I, Hardie D, Hsiao M, Martin D, York D, Goedhals D, San EJ, Giovanetti M, Lourenco J, Alcantara LCJ, de Oliveira T, Nature Medicine (2021), https://doi.org/10.1038/s41591-021-01255-3:.

Current Affairs of Microbial Genome-Wide Association Studies: Approaches, Bottlenecks and Analytical Pitfalls.
San EJ, Baichoo S, Kanzi A, Moosa Y, Lessells R, Fonseca V, Mogaka J, Power R, de Oliveira T, Front. Microbiol. (2020), https://doi.org/10.3389/fmicb.2019.03119:.

Analysis of the microarray gene expression for breast cancer progression after the application modified logistic regression.
Morais-Rodrigues F, Silv Erio-Machado R, Kato RB, Rodrigues DLN, Valdez-Baez J, Fonseca V, San EJ, Gomes LGR, Dos Santos RG, Vinicius Canário Viana M, da Cruz Ferraz Dutra J, Teixeira Dornelles Parise M, Parise D, Campos FF, de Souza SJ, Ortega JM, Barh D, Ghosh P, Azevedo VAC, Dos Santos MA, Gene (2020), 144168. doi: 10.1016/j.gene.2019.144168.:.

Mosquito-Borne Viral Diseases: Control and Prevention in the Genomics Era.
Fonseca V, Xavier J, San EJ, de Oliveira T, de Filippis AMB, Alcantara LCJ, Giovanetti M, Current Topics in the Epidemiology of Vector-Borne (2019), DOI: 10.5772/intechopen.88769:.

A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes.
Fonseca V, Libin PJK, Theys K, Faria NR, Nunes MRT, Restovic MI, Freire M, Giovanetti M, Cuypers L, Nowé A, Abecasis A, Deforche K, Santiago GA, Siqueira IC, San EJ, Machado KCB, Azevedo V, Filippis AMB, Cunha RVD, Pybus OG, Vandamme AM, Alcantara LCJ, de Oliveira T, PLoS Negl Trop Dis (2019), 13(5):e0007231: doi: 10.1371/journal.pntd.0007231.

News Section from Bioafrica and SATuRN websites


Why Experts Want to Rename Monkeypox - New York Times - 2022-08-23

A Virus Variant by Any Other Name - Please - The New York Times - 2021-03-03

South African scientists on pandemic’s frontline - Financial Times - 2021-02-15

The New Covid-19 Strain in South Africa: What We Know - The Wall Street Journal - 2021-01-11

KRISP produces over 1000 HIV-1 genomes in record time - SAMRC Press Release - 2020-12-03

The Pros and Cons of high-speed science - Daily Maverick - 2020-04-24

SA scientists on breaking the Covid-19 code - Saturday Independent - 2020-04-21

Odd drop in how Covid-19 numbers grow - Mail & Guadian - 2020-04-02

Social media helped scientists with coronavirus - Independent on Saturday - 2020-02-15

KRISP 2020 - Strategy Meeting - KRISP News - 2019-11-29

KRISP Preparing Next Generation Scientists - UKZN Ndaba News - 2018-10-18

South Africa's bid to end AIDS - Science - 2016-06-29

21st International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME) - Rega Institute & Korea University College of Medicine - 2016-03-15

Case book tackles HIV and TB drug resistance - Zululand Observer - 2013-04-15

Searching for Virus Phylotypes - Pirate Science - 2013-01-22

The Machine That Will Help End TB - MIT Technology review - 2012-12-11


Blogs from Bioafrica and SATuRN websites


Social Worker perspective: Adolescents on Antiretroviral (ARV) therapy - a VideoBlog - by Pretty Nkosi, Nokuthula Skhosana, Lungani Ndwandwe and Tulio de Oliveira - 2012-02-10

KRISP has been created by the coordinated effort of the University of KwaZulu-Natal (UKZN), the Technology Innovation Agency (TIA) and the South African Medical Research Countil (SAMRC).

Location: K-RITH Tower Building
Nelson R Mandela School of Medicine, UKZN
719 Umbilo Road, Durban, South Africa.
Director: Prof. Tulio de Oliveira