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

Author

Ratmann, O., Grabowski, M.K., Hall, M., Golubchik, T., Wymant, C., Abeler-Dörner, L., Bonsall, D., Hoppe, A., Brown, A.L., de Oliveira, T., Gall, A., Kellam, P., Pillay, D., Kagaayi, J., Kigozi, G., Quinn, T.C., Wawer, M.J., Laeyendecker, O., Serwadda, D., Gray, R.H., Fraser, C., Ayles, H., Bowden, R., Calvez, V., Cohen, M., Dennis, A., Essex, M., Fidler, S., Frampton, D., Hayes, R., Herbeck, J.T., Kaleebu, P., Kityo, C., Lingappa, J., Novitsky, V., Paton, N., Rambaut, A., Seeley, J., Ssemwanga, D., Tanser, F., Nakigozi, G., Ssekubugu, R., Nalugoda, F., Lutalo, T., Galiwango, R., Makumbi, F., Sewankambo, N.K., R. Tobian, A.A., Reynolds, S.J., Chang, L.W., Nabukalu, D., Ndyanabo, A., Ssekasanvu, J., Nakawooya, H., Nakukumba, J., Kigozi, G.N., Nantume, B.S., Resty, N., Kambasu, J., Nalugemwa, M., Nakabuye, R., Ssebanobe, L., Nankinga, J., Kayiira, A., Nanfuka, G., Ahimbisibwe, R., Tomusange, S., Galiwango, R.M., Kalibbali, S., Nakalanzi, M., Otobi, J.O., Ankunda, D., Ssembatya, J.L., Ssemanda, J.B., Kairania, R., Kato, E., Kisakye, A., Batte, J., Ludigo, J., Nampijja, A., Watya, S., Nehemia, K., Anyokot, M., Mwinike, J., Kibumba, G., Ssebowa, P., Mondo, G., Wasswa, F., Nantongo, A., Kakembo, R., Galiwango, J., Ssemango, G., Redd, A.D., Santelli, J., Kennedy, C.E., and Wagman, J.

Abstract

To prevent new infections with human immunodeficiency virus type 1 (HIV-1) in sub-Saharan Africa, UNAIDS recommends targeting interventions to populations that are at high risk of acquiring and passing on the virus. Yet it is often unclear who and where these ‘source’ populations are. Here we demonstrate how viral deep-sequencing can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks. We are able to deep-sequence virus from a large population-based sample of infected individuals in Rakai District, Uganda, reconstruct partial transmission networks, and infer the direction of transmission within them at an estimated error rate of 16.3% [8.8–28.3%]. With this error rate, deep-sequence phylogenetics cannot be used against individuals in legal contexts, but is sufficiently low for population-level inferences into the sources of epidemic spread. The technique presents new opportunities for characterizing source populations and for targeting of HIV-1 prevention interventions in Africa.

