PUBLICATIONS SPOTLIGHT

PUBLICATIONS

Reduced efficacy of HIV-1 integrase inhibitors in patients with drug resistance mutations in reverse transcriptase

Siedner MJ, Moorhouse MA, Simmons B, de Oliveira T, Lessells R, Giandhari J, Kemp SA, Chimukangara B, Akpomiemie G, Serenata Cm, Venter WDF, HillA, Gupta RK, Nature Communications (2020), https://doi.org/10.1038/s41467-020-19801-x:

HIV infection alters SARS-CoV-2 responsive immune parameters but not clinical outcomes in COVID-19 disease

Karim F, Gazy I, Cele S, Zungu Y, Krause R, Bernstein M, Ganga Y, Rodel H, Mthabela N, Mazibuko M, Khan K, Muema D, Ramjit D, Lustig G, Ndung'u T, Hanekom W, Gosnell BI, COMMIT-KZN Team, Wong E, de Oliveira T, Moosa MYS, Leslie A, Kløverpris H, Sigal A, medRxiv (2020), doi: https://doi.org/10.1101/2020.11.23.20236828:

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:

Cost-effectiveness of public health strategies for COVID-19 epidemic control in South Africa: a microsimulation modelling study

Reddy KP, Shebl FM, Foote JHA, Harling G, Scott JA, Panella C, Fitzmaurice KP, Flanagan C, Hyle EP, Neilan AM, Mohareb AM, Bekker L-G, Lessells R, Ciaranello AL, Wood R, Losina E, Freedberg KA, Kazemian P, Siedner MJ , Lancet Global Health (2020), https://doi.org/10.1016/S2214-109X(20)30452-6:

Portable sequencing in the field and the classroom: a retrospective examination of the circulation of DENV1 and DENV2 in Brazil

Adelino TER, Giovanetti M, Fonseca V, Xavier J, Salgado A, Nascimento V, Demarchi LH, Oliveira M, Silva V, Mello A, Muricy G, Santos R, Oliveira E, Junior JAC, Iani F, de Filippis AMB, Abreu AL, de Jesus R, Albuquerque CF, Rico J, Said R, Silva J, Moura N, Leite P, Vinhal L, Kashima S, Martinez AA, Khouri F, Vazquez C, Cunha R, Araujo E, Tosta S, Fabri A, Chalhoub F, Lemos P, de Bruycker-Nogueira F, Lichs G, Zardin M, Cardozo F, Goncalves C, Fernandez Z, Slavov S, Pereira LA, Mendonca AF, Pereira F, Magalhaes J, de Castro A, Lima M, Nogueira R, Goes A, Azevedo V, Ramalho D, Oliveira W, Medeiros A, Pimentel V, Latin American Genomic Surveillance Arboviral Network, Holmes EC, de Oliveira T, Lourenco J, Alcantara LCJ, medRxiv (2020), https://doi.org/10.1101/2020.09.01.20183301:

Adding a Voice to the Unique Ethical Considerations in Molecular HIV Surveillance

Mutenherwa F, Wassenaar D, de Oliveira T, The American Journal of Bioethics (2020), https://doi.org/10.1080/15265161.2020.1806399:

Detection of Inducible Replication-Competent HIV-1 Subtype C Provirus Despite Long-Term Antiretroviral Treatment in Perinatally Infected Adolescents in Botswana

Koofhethile CK, Moyo S, Kotokwe KP, Chang C, Mokgethi P, Muchoba L, Mokgweetsi S, Makhema J, Lockman S, Gaseitsiwe S, de Oliveira T, Essex M, Shapiro R, Kanki P, Novitsky V, AIDS Res Hum Retroviruses (2020), doi: 10.1089/AID.2020.0097:

Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance

Kanzi AM, San JE , Chimukangara B, Wilkinson E, Ramsuran V, de Oliveira T, Frontiers in Genetics (2020), 11: 1250, https://doi.org/10.3389/fgene.2020.544162:

Impact of pretreatment low-abundance HIV-1 drug-resistant variants on virological failure among HIV-1/TB-co-infected individuals

Chimukangara B, Giandhari J, Lessells J, Yende-Zuma N, Sartorius B, Samuel R, Khanyile KS, Stray-Pedersen B, Moodley P, Metzner KJ, Padayatchi N, Naidoo K, de Oliveira T, Journal of Antimicrobial Chemotherapy (2020), 75, 11:3319–3326, https://doi.org/10.1093/jac/dkaa343

Unlocking the efficiency of genomics laboratories with robotic liquid-handling

Tegally H, San JE, Giandhari J, de Oliveira T, BMC Genomics (2020), 729:https://doi.org/10.1186/s12864-020-07137-1

Fatal outcome of chikungunya virus infection in Brazil

Lima STS, Souza WM, Cavalcante JW, Candido DS, Fumagalli MJ, Carrera JP, Mello LMS, Araújo FMC, Ramalho ILC, Barreto FKA, Braga DNM, Simião AR, Silva MJM, Oliveira RMAB, Lima CPS, Lins CS, Barata RR, Melo MNP, Souza MPC, Franco LM, Távora FRF, Lemos DRQ, Alencar CHM, Jesus R, Fonseca V, Dutra LH, Abreu AL, Araújo ELL, Freitas ARR, Júnior JLSGV, Pybus OG, Figueiredo LTM, Faria NR, Nunes MRT, Cavalcanti LPG, Miyajima F., Clinical Infectious Diseases (2020), ciaa1038 DOI: https://doi.org/10.1093/cid/ciaa1038:

