Skip directly to site content Skip directly to page options Skip directly to A-Z link Skip directly to A-Z link Skip directly to A-Z link
Volume 26, Number 10—October 2020
Dispatch

Main Routes of Entry and Genomic Diversity of SARS-CoV-2, Uganda

Daniel Lule Bugembe1, John Kayiwa1, My V.T. Phan1, Phiona Tushabe, Stephen Balinandi, Beatrice Dhaala, Jonas Lexow, Henry Mwebesa, Jane Aceng, Henry Kyobe, Deogratius Ssemwanga, Julius Lutwama, Pontiano Kaleebu, and Matthew CottenComments to Author 
Author affiliations: UK Medical Research Council–Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda (D. Lule Bugembe, B. Dhaala, J. Lexow, D. Ssemwanga, P. Kaleebu, M. Cotten); Uganda Virus Research Institute, Entebbe (J. Kiyawa, P. Tushabe, S. Balinandi, D. Ssemwanga, J. Lutwama, P. Kaleebu); Erasmus Medical Center, Rotterdam, the Netherlands (M.V.T. Phan); Uganda Ministry of Health, Kampala, Uganda (H. Mwebesa, J. Aceng, H. Kyobe); UK Medical Research Council–University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK (M. Cotten)

Main Article

Table

Summary characteristics of SARS-CoV-2 genomes obtained from 20 persons entering Uganda*

Genome GISAID ID† Sample date Ct Patient age, y Patient travel history Lineage‡
hCoV-19/Uganda/UG001/2020 EPI_ISL_451183 2020 Mar 23 19 48 Miami to Istanbul A
hCoV-19/Uganda/UG002/2020 EPI_ISL_451184 2020 Mar 26 19 43 Dubai A
hCoV-19/Uganda/UG003/2020 EPI_ISL_451185 2020 Mar 27 22 10 UK B.1.1
hCoV-19/Uganda/UG004/2020 EPI_ISL_451186 2020 Mar 27 18 25 UK to NL to Rwanda B.1.1.1
hCoV-19/Uganda/UG005/2020 EPI_ISL_451187 2020 Mar 27 18 26 UK to NL to Rwanda B
hCoV-19/Uganda/UG006/2020 EPI_ISL_451188 2020 Mar 30 23 27 UK to NL to Rwanda B
hCoV-19/Uganda/UG007/2020 EPI_ISL_451189 2020 Mar 30 21 8 UK to NL to Rwanda B.1.1.1
hCoV-19/Uganda/UG008/2020 EPI_ISL_451190 2020 Mar 30 22 7 UK to NL to Rwanda B.1.1.1
hCoV-19/Uganda/UG009/2020 EPI_ISL_451191 2020 Mar 30 20 9 UK to NL to Rwanda B.1.1.1
hCoV-19/Uganda/UG010/2020 EPI_ISL_451192 2020 Mar 30 22 27 UK to NL to Rwanda B.1.1.1
hCoV-19/Uganda/UG011/2020 EPI_ISL_451193 2020 Mar 30 21 29 Contact B.4
hCoV-19/Uganda/UG012/2020 EPI_ISL_451194 2020 Mar 22 24 37 Dubai A
hCoV-19/Uganda/UG013/2020 EPI_ISL_451195 2020 Mar 22 23 35 Dubai B
hCoV-19/Uganda/UG014/2020 EPI_ISL_451196 2020 Mar 25 27 31 Dubai B.1.1.1
hCoV-19/Uganda/UG015/2020 EPI_ISL_451197 2020 Apr 27 16 27 Kenya, by truck B.1
hCoV-19/Uganda/UG016/2020 EPI_ISL_451198 2020 Apr 27 19 52 Kenya, by truck B.1
hCoV-19/Uganda/UG017/2020 EPI_ISL_451199 2020 Apr 20 22 42 Tanzania, by truck A
hCoV-19/Uganda/UG018/2020 EPI_ISL_451200 2020 May 1 28 22 Tanzania, by truck B.1
hCoV-19/Uganda/UG019/2020 EPI_ISL_451201 2020 Apr 30 29 39 Kenya, by truck B.1
hCoV-19/Uganda/UG020/2020 EPI_ISL_451202 2020 May 1 25 47 Kenya, by truck B.1

*Ct, cycle threshold (based on diagnostic real-time reverse transcription PCR; NL, the Netherlands; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; UK, United Kingdom.
†Virus genomes sequences available from GISAID (https://www.gisaid.org).
‡SARS-CoV-2 lineages determined by using CoV-GLUE (13).

Main Article

References
  1. Edward  C. Holmes, Yong-Zhen Zhang EC. Initial genome release of novel coronavirus [cited 2020 May 7]. http://virological.org/t/initial-genome-release-of-novel-coronavirus/319
  2. Zhu  N, Zhang  D, Wang  W, Li  X, Yang  B, Song  J, et al.; China Novel Coronavirus Investigating and Research Team. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med. 2020;382:727–33. DOIPubMedGoogle Scholar
  3. Li  Q, Guan  X, Wu  P, Wang  X, Zhou  L, Tong  Y, et al. Early transmission dynamics in Wuhan, China, of novel coronavirus–infected pneumonia. N Engl J Med. 2020;382:1199–207. DOIPubMedGoogle Scholar
  4. Yang  X, Yu  Y, Xu  J, Shu  H, Xia  J, Liu  H, et al. Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study. Lancet Respir Med. 2020;8:475–81. DOIPubMedGoogle Scholar
  5. Johns Hopkins University Center for Systems Science and Engineering. COVID-19 dashboard. 2020 [cited 2020 May 7]. https://www.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6
  6. World Health Organization. COVID-19 cases top 10,000 in Africa. 2020 [cited 2020 May 7]. https://www.afro.who.int/news/covid-19-cases-top-10-000-africa
  7. Corman  VM, Landt  O, Kaiser  M, Molenkamp  R, Meijer  A, Chu  DK, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 2020;25:25. DOIPubMedGoogle Scholar
  8. Shu  Y, McCauley  J. GISAID: Global initiative on sharing all influenza data - from vision to reality. Euro Surveill. 2017;22:30494. DOIPubMedGoogle Scholar
  9. Katoh  K, Standley  DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80. DOIPubMedGoogle Scholar
  10. Stamatakis  A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3. DOIPubMedGoogle Scholar
  11. Nguyen  L-T, Schmidt  HA, von Haeseler  A, Minh  BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32:268–74. DOIPubMedGoogle Scholar
  12. Rambaut  A. FigTree. 2019 [cited 2020 May 7]. http://tree.bio.ed.ac.uk/software/figtree
  13. Josh  B. Singer, Gifford R, Cotten M, Robertson DL. CoV-GLUE project. 2020 [cited 2020 May 7]. http://cov-glue.cvr.gla.ac.uk

Main Article

1These first authors contributed equally to this article.

Page created: June 30, 2020
Page updated: September 17, 2020
Page reviewed: September 17, 2020
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
file_external