Genomic epidemiology of early SARS-CoV-2 transmission dynamics in Bangladesh

L. Carnegie; J. T. McCrone; L. du Plessis; M. Hasan; M.Z. Ali; R. Begum; M.Z. Hassan; S. Islam; M.H. Rahman; A.S.M. Uddin; M.S. Sarker; T. Das; M. Hossain; M. Khan; M.H. Razu; A. Akram; S. Arina; E. Hoque; M.M.A. Molla; T. Nafisaa; P. Angra; A. Rambaut; S.T. Pullan; K.L. Osman; M.A. Hoque; P. Biswas; M.S. Flora; J. Raghwani; G. Fournié; M.A. Samad; S.C. Hill

doi:10.1186/s12985-024-02560-2

Genomic epidemiology of early SARS-CoV-2 transmission dynamics in Bangladesh

L. Carnegie^*, J. T. McCrone, L. du Plessis, M. Hasan, M.Z. Ali, R. Begum, M.Z. Hassan, S. Islam, M.H. Rahman, A.S.M. Uddin, M.S. Sarker, T. Das, M. Hossain, M. Khan, M.H. Razu, A. Akram, S. Arina, E. Hoque, M.M.A. Molla, T. NafisaaP. Angra, A. Rambaut, S.T. Pullan, K.L. Osman, M.A. Hoque, P. Biswas, M.S. Flora, J. Raghwani, G. Fournié, M.A. Samad^*, S.C. Hill^*

^*Corresponding author for this work

School of Biological Sciences

Research output: Contribution to journal › Article › peer-review

Abstract / Description of output

Background
Genomic epidemiology has helped reconstruct the global and regional movement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, there is still a lack of understanding of SARS-CoV-2 spread in some of the world’s least developed countries (LDCs).
Methods
To begin to address this disparity, we studied the transmission dynamics of the virus in Bangladesh during the country’s first COVID-19 wave by analysing case reports and whole-genome sequences from all eight divisions of the country.
Results
We detected>50 virus introductions to the country during the period, including during a period of national lockdown. Additionally, through discrete phylogeographic analyses, we identified that geographical distance and population -density and/or -size influenced virus spatial dispersal in Bangladesh.
Conclusions
Overall, this study expands our knowledge of SARS-CoV-2 genomic epidemiology in Bangladesh, shedding light on crucial transmission characteristics within the country, while also acknowledging resemblances and differences to patterns observed in other nations.

Original language	English
Article number	291
Number of pages	13
Journal	Virology Journal
Volume	21
Issue number	1
DOIs	https://doi.org/10.1186/s12985-024-02560-2
Publication status	Published - 13 Nov 2024

Keywords / Materials (for Non-textual outputs)

SARS-CoV-2
Phylodynamics
Bangladesh
Genomic epidemiology

Access to Document

10.1186/s12985-024-02560-2

s12985-024-02560-2Final published version, 4.14 MBLicence: Creative Commons: Attribution (CC-BY)

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Carnegie, L., McCrone, J. T., du Plessis, L., Hasan, M., Ali, M. Z., Begum, R., Hassan, M. Z., Islam, S., Rahman, M. H., Uddin, A. S. M., Sarker, M. S., Das, T., Hossain, M., Khan, M., Razu, M. H., Akram, A., Arina, S., Hoque, E., Molla, M. M. A., ... Hill, S. C. (2024). Genomic epidemiology of early SARS-CoV-2 transmission dynamics in Bangladesh. Virology Journal, 21(1), Article 291. https://doi.org/10.1186/s12985-024-02560-2

@article{9c778d9f00544451a12789f5c0ae849d,

title = "Genomic epidemiology of early SARS-CoV-2 transmission dynamics in Bangladesh",

abstract = "Background Genomic epidemiology has helped reconstruct the global and regional movement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, there is still a lack of understanding of SARS-CoV-2 spread in some of the world{\textquoteright}s least developed countries (LDCs). Methods To begin to address this disparity, we studied the transmission dynamics of the virus in Bangladesh during the country{\textquoteright}s first COVID-19 wave by analysing case reports and whole-genome sequences from all eight divisions of the country. Results We detected>50 virus introductions to the country during the period, including during a period of national lockdown. Additionally, through discrete phylogeographic analyses, we identified that geographical distance and population -density and/or -size influenced virus spatial dispersal in Bangladesh. Conclusions Overall, this study expands our knowledge of SARS-CoV-2 genomic epidemiology in Bangladesh, shedding light on crucial transmission characteristics within the country, while also acknowledging resemblances and differences to patterns observed in other nations. ",

keywords = "SARS-CoV-2, Phylodynamics, Bangladesh, Genomic epidemiology",

author = "L. Carnegie and McCrone, {J. T.} and {du Plessis}, L. and M. Hasan and M.Z. Ali and R. Begum and M.Z. Hassan and S. Islam and M.H. Rahman and A.S.M. Uddin and M.S. Sarker and T. Das and M. Hossain and M. Khan and M.H. Razu and A. Akram and S. Arina and E. Hoque and M.M.A. Molla and T. Nafisaa and P. Angra and A. Rambaut and S.T. Pullan and K.L. Osman and M.A. Hoque and P. Biswas and M.S. Flora and J. Raghwani and G. Fourni{\'e} and M.A. Samad and S.C. Hill",

note = "We thank the Child Health Research Foundation (CHRF), Bangladesh, for allowing us to use their data on the GISAID EpiCoV database (accession numbers in Table S7-S8). We also acknowledge the use of additional sequences from the GISAID EpiCoV database for the global dataset used in our lineage analyses and provide accession numbers and acknowledgements in the supplementary electronic material (Table S7-S8). We thank the Directorate General of Health Services (DGHS) and Institute of Epidemiology Disease Control and Research (IEDCR) Bangladesh, DGHS, Ministry of Health and Family Welfare for sharing COVID-19 samples and data. ",

year = "2024",

month = nov,

day = "13",

doi = "10.1186/s12985-024-02560-2",

language = "English",

volume = "21",

journal = "Virology Journal",

issn = "1743-422X",

publisher = "BioMed Central",

number = "1",

}

Carnegie, L, McCrone, JT, du Plessis, L, Hasan, M, Ali, MZ, Begum, R, Hassan, MZ, Islam, S, Rahman, MH, Uddin, ASM, Sarker, MS, Das, T, Hossain, M, Khan, M, Razu, MH, Akram, A, Arina, S, Hoque, E, Molla, MMA, Nafisaa, T, