About Emmanuel James San
sanemmanueljames@gmail.com +27 (0) 72 529 0848
Background:
San James is Pursuing a PhD in Medicine, Majoring in Virology at the Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, South Africa and is a Bioinformatics Research Associate at the Kwazulu Natal Research and Innovation Sequencing Platform. Owing to his experience working as a Systems Analyst and Programmer with the Infectious Diseases Research Collaboration where he participated in exciting projects such the development of a clinical data visualization platform and Data Management Specialist at Global Health Uganda, he developed a keen interest bioinformatics research especially in the areas of Bioinformatics Software and Pipelines Development, Next Generation Sequence Data Management and Analysis (Phylogenetics, Recombinants and Drug Resistance), and High Performance Computing for Data Intensive Projects. His PhD research focus is in Microbial Classification and Detection, Development of SOPs for Sequence Analysis Projects, Validation of Existing Pipelines and setting up a standardized and structured bioinformatics environment.
Affiliations:
KRISP - KwaZulu-Natal Research and Innovation Sequencing Platform, UKZN, Durban, South Africa.
Department of Virology, National Health Laboratory Service (NHLS), Durban, South Africa (PhD Fellow).
Education:
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
PUBLICATIONS
A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa
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Wilkinson E, Giovanetti M, Tegally H, San EJ, Lessells R, Abdoul K. Sangare, Abdoul-Salam Ouedraogo, Abdul K. Sesay, Abechi Priscilla, Adedotun-Sulaiman Kemi, Adewunmi M. Olubusuyi, Adeyemi O.O. Oluwapelumi, Adnène Hammami, Adrienne A. Amuri, Ahmad Sayed, Ahmed E.O. Ouma, Aida Elargoubi, Ajayi N. Anthony, Ajogbasile F. Victoria, Akano Kazeem, Akpede George, Alexander J. Trotter, Ali A. Yahaya, Alpha K. Keita, Amadou Diallo, Amadou Kone, Amal Souissi, Amel Chtourou, Ana V. Gutierrez, Andrew J. Page, Anika Vinze, Arash Iranzadeh, Arnold Lambisia, Arshad Ismail, Audu Rosemary, Augustina Sylverken, Ayoade Femi, Azeddine Ibrahimi, Baba Marycelin, Bamidele S. Oderinde, Bankole Bolajoko, Beatrice Dhaala, Belinda L. Herring, Berthe-Marie Njanpop-Lafourcade, Bronwyn Kleinhans, Bronwyn McInnis, Bryan Tegomoh, Cara Brook, Catherine B. Pratt, Cathrine Scheepers, Chantal G. Akoua-Koffi, Charles N. Agoti, Christophe Peyrefitte, Claudia Daubenberger, Collins M. Moranga, D. James Nokes, Daniel G. Amoako, Daniel L. Bugembe, Danny Park, David Baker, Deelan Doolabh, Deogratius Ssemwanga, Derek Tshiabuila, Diarra Bassirou, Dominic S.Y. Amuzu, Dominique Goedhals, Donwilliams O. Omuoyo, Dorcas Maruapula, Ebenezer Foster-Nyarko, Eddy K. Lusamaki, Edgar Simulundu, Edidah M. Ong'era, Edith N. Ngabana, Edwin Shumba, Elmostafa El Fahime, Emmanuel Lokilo, Enatha Mukantwari, Eromon Philomena, Essia Belarbi, Etienne Simon-Loriere, Etilé A. Anoh, Fabian Leendertz, Faida Ajili, Fakayode O. Enoch, Fares Wasfi, Fatma Abdelmoula, Fausta S. Mosha, Faustinos T. Takawira, Fawzi Derrar, Feriel Bouzid, Folarin Onikepe, Fowotade Adeola, Francisca M. Muyembe, Frank Tanser, Fred A. Dratibi, Gabriel K. Mbunsu, Gaetan Thilliez, Gemma L. Kay, George Githinji, Gert van Zyl, Gordon A. Awandare, Grit Schubert, Gugu P. Maphalala, Hafaliana C. Ranaivoson, Hajar Lemriss, Happi