NEWS SPOTLIGHT

KRISP NEWS

26th International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME)

The VEME workshop faculty includes international leading researchers in virus evolution, molecular epidemiology, and bioinformatics. VEME has run for 26 years and it became known as one of the best workshops in the world. This year it will be presented in Panama and applicants from developing countries have priority.

ABBOTT- CERI/KRISP – Fellowship in Genomics (2-week short-term and 12-month long-term Fellowships)

Abbott are offering two long-term fellowships of 12 months and 5 short-term fellowships of 2 weeks. The fellowship will cover travel, accommodation, and a daily stipend.

Are new Omicron subvariants a threat? Here's how scientists are keeping watch

In South Africa, a network of researchers are studying whether new lineages BA.4 and BA.5 escape immunity from COVID-19 vaccines and prior infections.

Omicron’s new sub-lineages in SA: Continued evolution of the virus ‘entirely expected’

Two new sub-lineages of the Omicron variant have been detected in SA and some other countries. However, KRISP scientists say there is no cause for alarm at this stage. Known as BA.4 and BA.5, the team will continue to track their spread and study their properties. The detection of two new sub-lineages of the Omicron variant in South Africa serves as a reminder that the virus will continue to evolve and change over time.

'No cause for alarm' as scientists find two new Omicron strains in SA

South African scientists have discovered two new sublineages of the Omicron coronavirus variant, said Tulio de Oliveira, who runs gene-sequencing institutions in the country.

Prof Tulio de Oliveira: saving lives by searching for clues in pandemics

In Covid-19 history, Stellenbosch University (SU) bioinformatician Prof Tulio de Oliveira will be remembered for first detecting the Beta variant of SARS-CoV-2 in late 2020. In November 2021, a few months after moving from the University of KwaZulu-Natal (UKZN) to SU's School for Data Science and Computational Thinking, he also detected the Omicron variant.

SAMRC Scientific Merit Awards: Prof Tulio de Oliveira is awarded a Gold Medal

The South African Medical Research Council strongly supports excellence in health research and has established a set of medal awards to recognise world-class science. The Awards are among South Africa’s most prestigious and are dedicated to contributions to health research in South Africa.

PUBLICATIONS SPOTLIGHT

KRISP SCIENTIFIC PUBLICATIONS

Continued Emergence and Evolution of Omicron in South Africa: New BA.4 and BA.5 lineages.
Tegally H, Moir M, Everatt J, Giovanetti M, Scheepers C, Wilkinson E, Subramoney K, Moyo S, Amoako D, Althaus C, Anyaneji U, Kekana D, Viana R, Giandhari J, Maponga T, Maruapula D, Choga W, Mayaphi S, Mbhele N, Gaseitsiwe S, Msomi N, Naidoo Y, Pillay S, Sanko T, San J, Scott L, Singh L, Magini N, Smith-Lawrence P, Stevens W, Dor G, Tshiabuila D, Wolter N, Preiser W, Treurnicht F, Venter M, Davids M, Chiloane G, Mendes A, McIntyre C, O'Toole A, Ruis C, Peacock T, Roemer C, Williamson C, Pybus O, Bhiman J, Glass A, Martin D, Rambaut A, Gaseitsiwe S, von Gottberg A, Baxter C, Lessells R, de Oliveira T, medRxiv (2022), MEDRXIV-2022-274406v1-deOliveira:.

Effectiveness of the Ad26.COV2.S vaccine in health-care workers in South Africa (the Sisonke study): results from a single-arm, open-label, phase 3B, implementation study.
Bekker LG, Garrett N, Goga A, Fairall L, Reddy T, Yende-Zuma N, Kassanjee R, Collie S, Sanne I, Boulle A, Seocharan I, Engelbrecht I, Davies MA, Champion J, Chen T, Bennett S, Mametja S, Semenya M, Moultrie H, de Oliveira T, Lessells R, Cohen C, Jassat W, Groome M, Von Gottberg A, Le Roux E, Khuto K, Barouch D, Mahomed H, Wolmarans M, Rousseau P, Bradshaw D, Mulder M, Opie J, Louw V, Jacobson B, Rowji P, Peter JG, Takalani A, Odhiambo J, Mayat F, Takuva S, Corey L, Gray GE, Lancet (2022), 399(10330):1141-1153. doi: 10.1016/S0140-6736(22)00007-1:.

The geography and inter-community configuration of new sexual partnership formation in a rural South African population over fourteen years (2003–2016).
Kim H-Y, Cuadros D, Wilkinson E, Junqueira DM, de Oliveira T, Tanser F, PLoS Global Public Health (2022), https://doi.org/10.1371/journal.pgph.0000055:.

Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage.
Scheepers C, Everatt J, Amoako DG, Tegally H, Wibmer CK, Mnguni A, Ismail A, Mahlangu B, Lambson BE, Martin DP, Wilkinson E, San JE, Giandhari J, Manamela N, Ntuli N, Kgagudi P, Cele S, Richardson SI, Pillay S, Mohale T, Ramphal U, Naidoo Y, Khumalo ZT, Kwatra G, Gray G, Bekker LG, Madhi SA, Baillie V, Van Voorhis WC, Treurnicht FK, Venter M, Mlisana K, Wolter N, Sigal A, Williamson C, Hsiao NY, Msomi N, Maponga T, Preiser W, Makatini Z, Lessells R, Moore PL, de Oliveira T, von Gottberg A, Bhiman JN, Nature Commununications (2022), 13(1):1976. doi: 10.1038/s41467-022-29579-9:.

Genomic epidemiology reveals the impact of national and international restrictions measures on the SARS-CoV-2 epidemic in Brazil.
Giovanetti M, Slavov SN, Fonseca V, Wilkinson E, Tegally H, Patané JSL, Viala VL, San JE, Rodrigues ES, Vieira Santos E, Aburjaile F, Xavier J, Fritsch H, Ribeiro Adelino TE, Pereira F, Leal A, Campos de Melo Iani F, de Carvalho Pereira G, Vazquez C, Mercedes Estigarribia Sanabria G, de Oliveira EC, Demarchi L, Croda J, Dos Santos Bezerra R, Oliveira de Lima LP, Martins AJ, Dos Santos Barros CR, Marqueze EC, de Souza Todao Bernardino J, Moretti DB, Brassaloti RA, de Lello Rocha Campos Cassano R, Drummond Sampaio Corrêa Mariani P, Kitajima JP, Santos B, Proto-Siqueira R, Cantarelli VV, Tosta S, Brandão Nardy V, Reboredo de Oliveira da Silva L, Astete Gómez MK, Lima JG, Ribeiro AA, Guimarães NR, Watanabe LT, Barbosa Da Silva L, da Silva Ferreira R, F da Penha MP, Ortega MJ, Gómez de la Fuente A, Villalba S, Torales J, Gamarra ML, Aquino C, Martínez Figueredo GP, Fava WS, Motta-Castro ARC, Venturini J, do Vale Leone de Oliveira SM, Cavalheiro Maymone Gonçalves C, Debur Rossa MDC, Becker GN, Presibella MM, Marques NQ, Riediger IN, Raboni S, Coelho GM, Cataneo AHD, Zanluca C, Dos Santos CND, Assato PA, Allan da Silva da Costa F, Poleti MD, Chagas Lesbon JC, Mattos EC, Banho CA, Sacchetto L, Moraes MM, Tommasini Grotto RM, Souza-Neto JA, Nogueira ML, Fukumasu H, Coutinho LL, Calado RT, Neto RM, Bispo de Filippis AM, Venancio da Cunha R, Freitas C, Leonel Peterka CR, Rangel Fernandes CF, de Araújo WN, do Carmo Said RF, Almiron M, Campelo de Albuquerque E Melo CF, Lourenço J, de Oliveira T, Holmes EC, Haddad R, Sampaio SC, Elias MC, Kashima S, de Alcantara LCJ, Covas DT, medRxiv [Preprint] (2022), 28:2021.10.07.21264644. doi: 10.1101/2021.10.07.21264644:.

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:.

Selection analysis identifies clusters of unusual mutational changes in Omicron lineage BA.1 that likely impact Spike function.
Martin DP, Lytras S, Lucaci AG, Maier W, Grüning B, Shank SD, Weaver S, MacLean OA, Orton RJ, Lemey P, Boni MF, Tegally H, Harkins GW, Scheepers C, Bhiman JN, Everatt J, Amoako DG, San JE, Giandhari J, Sigal A; NGS-SA, Williamson C, Hsiao NY, von Gottberg A, De Klerk A, Shafer RW, Robertson DL, Wilkinson RJ, Sewell BT, Lessells R, Nekrutenko A, Greaney AJ, Starr TN, Bloom JD, Murrell B, Wilkinson E, Gupta RK, de Oliveira T, Kosakovsky Pond SL, Mol Biol Evol. (2022), doi: 10.1093/molbev/msac061:.

KRISP VIDEOS

8th SAMRC Scientific Merit Awards - Prof Tulio de Oliveira - Gold Award
By: Tulio de Oliveira

KRISP BIOINFORMATICS TOOLS