WASHINGTON STATE CONVENTION CENTER Seattle, Washington March 4–7, 2019 MAPPING OF HIV-1C TRANSMISSION NETWORKS IN BOTSWANA Conference on Retroviruses and Opportunistic Infections 875 V. Novitsky1,2, M. Zahralban-Steele2, S. Moyo1,2, T. Nkhisang1, D. Maruapula1, M.F. McLane2, J. Leidner3, K. Bennett4, T. Gaolathe1, E. Kadima1, S. Lockman1,2,5, J. Makhema1,2, S. Gaseitsiwe1,2, V. DeGruttola2, and M. Essex1,2 1Botswana Harvard AIDS Institute, Gaborone, Botswana 2Harvard TH Chan School of Public Health, Boston, MA 3Goodtables Data Consulting LLC, Norman, OK 4Bennett Statistical Consulting, Inc., Ballston Lake, NY 5Brigham and Women’s Hospital, Boston, MA

ABSTRACT RESULTS RESULTS Background: Better understanding of the structure and dynamics of HIV transmission networks is essen- Number of identified HIV-1C lineages was associated with the number of generated viral tial for preventing new viral transmissions and for ultimate control of the HIV epidemic. Phylogenetic map- sequences per community ping of HIV transmission networks is a promising approach that could help to stop the spread of HIV. Complexity of HIV-1C 10.0 rho = 0.99 Methods: We obtained near full-length HIV-1C sequences from 6,149 HIV-infected individuals participat- 500 p < 0.0001 ing in five studies in Botswana from 1996 to 2018, including 5,440 participants from the Botswana Combi- 7.5 Transmission Network 400 nation Prevention Project (BCPP) sampled in 2013–2018. HIV-1C sequences included 142 seroconvert- Shakawe ers identified in the BCPP study. In addition, 696 non-Botswana HIV-1C sequences were retrieved from 300 5.0 Los-Alamos database and included in analyses. Phylogenetic relationships among viral sequences were in Botswana Count 200 estimated by maximum likelihood using RAxML v.8 and the GTR+Γ4+Ι model. Given the predominantly per community 2.5 heterosexual mode of virus transmission, cross-sectional nature of sampling, relatively high genotyping Viral links between communities represent 100 Number of viral sequences density, and use of near full-length HIV-1 genomes, we defined a cluster as a phylogenetically distinct phylogenetically distinct HIV-1C lineages. 0.0 viral lineage that gives rise to a monophyletic subtree of the overall phylogeny with bootstrap support of Each color indicates a separate viral lineage. 40 80 120 0.20 0.25 0.30 0.35 0.40 0.45 splits >=0.80. Links within communities are not shown. Number of identified lineages per community Lineages normalized by the number of sequences

Results: We identified 966 phylogenetically distinct HIV-1C lineages circulating in Botswana by mid-2018. Gumare The vast majority of identified lineages, n=961, were comprised at least 50% of Botswana sequences and Breadth of viral lineage spread varied from 2 to 19 members per cluster. Dyads accounted for 63% of identified HIV-1C lineages. The median of identified viral lineages per community in Botswana was 48 (IQR 28–83). About 27% (n=260) 10.0 of identified viral lineages were found in a single community. The majority of identified viral lineages were spread across multiple Botswana communities. About half (52%; n=74) of BCPP seroconverters were Gweta Nata found in 68 clusters, including 9 clusters spread in a single community. Men in clusters (median age 41 Nkange 7.5 years old; IQR 35–47) were about 4 years older than women (median age 37 years old; IQR 31–43; p<0.0001). In clusters with seroconverters, both men and women were younger than in clusters without seroconverters (p<0.0001 for both comparisons). 5.0

Conclusions: A large number of phylogenetically distinct HIV-1C lineages have been circulating in Bo- Sebina Masunga tswana by mid-2018. The majority (73%) of identified viral lineages were spread across multiple commu- nities, highlighting the complexity of the HIV-1C transmission network. Clustered men were about 4 years Mathangwane 2.5 older than clustered women; and clustered men and women were both younger than non-clustered. Rakops Tati Siding per viral lineage Number of communities METHODS 2 3 4 5 6 7 8 9 12 13 14 15 16 19 Mmandunyane Members per cluster (cluster size) Near full-length HIV-1C sequences were obtained from blood specimens sampled within five Botswana- Harvard AIDS Institute Partnership (BHP) studies during 1996–2018. All studies included HIV genotyping as one of their core components, and were approved by IRBs in Botswana and at the Harvard T.H. Chan School Mmadinare of Public Health. All participants signed the written consent form for viral genotyping. All HIV-1C sequences in Proportions of viral lineages across single and multiple communities this study were represented by a single sequence per participant. Sefophe Tsetsebjwe Proportion of viral lineages spread across single communities We used sequence length of >=7,000 bp, the LANL HIV-1 Database criterion for definition of the near full-length Proportion of viral lineages spread across multiple communities HIV genome. A total of 6,848 near full-length HIV-1C genome sequences included 6,152 (90%) sequences from Maunatlala Botswana (representing 6,149 participants, as 3 dual infections with distinct HIV-1C were identified) and 696 (10%) sequences from outside of Botswana. 8 Ramokgonami Lerala Multiple sequence alignment (MSA) 6 MSA was generated by aligning 6,848 near full-length HIV-1C sequences to the majority HIV-1C consensus se- Sefhare quence using mafft with option --keeplength and gap extension option --op 0.75. The MSA corresponded to Shoshong HXB2 nt positions 790 (the first codon encoding HIV-1 gag) to 9,632 (end of R in 3’ LTR) and had a length of 4 8,827 bp. density RESULTS 2

Overall, we identified 1,053 phylogenetically distinct HIV-1C lineages that included 45% (3,052 of 6,848) of ana- 6,152 near full-length HIV-1C sequences from Botswana 0 lyzed near full-length HIV-1C genome sequences. In Botswana, we identified 966 lineages. HIV-1C lineages cir- Letlhakeng Lentsweletau 0.00 0.25 0.50 0.75 1.00 culating in Botswana by mid-2018 included 2,702 of 6,152 HIV-1C sequences sampled in Botswana communi- 2,718 (44%) of sequences in clusters Proportion of viral lineages identified across communities ties. The majority of identified lineages, 961, were comprised at least 50% of Botswana sequences, while 945 Sampling: 1996 - 2018 Bokaa The diversity of viral lineage of identified lineages were exclusively of Botswana origin. Molepolole Mochudi spread was high. The median In this study, we focused on the 961 lineages that were comprised at least 50% of Botswana sequences; the set 961 phylogenetically distinct lineages Metsimotlhabe of circulating HIV-1C lineages of 2,718 sequences included 2,697 sequences from Botswana. The presence of multiple HIV-1C lineages circu- 2 to 19 members per cluster Oodi per community was 48 (IQR Age and gender in HIV-1C clusters lating in Botswana communities by mid-2018 is illustrated by identified phylogenetically distinct HIV-1C lineages Mmankgodi Gaborone 28–83), ranging from 11 and their links among Botswana communities. The abundance and broad spread of identified viral lineages Dyads: 63% (605 of 961) Ranaka (Ranaka) to 150 (Lerala). Overall in clusters, In 66% (n=353) clusters In 34% (n=184) clusters Clusters with seroconverters are younger across Botswana communities suggests high complexity in the HIV-1C transmission network in Botswana. included 44% (1,205 of 2,718) of clustered sequences men are older than women men are older than women women are older than men than clusters without seroconverters 0.04 Women Women Women without seroconv. Each color indicates a separate phylogenetically distinct HIV-1C lineage spreading across 34 Botswana com- 0.04 Otse Men 0.04 Men Men with seroconv. munities, including the 30 BCPP communities. Viral links within communities are not shown on the map for sim- Molapowabojang We found that 27% (260 of 961) of identified viral lineages were 0.03 0.04 0.03 plicity. Lobatse found in single communities. Those included one lineage with 7 0.03 0.02 Mmathethe 0.02 0.02 density A. Genotyping density, % B. Sequencing of collected RBD, % members (Lerala), three lineages with 5 members each 0.02 Ranaka 5.9 Ranaka 58.9 Digawana 0.01 Digawana 14 Digawana 38.4 0.01 0.01 Molapowabojang 6.2 Molapowabojang 75.3 (Gumare, Mmankgodi, and Sefhare), four lineages with 4 mem- Otse 21.7 Otse 55.9 Letlhakeng 10 Letlhakeng 67.8 0.00 0.00 0.00 0.00 Lentsweletau 49 Lentsweletau 65.1 bers each (Lentsweletau, Mmathethe, Lerala, and Ramokg- Bokaa 10.2 Bokaa 67.8 20 30 40 50 60 20 30 40 50 60 20 30 40 50 60 20 30 40 50 60 Oodi 10.5 Oodi 25.9 Median age in clusters, years Median age in clusters, years Median age in clusters, years Age at interview, years Mmathethe 26.9 Mmathethe 33.9 onami), 36 lineages with 3 members each, and 216 dyads. In- Mmankgodi 29.5 Mmankgodi 43.2 Sefophe 15.7 Sefophe 81.8 Lerala 41 Lerala 62.3 terestingly, 36% (216 of 605) of dyads were found in a single Ramokgonami 43.4 Ramokgonami 64.1 Maunatlala 62.1 Maunatlala 60.2 Mmadinare 5.9 Mmadinare 78.8 Shoshong 5.7 Shoshong 8.4 community.

Communities Metsimotlhabe 4.4 Metsimotlhabe 59.7 Tati_Siding 25.6 Tati_Siding 55.1 Sebina 14.6 Sebina 73 Nkange 24.9 Nkange 49 Mmandunyane 12.6 Mmandunyane 68.3 Mathangwane 29.1 Mathangwane 42.1 Rakops 15.1 Rakops 72.8 Among viral lineages with 3 members, 42% were found in two communities and 39% in three communities. More than 90% of HIV-1C lin- Gweta 21.1 Gweta 35.7 ACKNOWLEDGEMENTS Shakawe 26.7 Shakawe 34.6 Gumare 28.6 Gumare 29.4 eages with 4+ members were spread across multiple communities, and all viral lineages with 8+ members were found in multiple Tsetsebjwe 14.6 Tsetsebjwe 65.1 Sefhare 23 Sefhare 48.9 This study was supported by the US President’s Emergency Plan for AIDS Relief (PEPFAR) through CDC under Nata 10.7 Nata 42.2 communities/villages in Botswana. Masunga 26.9 Masunga 36.7 the terms of cooperative agreement U01 GH000447, in part by NIH-funded AI47067, AI092715 and AI083036, 0 25 50 75 100 0 25 50 75 100 Density, % Density, % and through collaboration with PANGEA HIV consortium.