Anise, Haruka Abe, Hela H. Karray, Hellen Nansumba, Hesham A. Elgahzaly, Hlanai Gumbo, Ibtihel Smeti, Ikhlas B. Ayed, Ikponmwosa Odia, Ilhem Boutiba-Ben Boubaker, Imed Gaaloul, Inbal Gazy, Innocent Mudau, Isaac Ssewanyana, Iyaloo Konstantinus, Jean B. Lekana-Douk, Jean-Claude C. Makangara, Jean-Jacques M. Tamfum, Jean-Michel Heraud, Jeffrey G. Shaffer, Giandhari J, Jingjing Li, Jiro Yasuda, Joana Q. Mends, Jocelyn Kiconco, John M. Morobe, John O. Gyapong, Johnson C. Okolie, John T. Kayiwa, Johnathan A. Edwards, Jones Gyamfi, Jouali Farah, Joweria Nakaseegu, Joyce M. Ngoi, Joyce Namulondo, Julia C. Andeko, Julius J. Lutwama, Justin OGrady, Katherine Siddle, Kayode T. Adeyemi, Kefentse A. Tumedi, Khadija M. Said, Kim Hae-Young, Kwabena O. Duedu, Lahcen Belyamani, Lamia Fki-Berrajah, Lavanya Singh, Leonardo de O. Martins, Lynn Tyers, Magalutcheemee Ramuth, Maha Mastouri, Mahjoub Aouni, Mahmoud el Hefnawi, Maitshwarelo I. Matsheka, Malebogo Kebabonye, Mamadou Diop, Manel Turki, Marietou Paye, Martin M. Nyaga, Mathabo Mareka, Matoke-Muhia Damaris, Maureen W. Mburu, Maximillian Mpina, Mba Nwando, Michael Owusu, Michael R. Wiley, Mirabeau T. Youtchou, Mitoha O. Ayekaba, Mohamed Abouelhoda, Mohamed G. Seadawy, Mohamed K. Khalifa, Mooko Sekhele, Mouna Ouadghiri, Moussa M. Diagne, Mulenga Mwenda, Mushal Allam, My V.T. Phan, Nabil Abid, Nadia Touil, Nadine Rujeni, Najla Kharrat, Nalia Ismael, Ndongo Dia, Nedio Mabunda, Nei-yuan Hsiao, Nelson B. Silochi, Ngoy Nsenga, Nicksy Gumede, Nicola Mulder, Nnaemeka Ndodo, Norosoa H Razanajatovo, Nosamiefan Iguosadolo, Oguzie Judith, Ojide C. Kingsley, Okogbenin Sylvanus, Okokhere Peter, Oladiji Femi, Olawoye Idowu, Olumade Testimony, Omoruyi E. Chukwuma, Onwe E. Ogah, Onwuamah Chika, Oshomah Cyril, Ousmane Faye, Oyewale Tomori, Pascale Ondoa, Patrice Combe, Patrick Semanda, Paul E. Oluniyi, Paulo Arnaldo, Peter K. Quashie, Philippe Dussart, Phillip A. Bester, Placide K. Mbala, Reuben Ayivor-Djanie, Richard Njouom, Richard O. Phillips, Richmond Gorman, Robert A. Kingsley, Rosina A.A. Carr, Saâd El Kabbaj, Saba Gargouri, Saber Masmoudi, Safietou Sankhe, Salako B. Lawal, Samar Kassim, Sameh Trabelsi, Samar Metha, Sami Kammoun, Sanaâ Lemriss, Sara H.A. Agwa, Sébastien Calvignac-Spencer, Stephen F. Schaffner, Seydou Doumbia, Sheila M. Mandanda, Sherihane Aryeetey, Shymaa S. Ahmed, Siham Elhamoumi, Soafy Andriamandimby, Sobajo Tope, Sonia Lekana-Douki, Sophie Prosolek, Soumeya Ouangraoua, Steve A. Mundeke, Steven Rudder, Sumir Panji, Sureshnee Pillay, Susan Engelbrecht, Susan Nabadda, Sylvie Behillil, Sylvie L. Budiaki, Sylvie van der Werf, Tapfumanei Mashe, Tarik Aanniz, Thabo Mohale, Thanh Le-Viet, Tobias Schindler, Ugochukwu J. Anyaneji, Ugwu Chinedu, Ramphal U, Uwanibe Jessica, Uwem George, Fonseca V, Vincent Enouf, Vivianne Gorova, Wael H. Roshdy, William K. Ampofo, Wolfgang Preiser, Wonderful T. Choga, Yaw Bediako, Yeshnee Naidoo, Yvan Butera, Zaydah R. de Laurent, Amadou A. Sall, Ahmed Rebai, Anne von Gottberg, Bourema Kouriba, Carolyn Williamson, Daniel J. Bridges, Ihekweazu Chikwe, Jinal Bhiman, Madisa Mine, Matthew Cotten, Sikhulile Moyo, Simani Gaseitsiwe, Ngonda Saasa, Pardis C. Sabeti, Pontiano Kaleebu, Yenew K. Tebeje, Sofonias K. Tessema, Happi Christian, John Nkengasong, de Oliveira T, Science (2021), DOI: 10.1126/science.abj4336:.
The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages
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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.
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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 (2021), 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:.
High Resolution analysis of Transmission Dynamics of Sars-Cov-2 in Two Major Hospital Outbreaks in South Africa Leveraging Intrahost Diversity.
San EJ, Ngcapu S, Kanzi A, Tegally H, Fonseca V, Giandhari J, Wilkinson E, Chimukangara B, Pillay S, Singh L, Fish M, Gazy I, Khanyile KS, Lessells R, de Oliveira T, medRxiv (2020), https://doi.org/10.1101/2020.11.15.20231993:.
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
CERI: Realizing the Potential of Pathogen Genomics in Africa - Illumina - 2021-09-30
Unethical? Unnecessary? The COVID-19 vaccine booster debate intensifies - Science - 2021-08-27
Stellenbosch University 2 Postdoctoral Positions on Pathogen Genomics, Cape Town - PostDoc - 2021-07-30
Coronavirus variants get Greek names, but will scientists use them? - Nature - 2021-06-01
Whats unique about the bodys response to the 501Y.V2 variant? Find out - Bhekisisa - 2021-03-12
We Now Can See a Virus Mutate Like Never Before - The Atlantic - 2021-03-09
A Virus Variant by Any Other Name - Please - The New York Times - 2021-03-03
Covid variants: What are they and will vaccines work? - BBC - 2021-03-02
South African scientists on pandemics frontline - Financial Times - 2021-02-15
All These Mutant Virus Strains Need New Code Names - Wired - 2021-02-08
Worrisome New Coronavirus Strains Are Emerging. Why Now? - Wired - 2021-01-27
Alarming COVID variants show vital role of genomic surveillance - Nature - 2021-01-17
Will vaccines work against the new COVID variants? Scientists race to find out - Bhekisisa - 2021-01-15
As Coronavirus Mutates, the World Stumbles Again to Respond - The New York Times - 2021-01-15
Could new COVID variants undermine vaccines? Labs scramble to find out - Nature - 2021-01-14
WHO calls for new names for Covid variants to avoid country stigma - The Telegraph - 2021-01-12
The New Covid-19 Strain in South Africa: What We Know - The Wall Street Journal - 2021-01-11
Got questions about the new Covid-19 variant in South Africa? Health department has lots of answers - Department of Health - 2020-12-19
KRISP produces over 1000 HIV-1 genomes in record time - SAMRC Press Release - 2020-12-03
Accelerating genomics-based surveillance for COVID-19 response in Africa - Lancet Microbe - 2020-08-25
South Africa joins 'Big 5' COVID-19 countries - Mybroadband - 2020-07-18
Experts question underreported' virus deaths in South Africa - Businesstech - 2020-07-18
South Africa Data May Underreport Virus Deaths, Experts Say - Bloomberg - 2020-07-18
Initial COVID-19 Infections In CT Came From Europe, Researchers Find - EWN - 2020-07-17
En Afrique du Sud, l'espoir ténu du BCG, « boosteur » du système immunitaire contre le Covid-19 - Le Monde - 2020-06-17
En Afrique du Sud, des chercheurs remontent la piste du coronavirus - Le Monde - 2020-06-06
South Africa: Protecting Healthcare Workers 'Not Rocket Science' - All Africa - 2020-06-02
Coronavirus in South Africa: Eight lessons for the rest of the continent - BBC - 2020-05-30
Three detectives', a virus and the patient who infected an entire hospital | Future Planet - Future Planet - 2020-05-27
