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A1 Pairwise diversity and tMRCA as potential markers of HIV infection recency

Sikhulile Moyo, Eduan Wilkinson, Alain Vandormael, Rui Wang, Jia Weng, Kenanao P Kotokwe, Simani Gaseitsiwe, Rosemary Musonda, Joseph Makhema, Max Essex, Susan Engelbrecht, Tulio de Oliveira and Vladimir Novitsky.

in Virus Evolution

P ublished online April 2018 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 173 words.

A10 Using the molecular epidemiology of HIV transmission in New South Wales to inform public health response: Assessing the representativeness of linked phylogenetic data

Angie Pinto, Francesca Di Giallonardo, Phillip Keen, Craig Cooper, Barbara Telfer, David Cooper, Andrew Grulich and Anthony Kelleher.

in Virus Evolution

P ublished online April 2018 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 330 words.

A11 The 1988 Elista outbreak and the epidemiology of HIV subtype G in Russia

Ekaterina Serova, Anastasia Murzakova, Marina Nossik, Andrey Shemshura, Georgii Bazykin and Dmitry Kireev.

in Virus Evolution

P ublished online April 2018 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 361 words.

A12 Transmitted HLA pre-adapted polymorphisms in the GAG protein influences viral evolution in the new host

D Mónaco, D Dilernia, A Gartland, K Qin, K Dennis, J Tang, J Gilmour, A Bansal, S Allen, P Goepfert and E Hunter.

in Virus Evolution

P ublished online April 2018 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 354 words.

A13 Social affects phylogeny: Exploration of ongoing and active transmission chains

M Siljic, V Cirkovic, S Lukovic, D Salemovic, I Pesic-Pavlovic, D J Jevtivic and M Stanojevic.

in Virus Evolution

P ublished online April 2018 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 369 words.

A14 Ultra-wide and ultra-deep sequencing increases the detection rate of dual HIV-1 infections and recombinants

K Van Laethem, A Thielen, Y Schrooten, F Ferreira, L Vinken and M Daümer.

in Virus Evolution

P ublished online April 2018 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 359 words.

A15 HIV-1 whole-genome NGS analysis to characterize virus evolution following dendritic cell immunotherapy and analytical treatment interruption

C Lungu, P H M Boers, C M E Schapendonk, S L Smits, D A M C van de Vijver and R A Gruters.

in Virus Evolution

P ublished online April 2018 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 297 words.

A16 Primary drug resistance among children infected with HIV-1 in Mozambique: Impact of maternal and neonatal prophylaxis

Nália Ismael, Dulce Bila, Nedio Mabunda, Martina Penazzato and Adolfo Vubil.

in Virus Evolution

P ublished online April 2018 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 419 words.

A17 Transmitted drug-resistant mutations among recently infected HIV-1 patients in Israel, 2000–2014

Roy Moscona, Daniela Ram, Marina Wax, Efrat Bucris, Itzchak Levy, Ella Mendelson and Orna Mor.

in Virus Evolution

P ublished online April 2018 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 310 words.

A18 HIV-1 genetic diversity and drug resistance in Haiti

G Delva, M Charles and C Yang.

in Virus Evolution

P ublished online April 2018 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 179 words.

A19 The impact of HIV-1 on the evolution of Mycobacterium tuberculosis

Anastasia Koch, Daniela Brites, David Stucki, Joanna C Evans, Ronnett Seldon, Alexa Heekes, Nicola Mulder, Mark Nicol, Tolu Oni, Digby F Warner, Valerie Mizrahi, Julian Parkhill, Sebastien Gagneux, Darren P Martin and Robert J Wilkinson.

in Virus Evolution

P ublished online April 2018 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 232 words.

A2 Optimization of the results generated by large-scale sequencing for the study of drug resistance in HIV infection: A systematic review

J A Fernández-Caballero, N Chueca, E Poveda and F García.

in Virus Evolution

P ublished online April 2018 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 316 words.

A20 Deep sequencing reveals viral evolution in GAG within protective HLA Alleles B*57: 02, B*58: 01, and B*7 supertype individuals acutely infected with HIV-1 subtype C in Durban, South Africa

K Gounder, V Naidoo, N Padayachi, Q Mthethwa, D Dilernia, E Hunter, B Walker and T Ndung’u.

in Virus Evolution

P ublished online April 2018 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 362 words.

A21 Evolvability of HIV-1 is influenced by codon pair usage

M Nevot, M Parera, G Martrus and M A Martínez.

in Virus Evolution

P ublished online April 2018 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 318 words.

A22 Spatio-temporal history of the HIV-1 circulating recombinant form 35_AD in Afghanistan and Iran

S Eybpoosh, E Mostafavi, K Azadmanesh and A-A Haghdoost.

in Virus Evolution

P ublished online April 2018 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 429 words.

A23 Large phylogenetic clusters highlight the HIV-1 epidemic in Canadian at risk populations

Rupert Capina, Francois Cholette, Eric Enns, Christina Daniuk, Tracy Taylor, James Brooks, P Richard Harrigan and Paul Sandstrom.

in Virus Evolution

P ublished online April 2018 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 281 words.

A24 Role of phylogenetic analysis in epidemiological case definitions during an outbreak of HIV-1 in people who inject drugs in Ireland

L Dunford, A Waters, M Neary, J Dean, C Giese, D Igoe, C Hurley, K O’Donnell, M Fitzgerald and C De Gascun.

in Virus Evolution

P ublished online April 2018 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 286 words.

A25 Analysis of non-structural genes subtype A1 HIV-1 circulating in Russia

K Gromov, A Murzakova, D Kireev and E Kazennova.

in Virus Evolution

P ublished online April 2018 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 300 words.

A26 Probing the compartmentalization of HIV-1 in the central nervous system through its neutralization properties

K Stefic, A Chaillon, M Bouvin-Pley, A Moreau, M Braibant, F Bastides, G Gras, L Bernard and F Barin.

in Virus Evolution

P ublished online April 2018 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 333 words.

A27 Exploring novel mechanisms of HIV-2 mutagenesis

M E Meissner, S Baliga, M Roth, J Baller and L M Mansky.

in Virus Evolution

P ublished online April 2018 .

Journal Article. Subjects: Public Health and Epidemiology; Epidemiology; Evolutionary Biology; Genetics and Genomics; Microbiology. 345 words.