Published
2019

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

Author

Ratmann, O., Grabowski, M.K., Hall, M., Golubchik, T., Wymant, C., Abeler-Dörner, L., Bonsall, D., Hoppe, A., Brown, A.L., de Oliveira, T., Gall, A., Kellam, P., Pillay, D., Kagaayi, J., Kigozi, G., Quinn, T.C., Wawer, M.J., Laeyendecker, O., Serwadda, D., Gray, R.H., Fraser, C., Ayles, H., Bowden, R., Calvez, V., Cohen, M., Dennis, A., Essex, M., Fidler, S., Frampton, D., Hayes, R., Herbeck, J.T., Kaleebu, P., Kityo, C., Lingappa, J., Novitsky, V., Paton, N., Rambaut, A., Seeley, J., Ssemwanga, D., Tanser, F., Nakigozi, G., Ssekubugu, R., Nalugoda, F., Lutalo, T., Galiwango, R., Makumbi, F., Sewankambo, N.K., R. Tobian, A.A., Reynolds, S.J., Chang, L.W., Nabukalu, D., Ndyanabo, A., Ssekasanvu, J., Nakawooya, H., Nakukumba, J., Kigozi, G.N., Nantume, B.S., Resty, N., Kambasu, J., Nalugemwa, M., Nakabuye, R., Ssebanobe, L., Nankinga, J., Kayiira, A., Nanfuka, G., Ahimbisibwe, R., Tomusange, S., Galiwango, R.M., Kalibbali, S., Nakalanzi, M., Otobi, J.O., Ankunda, D., Ssembatya, J.L., Ssemanda, J.B., Kairania, R., Kato, E., Kisakye, A., Batte, J., Ludigo, J., Nampijja, A., Watya, S., Nehemia, K., Anyokot, M., Mwinike, J., Kibumba, G., Ssebowa, P., Mondo, G., Wasswa, F., Nantongo, A., Kakembo, R., Galiwango, J., Ssemango, G., Redd, A.D., Santelli, J., Kennedy, C.E., Wagman, J., Ratmann, O., Grabowski, M.K., Hall, M., Golubchik, T., Wymant, C., Abeler-Dörner, L., Bonsall, D., Hoppe, A., Brown, A.L., de Oliveira, T., Gall, A., Kellam, P., Pillay, D., Kagaayi, J., Kigozi, G., Quinn, T.C., Wawer, M.J., Laeyendecker, O., Serwadda, D., Gray, R.H., Fraser, C., Ayles, H., Bowden, R., Calvez, V., Cohen, M., Dennis, A., Essex, M., Fidler, S., Frampton, D., Hayes, R., Herbeck, J.T., Kaleebu, P., Kityo, C., Lingappa, J., Novitsky, V., Paton, N., Rambaut, A., Seeley, J., Ssemwanga, D., Tanser, F., Nakigozi, G., Ssekubugu, R., Nalugoda, F., Lutalo, T., Galiwango, R., Makumbi, F., Sewankambo, N.K., R. Tobian, A.A., Reynolds, S.J., Chang, L.W., Nabukalu, D., Ndyanabo, A., Ssekasanvu, J., Nakawooya, H., Nakukumba, J., Kigozi, G.N., Nantume, B.S., Resty, N., Kambasu, J., Nalugemwa, M., Nakabuye, R., Ssebanobe, L., Nankinga, J., Kayiira, A., Nanfuka, G., Ahimbisibwe, R., Tomusange, S., Galiwango, R.M., Kalibbali, S., Nakalanzi, M., Otobi, J.O., Ankunda, D., Ssembatya, J.L., Ssemanda, J.B., Kairania, R., Kato, E., Kisakye, A., Batte, J., Ludigo, J., Nampijja, A., Watya, S., Nehemia, K., Anyokot, M., Mwinike, J., Kibumba, G., Ssebowa, P., Mondo, G., Wasswa, F., Nantongo, A., Kakembo, R., Galiwango, J., Ssemango, G., Redd, A.D., Santelli, J., Kennedy, C.E., and Wagman, J.

Abstract

To prevent new infections with human immunodeficiency virus type 1 (HIV-1) in sub-Saharan Africa, UNAIDS recommends targeting interventions to populations that are at high risk of acquiring and passing on the virus. Yet it is often unclear who and where these ‘source’ populations are. Here we demonstrate how viral deep-sequencing can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks. We are able to deep-sequence virus from a large population-based sample of infected individuals in Rakai District, Uganda, reconstruct partial transmission networks, and infer the direction of transmission within them at an estimated error rate of 16.3% [8.8–28.3%]. With this error rate, deep-sequence phylogenetics cannot be used against individuals in legal contexts, but is sufficiently low for population-level inferences into the sources of epidemic spread. The technique presents new opportunities for characterizing source populations and for targeting of HIV-1 prevention interventions in Africa.

3. Timing for maximum anaesthetic effect of topical cream during early infant circumcision (EIC) in Rakai, Uganda.

Author

Kiboneka S, Anok A, Nakabuye R, Odiya S, Magembe J, Nazziwa R, Ddamulira C, Mulooki A, Galiwango RM, Watya S, Li PS, Lee RK, Gray RH, Kigozi G, and Kankaka EN

Abstract

Objectives: The objective of this study is to determine the optimal timing for device-based infant circumcision under topical anaesthesia., Subjects/patients: We include infants aged 1-60 days who were enrolled in a field study of the no-flip ShangRing device at four hospitals in the Rakai region of south-central Uganda, between 5 February 2020 and 27 October 2020., Methods: Two hundred infants, aged 0-60 days, were enrolled, and EMLA cream was applied on the foreskin and entire penile shaft. The anaesthetic effect was assessed every 5 min by gentle application of artery forceps at the tip of the foreskin, starting at 10 min post-application until 60 min, the recommended time to start circumcision. The response was measured using the Neonatal Infant Pain Scale (NIPS). We determined the onset and duration of anaesthesia (defined as <20% of infants with NIPS score >4) and maximum anaesthesia (defined as <20% of infants with NIPS score >2)., Results: Overall, NIPS scores decreased to a minimum and reversed before the recommended 60 min. Baseline response varied with age, with minimal response among infants aged 40 days. Overall, anaesthesia was achieved after at least 25 min and lasted 20-30 min. Maximum anaesthesia was achieved after at least 30 min (except among those aged >45 days where it was not achieved) and lasted up to 10 min., Conclusion: The optimal timing for maximum topical anaesthesia occurred before the recommended 60 min of waiting time. A shorter waiting time and speed may be efficient for mass device-based circumcision., (© 2023 The Authors. BJUI Compass published by John Wiley & Sons Ltd on behalf of BJU International Company.)

Published
2023
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4. ShangRing versus Mogen clamp for early infant male circumcision in eastern sub-Saharan Africa: a multicentre, non-inferiority, adaptive, randomised controlled trial.

Author

Basourakos SP, Nang QG, Ballman KV, Al Awamlh OAH, Punjani N, Ho K, Barone MA, Awori QD, Ouma D, Oketch J, Christensen AE, Hellar A, Makokha M, Isangu A, Salim R, Lija J, Gray RH, Kiboneka S, Anok A, Kigozi G, Nakabuye R, Ddamulira C, Mulooki A, Odiya S, Nazziwa R, Goldstein M, Li PS, and Lee RK

Subjects
Adolescent, Adult, Humans, Infant, Infant, Newborn, Kenya, Male, Pain etiology, Uganda, Anesthesia, Circumcision, Male adverse effects
Abstract

Background: Use of medical devices represents a unique opportunity to facilitate scale-up of early infant male circumcision (EIMC) across sub-Saharan Africa. The ShangRing, a circumcision device prequalified by WHO, is approved for use in adults and adolescents and requires topical anaesthesia only. We aimed to investigate the safety and efficacy of the ShangRing versus the Mogen clamp for EIMC in infants across eastern sub-Saharan Africa., Methods: In this multicentre, non-inferiority, open-label, randomised controlled trial, we enrolled healthy male infants (aged <60 days), with a gestational age of at least 37 weeks and a birthweight of at least 2·5 kg, from 11 community and referral centres in Kenya, Tanzania, and Uganda. Infants were randomly assigned (1:1) by a computer-generated text message service to undergo EIMC by either the ShangRing or the Mogen clamp. The primary endpoint was safety, defined as the number and severity of adverse events (AEs), analysed in the intention-to-treat population (all infants who underwent an EIMC procedure) with a non-inferiority margin of 2% for the difference in moderate and severe AEs. This trial is registered with Clinical., Trials: gov, NCT03338699, and is complete., Findings: Between Sept 17, 2018, and Dec 20, 2019, a total of 1420 infants were assessed for eligibility, of whom 1378 (97·0%) were enrolled. 689 (50·0%) infants were randomly assigned to undergo EIMC by ShangRing and 689 (50·0%) by Mogen clamp. 43 (6·2%) adverse events were observed in the ShangRing group and 61 (8·9%) in the Mogen clamp group (p=0·078). The most common treatment-related AE was intraoperative pain (Neonatal Infant Pain Scale score ≥5), with 19 (2·8%) events in the ShangRing and 23 (3·3%) in the Mogel clamp group. Rates of moderate and severe AEs were similar between both groups (29 [4·2%] in the ShangRing group vs 30 [4·4%] in the Mogen clamp group; difference -0·1%; one-sided 95% CI upper limit of 1·7%; p=0·89). No treatment-related deaths were reported., Interpretation: Use of the ShangRing device for EIMC showed safety, achieved high caregiver satisfaction, and did not differ from the Mogen clamp in other key measures. The ShangRing could be used by health systems and international organisations to further scale up EIMC across sub-Saharan Africa., Funding: Bill & Melinda Gates Foundation., Competing Interests: Declaration of interests We declare no competing interests., (Copyright © 2022 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.)

Published
2022
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