Yellow fever transmission in non-human primates, Bahia, Northeastern Brazil

Goes de Jesus J, Gräf T, Giovanetti M, Mares-Guia MA, Xavier J, Lima Maia M, Fonseca V, Fabri A, Santos RF, Pereira FM, Santos LFO, Silva LRO, Maia ZPG, Cerqueira JXG, Thèze J, Abade L, Cordeiro MCS, Torquato SSC, Santana EB, Silva NSJ, Dourado RSO, Alves AB, Guedes AS, Filho PMC, Faria NR, Campelo de Albuquerque CF, Abreu AL, Romano APM, Croda J, Said RFC, Cunha GM, Cerqueira JMF, Mello ALS, Filippis AMB, Alcantara LCJ., PLoS Negl Trop Dis (2020), 14(8): e0008405. https://doi.org/10.1371/journal.pntd.0008405:14(8): e0008405

Accelerating genomics-based surveillance for COVID-19 response in Africa

Tessema SK, Inzaule SC, Christoffels A, Kebede Y, de Oliveira T, Ouma AEO, Happi CT, Nkengasong JN, Lancet Microbe (2020), https://doi.org/10.1016/S2666-5247(20)30117-8:

A genomics network established to respond rapidly to public health threats in South Africa

Msomi N, Mlisana K, Willianson C, Bhiman JN, Goedhals D, Engelbrecht S, Van Zyl G, Preiser W, Hardie D, Hsiao M, Mulder N, Martin D, Christoffels A, York D, Giandhari J, Wilkinson E, Pillay S, Tegally H, James SE, Kanzi A, Lessells RJ, de Oliveira T, Lancet Microbe (2020), https://doi.org/10.1016/S2666-5247(20)30116-6:

Exposure to waste sites and their impact on health: a panel and geospatial analysis of nationally representative data from South Africa, 2008–2015

Tomita A, Cuadros DF, Burns JK, Tanser F, Slotow R, Lancet Planetary Health (2020), 4: e223–34:

Neurocognitive functioning in MDR-TB patients with and without HIV in KwaZulu-Natal, South Africa

Ramlall S, Lessells RJ, Naidu T, Mthembu SS, Padayatchi N, Burns JK, Tomita A, Tropical Medicine and International Health (2020), 25 (8), 919–927 :

Opportunities and Challenges in HIV Treatment as Prevention Research: Results from the ANRS 12249 Cluster-Randomized Trial and Associated Population Cohort

Tanser F, Kim H-Y, Vandormael A, Iwuji C, Barnighausen T, Current HIV/AIDS Reports (2020), 17:97–108 https://doi.org/10.1007/s11904-020-00487-1:

Spatial clustering of food insecurity and its association with depression: a geospatial analysis of nationally representative South African data, 2008–2015

Tomita A, Cuadros DF, Mabhaudhi T, Sartorius B, Ncama BP, Dangour AD, Tanser F, Modi AT, Slotow R, Burns JK , Scientific Reports (2020), (2020) 10:13771. https://doi.org/10.1038/s41598-020-70647-1:

HIV incidence declines in a rural South African population: a G-imputation approach for inference

Vandormael A, Cuadros D, Dobra A, Barnighausen T, Tanser F, BMC Public Health (2020), 20:1205 https://doi.org/10.1186/s12889-020-09193-4:

Attitude and preferences towards oral and long-acting injectable antipsychotics in patients with psychosis in KwaZulu-Natal, South Africa

Roopun KR, Tomita A, Paruk S, South African Journal of Psychiatry (2020), 6(0), a1509. https://doi.org/ 10.4102/sajpsychiatry. v26i0.1509:

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, Genes (2020), doi: https://doi.org/10.3390/genes11080949:11(8), 949

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, IJID (2020), doi: https://doi.org/10.1016/j.ijid.2020.11.128:

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, Emerging Microbes & Infections (2020), vol 9:

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:

Naturally Occurring Oxazole-Containing Peptides

Mhlongo JT, Brasil E, de la Torre BG, Albericio F, Mar Drugs (2020), 18(4). pii: E203. doi: 10.3390/md18040203:

New Genomes from The Congo Basin Expand History of CRF01_AE Origin and Dissemination

Junqueira DM, Wilkinson E, Vallari AS, Deng XD, Achari A, Yu G, McArthur C, Kaptué L, Mbanya DN, Chiu C, Cloherty G, de Oliveira T, Rodgers MA, AIDS Res Hum Retroviruses (2020), doi: 10.1089/AID.2020.0031:

Symptom and digital chest X-ray TB screening in South African prisons: yield and cost-effectiveness

Kim HY, Zishiri V, Page-Shipp L, Makgopa S, Churchyard GJ, Dowdy D, Charalambous S, Hoffmann CJ, Int J Tuberc Lung Dis. (2020), 24(3):295-302. doi: 10.5588/ijtld.19.0214: