PUBLICATIONS SPOTLIGHT

PUBLICATIONS

The Role of Adverse Childhood Experiences on Perinatal Substance Use Behaviour in KwaZulu-Natal Province, South Africa.

Bhengu BS, Tomita A, Mashaphu S, Paruk S, AIDS Behav. (2019), doi: 10.1007/s10461-019-02661-y:

Space-time clustering of recently diagnosed tuberculosis and impact of ART scale-up: Evidence from an HIV hyper-endemic rural South African population

Tomita A, Smith CM, Lessells RJ, Pym A, Grant AD, de Oliveira T, Tanser F , Scientific Reports (2019), https://doi.org/10.1038/s41598-019-46455-7:

Whole genome sequencing for drug-resistant tuberculosismanagement in South Africa: What gaps would this address andwhat are the challenges to implementation?

Dlamini MT, Lessells R, Iketleng T, de Oliveira T, Journal of Clinical TB and Other Mycobacterial Dis (2019), https://doi.org/10.1016/j.jctube.2019.100115:

The clinical presentation caused by truncating CHD8 variants.

Douzgou S, Liang HW, Metcalfe K, Somarathi S, Tischkowitz M, Mohamed W, Kini U, McKee S, Yates L, Bertoli M, Lynch SA, Holder S; Deciphering Developmental Disorders Study, Banka S, Clin Genet. (2019), 96(1):72-84. doi: 10.1111/cge.13554:

Phylodynamic analyses of Brazilian antigenic variants of infectious bursal disease virus

de Fraga AP, Graf T, Coltro VP, Ikuta N, Fonseca ASK, Majó N, Lunge VR, Infect Genet Evol. (2019), 73:159-166. doi: 10.1016/j.meegid.2019.04.020:

Predictors of quality of life among community psychiatric patients in a peri-urban district of Gauteng Province, South Africa.

Mapatwana D, Tomita A, Burns JK, Robertson LJ, Int J Soc Psychiatry (2019), 65(4):322-332. doi: 10.1177/0020764019842291

Bypassing Osmotic Shock Dilemma in a Polystyrene Resin Using the Green Solvent Cyclopentyl methyl Ether (CPME): A Morphological Perspective.

Al Musaimi O, El-Faham A, Almarhoon Z, Basso A, de la Torre BG, Albericio F, Polymers (Basel) (2019), 11(5). pii: E874. doi: 10.3390/polym11050874.:

High rate of occult hepatitis B virus infection in hemodialysis units of KwaZulu-Natal, South Africa

Msomi N, Ndlovu K, Giandhari J, Wilkinson E, Parboosing R, Zungu S, Mlisana K, J Med Virol. (2019), doi: 10.1002/jmv.25510:

Circulation of chikungunya virus East/Central/South African lineage in Rio de Janeiro, Brazil

Xavier J, Giovanetti M, Fonseca V, Thézé J, Gräf T, Fabri A, Goes de Jesus J, Lima de Mendonça MC, Damasceno Dos Santos Rodrigues C, Mares-Guia MA, Cardoso Dos Santos C, Fraga de Oliveira Tosta S, Candido D, Ribeiro Nogueira RM, Luiz de Abreu A, Kleber Oliveira W, Campelo de Albuquerque CF, Chieppe A, de Oliveira T, Brasil P, Calvet G, Carvalho Sequeira P, Rodrigues Faria N, Bispo de Filippis AM, Alcantara LCJ, PLoS One (2019), 14(6):e0217871:

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

Neurocognitive Impairment Risk Among Individuals With Multiple Drug-Resistant Tuberculosis and Human Immunodeficiency Virus Coinfection: Implications for Systematic Linkage to and Retention of Care in Tuberculosis/Human Immunodeficiency Virus Treatment.

Tomita A, Ramlall S, Naidu T, Mthembu SS, Padayatchi N, Burns JK, J Nerv Ment Dis (2019), 207(4):307-310

Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis

Ratmann O, Grabowski KM, Hall M, Golubchik T, Wymant C, Abeler-Dorner L, Bonsall D, Hoppe A, Leigh Brown A, de Oliveira T, Gall A, Kellam P, Pillay D, Kagaayi J, Kigozi G, Quinn TC, Wawer MJ, Laeyendecker O, Serwadda D, Gray RH, Fraser C, PANGEA Consortium and Rakai Health Sciences Program , Nature Communications (2019), 10:1411:https://doi.org/10.1038/s41467-019-09139-4

Trends in Pretreatment HIV-1 Drug Resistance in Antiretroviral Therapy-naive Adults in South Africa, 2000–2016: A Pooled Sequence Analysis

Chimukangara B, Lessells RJ, Rhee S-Y, Giandhari J, Kharsany ABM, Naidoo K, Lewis L, Cawood C, Khanyile D, Ayalew KA, Diallo K, Samuel R, Hunt G, Vandormael A, Stray-Pedersen B, Gordon M, Makadzange T, Kiepiela P, Ramjee G, Ledwaba J, Kalimashe M, Morris L, Parikh UM, Mellors JW, Shafer RW, Katzenstein D, Moodley P, Gupta RK, Pillay D, Karim SSA, de Oliveira T, EClinicalMedicine (Lancet) (2019), DOI:https://doi.org/10.1016/j.eclinm.2019.03.006:

Effects of Migration on Risky Sexual Behavior and HIV Acquisition in South Africa: A Systematic Review and Meta-analysis, 2000-2017.

Dzomba A, Tomita A, Govender K, Tanser F, AIDS Behav. (2019), doi: 10.1007/s10461-018-2367-z:

Major depression and household food insecurity among individuals with multidrug-resistant tuberculosis (MDR-TB) in South Africa.

Tomita A, Ramlall S, Naidu T, Mthembu SS, Padayatchi N, Burns JK, Soc Psychiatry Psychiatr Epidemiol. (2019), doi: 10.1007/s00127-019-01669-y:

Effect of ART scale-up and female migration intensity on risk of HIV acquisition: results from a population-based cohort in KwaZulu-Natal, South Africa

Dzomba A, Tomita A, Vandormael A, Govender K, Tanser F, BMC Public Health (2019), 19(1):196:doi: 10.1186/s12889-019-6494-x

Effects of genetic variability on rifampicin and isoniazid pharmacokinetics in South African patients with recurrent tuberculosis

Naidoo A, Chirehwa M, Ramsuran V, McIlleron H, Naidoo K, Yende-Zuma N, Singh R, Ncgapu S, Adamson J, Govender K, Denti P, Padayatchi N, Pharmacogenomics (2019), doi: 10.2217/pgs-2018-0166:

Estimating trends in the incidence rate with interval censored data and time-dependent covariates

Vandormael A, Tanser F, Cuadros D, Dobra A, Stat Methods Med Res (2019), 962280219829892. doi: 10.1177/0962280219829892:

The Pharmaceutical Industry in 2018. An Analysis of FDA Drug Approvals from the Perspective of Molecules.

de la Torre B, Albericio F, Molecules (2019), 24(4): pii: E809. doi: 10.3390/molecules24040809.

Factors influencing HIV-1 phylogenetic clustering

Junqueira DM, Sibisi Z, Wilkinson E, de Oliveira T, Curr Opin HIV AIDS (2019), doi: 10.1097/COH.0000000000000540:

Early Genomic Detection of Cosmopolitan Genotype of Dengue Virus Serotype 2, Angola, 2018

Hill SC, Neto de Vasconcelos J, Granja BG, Thézé J, Jandondo D, Neto Z, Mirandela M, Sebastião CDS, Cândido ALM, Clemente C, Pereira da Silva S, de Oliveira T, Pybus OG, Faria NR, Afonso JM, Emerg Infect Dis. (2019), 25(4):784-787

The effect of interventions on the transmission and spread of HIV in South Africa: a phylodynamic analysis

Wilkinson E, Junqueira DM, Lessells R, Engelbrecht S, van Zyl G, de Oliveira T, Salemi M, Scientific Reports (2019), 9:2640:https://doi.org/10.1038/s41598-018-37749-3

Sociobehavioral and community predictors of unsuppressed HIV viral load: multilevel results from a hyperendemic rural South African population

Tomita A, Vandormael A, Bärnighausen T, Phillips A, Pillay D, De Oliveira T, Tanser F, AIDS (2019), 33(3):559–569

Spatial structure of depression in South Africa: A longitudinal panel survey of a nationally representative sample of households

Cuadros DF, Tomita A, Vandormael A, Slotow R, Burns JK, Tanser F, Scientific Reports (2019), 9(1):979:doi.org/10.1038/s41598-018-37791-1

Early detection of emergent extensively drug resistant tuberculosis (XDR-TB) by flow cytometry-based phenotyping and whole genome sequencing

O'Donnell MR, Larsen MH, Brown TS, Jain P, Munsamy V, Wolf A, Uccellini L, Karim F, de Oliveira T, Mathema B, Jacobs WR, Pym A, Antimicrob Agents Chemother. (2019), pii: AAC.01834-18.:doi: 10.1128/AAC.01834-18

Experts' Perspectives on Key Ethical Issues Associated With HIV Phylogenetics as Applied in HIV Transmission Dynamics Research

Mutenherwa F, Wassenaar DR, de Oliveira T, J Empir Res Hum Res Ethics (2019), 1556264618809608. doi: 10.1177/1556264618809608:

Moderate to high levels of pre-treatment HIV drug resistance in KwaZulu-Natal Province, South Africa

Chimukangara B, Kharsany AB, Lessells RJ, Naidoo K, Rhee SY, Manasa J, Gräf T, Lewis L, Cawood C, Khanyile D, Diallo K, Ayalew KA, Shafer R, Hunt G, Pillay D, Abdool SK, de Oliveira T, AIDS Research and Human Retroviruses (2019), https://doi.org/10.1089/AID.2018.0202:

Genome Detective: An Automated System for Virus Identification from High-throughput sequencing data.

Vilsker M, Moosa Y, Nooij S, Fonseca V, Ghysens Y, Dumon K, Pauwels R, Alcantara LC, Vanden Eynden E, Vandamme AM, Deforche K, de Oliveira T, Bioinformatics (2019), doi: 10.1093/bioinformatics/bty695:

Phylodynamic analysis and molecular diversity of the avian infectious bronchitis virus of chickens in Brazil

Fraga AP, Graf T, Pereira CS, Ikuta N, Fonseca ASK, Lunge VR, Infect Genet Evol. (2018), 61:77-83

Spatiotemporal and demographic history of the HIV-1 circulating recombinant form CRF31_BC in Brazil

Fritsch HM, Almeida SEM, Pinto AR, Graf T, Infect Genet Evol. (2018), 61:113-118