TIME 100: The 100 Most Influential People of 2022 - Prof Tulio de Oliveira and Sikhulile Moyo

NEWS SPOTLIGHT



Science



Nature



The Guardian

KRISP NEWS


NGS-BRICS Viral Sequencing and Phylogenetics Workshop, 26-30 Sept 2022

The BRICS Network for Genome Surveillance (NGS-BRICS) was established in 2021 and generates and investigates sequence data of viral pathogens of public health importance, such as COVID-19. In the interest of increasing bioinformatics and experimental expertise within BRICS countries. Applications close on 1st of August 2022.


Postdoctoral Research Fellowship: Infectious Disease Management

The Centre for Epidemic Response and Innovation (CERI) is seeking to appoint a post-doctoral fellow with great potential and ambition to become a leading scientist. The position will work with some of the best genomics and bioinformatics scientists in the world. We aim to identify both pathogen and human genomic variation that are associated with the transmission and virulence of pathogens and the development of diseases.


CERI & KRISP Newsletter Aug/Sep 2022: Scientific research and surveillance efforts at CERI & KRISP remain under the global spotlight

This month we reflect on how much the world has changed over the last two years. It is still too early to declare the pandemic over, but it is time to begin thinking about what can be done better and how best to prepare for future threats to global health.


Genomics Africa Fellowships: 2-week short term fellowships and hands-on workshop on NGS sequencing

Individuals from organizations affiliated with the Abbott Pandemic Defense Coalition & Rockefeller Pandemic Prevention Institute will participate in long- and short-term training opportunities at CERI/KRISP.


Pandemic preparedness in a changing world: Fostering global collaboration to strengthen public health and respond to viral threats

The last 2 years have made us fully aware of the devastating effects that a global pandemic can have. We appear to be past the worst of it, but it’s too early to say that it’s over. It is not too early, however, to begin thinking about what can be done better when the precursor to the next pandemic comes along.


The Virus Hunters Trying to Prevent the Next Pandemic

Nobody saw SARS-CoV-2 coming. In the early days of the pandemic, researchers were scrambling to collect samples from people who had mysteriously developed fevers, coughs, and breathing problems. Pretty soon, they realized that the disease-causing culprit was a new virus humans hadn’t seen before.


Tulio de Oliveira: collaborating to boost science in Africa

Bioinformatician and Director of CERI and KRISP, Prof Tulio de Oliveira is profiled in The Lancet. Article written by Udani Samarasekera, 6 August 2022.


PUBLICATIONS SPOTLIGHT


Nature


Nature


Science

KRISP SCIENTIFIC PUBLICATIONS


Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus.
Happi C, Adetifa I, Mbala P, Njouom R, Nakoune E, Happi A, Ndodo N, Ayansola O, Mboowa G, Bedford T, Neher RA, Roemer C, Hodcroft E, Tegally H, O'Toole Á, Rambaut A, Pybus O, Kraemer MUG, Wilkinson E, Isidro J, Borges V, Pinto M, Gomes JP, Freitas L, Resende PC, Lee RTC, Maurer-Stroh S, Baxter C, Lessells R, Ogwell AE, Kebede Y, Tessema SK, de Oliveira T, PLoS Biology (2022), doi: 10.1371/journal.pbio.3001769.:.



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:.



SARS-CoV-2 Genetic Diversity and Lineage Dynamics in Egypt during the First 18 Months of the Pandemic.
Roshdy WH, Khalifa MK, San JE, Tegally H, Wilkinson E, Showky SM, Darren P, Moir M, Naguib AEN, Gomaa MR, Fahim MAEH, Mohsen AGR, Hassany M, Lessells R, Al-Karmalawy AA, EL-Shesheny R, Kandeil AM, Ali MA, de Oliveira T, Viruses (2022), https://www.mdpi.com/1999-4915/14/9/1878:.



Building genomic sequencing capacity in Africa to respond to the SARS-CoV-2 pandemic.
de Oliveira T, Wilkinson E, Baxter C, Tegally H, Giandhari J, Naidoo Y, Pillay S, Science (2022), https://www.science.org/content/resource/pandemic-preparedness-changing-world-fostering-global-collaboration, 2022:.



Omicron BA.4/BA.5 escape neutralizing immunity elicited by BA.1 infection..
Khan K, Karim F, Ganga Y, Bernstein M, Jule Z, Reedoy K, Cele S, Lustig G, Amoako D, Wolter N, Samsunder N, Sivro A, San JE, Giandhari J, Tegally H, Pillay S, Naidoo Y, Mazibuko M, Miya Y, Ngcobo N, Manickchund N, Magula N, Karim QA, von Gottberg A, Abdool Karim SS, Hanekom W, Gosnell BI; COMMIT-KZN Team, Lessells RJ, de Oliveira T, Moosa MS, Sigal A, Nature Communications (2022), doi: 10.1038/s41467-022-32396-9:.



Genomic surveillance of Rift Valley fever virus: from sequencing to lineage assignment.
Juma J, Fonseca V, Konongoi SL, van Heusden P, Roesel K, Sang R, Bett B, Christoffels A, de Oliveira T, Oyola SO, BMC Genomics (2022), 23(1):520. doi: 10.1186/s12864-022-08764-6:.



HIV-1 Evolutionary Dynamics under Nonsuppressive Antiretroviral Therapy.
Kemp SA, Charles OJ, Derache A, Smidt W, Martin DP, Iwuji C, Adamson J, Govender K, de Oliveira T, Dabis F, Pillay D, Goldstein RA, Gupta RK, mBio (2022), 13(3):e0026922. doi: 10.1128/mbio.00269-22:.



KRISP VIDEOS


As the COVID pandemic recedes CERI & KRISP join the fight to control other outbreaks and epidemics
By: Tulio de Oliveira

KRISP BIOINFORMATICS TOOLS



Genome Detective Coronavirus Typing Tool

Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes



Genome Detective Dengue Virus Typing Tool

This is a beta version of our Dengue Virus Typing tool. For the mean time, this tool should be used for evaluation only. Please send feedback to Tulio de Oliveira.



Genome Detective Zika Typing Tool

This is the first version of the Zika typing tool, which uses phylogenetic analysis to identify the species and genotype of the virus.



Genome Detective Chikungunya Typing Tool

This is the first version of the Chikungunya typing tool, which uses phylogenetic analysis to identify the species and genotype of the virus.



Genome Detective Yellow Fever Virus Typing Tool

This is the first version of the Yellow Fever typing tool, which uses phylogenetic analysis to identify the species and genotype of the virus.



Genome Detective

This is the first version of our Arbovirus typing tool for Chikungunya, Dengue, Yellow Fever and Zika



REGA HIV Subtyping Tool V3 - Belgium Mirror

Phylogenetic tool to identify the HIV-1 subtypes and recombinants. Query sequences are analysed for recombination using bootscanning methods. The version 3 contains new CRFs (CRF01_AE to CRF47_BF).


MORE TOOLS


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