Between two devils: Why hospitals must act fast to prevent health worker deaths - Bhekisisa - 2020-05-25
Lockdown has stopped SA's flu season in its tracks - it's now several weeks late - Business Insider - 2020-05-25
Southern Africa: COVID-19 Roundup | Back to School - All Africa - 2020-05-23
More than 100 infections and 15 patient deaths in Covid-19 outbreak at St Augustine's Hospital - Times Live - 2020-05-20
Lockdown and other interventions potentially saved 20 000 lives - News24 - 2020-05-13
Covid-19: Infections could rise by 10% per day after lockdown lifts - top scientists - News24 - 2020-05-01
Coronavirus: 27 patients on ventilators as SA edges towards the end of 'hard' lockdown - News24 - 2020-04-28
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
Support South Africa's COVID-19 Scientists on the Frontline - BackaBuddy - 2020-04-19
Odd drop in how Covid-19 numbers grow - Mail & Guadian - 2020-04-02
What you need to know about Covid-19 to protect yourself - Mail and Guardian - 2020-03-24
Coronavirus testing: How it works, what it costs and when you need a test - Bhekisisa - 2020-03-11
Innovation Festival 2020, Durban, South Africa, 5-7 March 2020 - Innovate Durban - 2020-03-05
UKZN to launch health war room to tackle coronavirus - Raising News - 2020-03-05
UKZN scientists make the African Academy of Science's Top 40 List - The Mercury - 2020-02-25
UKZN professor & KRISP Group Leader Bags Prestigious Award - The Mercury - 2020-02-24
Social media helped scientists with coronavirus - Independent on Saturday - 2020-02-15
KRISP Newsletter Jan 2020: Reversing brain drain and training the next generation of scientists in South Africa and abroad. - KRISP Newsletter - 2020-02-04
KRISP 2020 - Strategy Meeting - KRISP News - 2019-11-29
Promotion Sanger Sequencing at KRISP - Jan to Dec 2020 - Promotion Sanger - 2019-11-13
Open Access Book Chapter - Mosquito-Borne Viral Diseases: Control and Prevention in the Genomics Era - KRISP News - 2019-10-03
KRISP Newsletter Sept 2019: KRISP Sale Brochure 2019-2020 and the launch of KRISP Business Development Unit - KRISP Newsletter - 2019-09-03
KRISP Road Shows Westville & Pietermaritzburg UKZN Campuses - KRISP News - 2019-07-30
Capillary Electrophoresis (i.e. Sanger Sequencing) Workshop II, Durban, South Africa, 27-28 June 2019 - KRISP Education - 2019-06-26
Capillary Electrophoresis (i.e. Sanger Sequencing) Training Workshop, Durban, South Africa, 24-25 June 2019 - KRISP Education - 2019-06-25
STEM Education: Training II - Quantitative PCR (qPCR), KRISP and ThermoScientific Workshop, Durban, South Africa, 21 June 2019 - KRISP & Thermo Fisher - 2019-06-21
STEM Education: Training I - Quantitative PCR (qPCR), KRISP and ThermoScientific Workshop, Durban, South Africa, 20 June 2019 - KRISP & Thermo Fisher - 2019-06-20
KRISP Newsletter May/June 2019: KRISP participation in BIO 2019, the largest biotechnology innovation convention in the world - KRISP Newsletter - 2019-06-20
KRISP among the first awards of The African Academy of Sciences and Royal Society £25M FLAIR scheme - Royal Society - 2019-04-06
KRISP provide access to high-throughput Sanger sequencing services - KRISP Services - 2019-04-01
KRISP & Thermo Fisher Scientific complete their 5th STEM training workshop in Africa - KRISP News - 2019-03-31
DNA Sequencing Fragment Analysis (i.e Microsatellite) Workshop, Durban, South Africa, 28-29 March 2019 - KRISP Education - 2019-03-28
Capillary Electrophoresis (i.e. Sanger Sequencing) Training Workshop, Durban, South Africa, 24-25 March 2019 - KRISP Education - 2019-03-25
Workshop in Translational Research, Health Innovation & Commercialization - KRISP Innovation - 2019-03-20
KRISP Preparing Next Generation Scientists - UKZN Ndaba News - 2018-10-18
In Epicenter of Global HIV Crisis, Multiple Partners and Age Disparity Part of Problem - Epoch Times - 2018-10-17
Innovation Festival 2018, Durban, South Africa, 28-30 June 2018. - KRISP News - 2018-06-28
KRISP gets two awards at SANTHE DELTA initiative - KRISP News - 2018-06-07
Nature paper: Renewing Felsenstein's phylogenetic bootstrap in the era of big data - KRISP Papers - 2018-04-18
Find Funding - List of Agencies in South Africa and abroad - - 2018-02-06
Science Discovery: Biomarkers for HIV treatment - KRISP News - 2018-01-19
SA study reveals important link between genes and Aids - KRISP News - 2018-01-19
Why some HIV-positive people develop AIDS quicker than others is now clearer - KRISP News - 2018-01-19
Prevention of HIV transmission by antiretroviral therapy - KRISP News - 2017-11-30
KRISP Newsletter - July 2017: news, videos, blogs, publications and training events - KRISP Newsletter - 2017-08-01
KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP) Established - KRISP News - 2017-07-12
Two manuscripts featured in the Lancet website front webpage on AIDS day. - The Lancet - 2016-12-01
PhD Fellowship II: Genomics, Bioinformatics, Epidemioloy and Phylogenetics - CAPRISA, UKZN & MRC Flagship - 2016-08-23
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
MOLECULAR EPIDEMIOLOGY: HIV family trees reveal viral spread. - Science - 2015-06-12
HIV 2015: Using Phylogenetics to Enhance the HIV Response, New York, June 4, 2015 - New York Academy of Sciences - 2015-06-04
Seminar: Virus and host genetics: where and how to look in big data for associations with infectious disease - KRISP Talks - 2015-02-13
Seminar: 30 years of HIV diversity research: a personal perspective - KRISP Talks - 2014-01-31
New Director named for leading HIV research centre in South Africa - Wellcome Trust - 2013-09-02
Infectious Disease Genomics and Global Health Wellcome Trust Conference - Wellcome Trust - 2013-05-24
Case book tackles HIV and TB drug resistance - Zululand Observer - 2013-04-15
PRESS RELEASE: Book Launch: HIV and TB Drug Resistance & Clinical Management Case Book - Africa Centre - 2013-03-06
Invitation to the launch of the HIV and TB drug resistance & clinical management case book - University of Pretoria - 2013-03-05
Searching for Virus Phylotypes - Pirate Science - 2013-01-22
The Machine That Will Help End TB - MIT Technology review - 2012-12-11
SATuRN at the 43rd Union World Conference on Lung Health - TB Union - 2012-11-20
Collaboration to Undertake HIV Resistance Testing in Africa - LabMedica - 2012-08-06
Life Tech, SATuRN Collaborate on Dx for Antiretroviral Resistance in HIV in Africa - GenomeWeb - 2012-07-26
Life Technologies and SATuRN Collaborate to Increase Access to HIV Testing in Africa - The Wall Street Journal - 2012-07-24
HIV drug resistance is spreading in Africa, experts say - Los Angeles Times - 2012-07-23
VIDEOS
Social Worker Workshop with Adolescents on ARVs in South Africa - YouTube - 2012-12-30
BLOGS
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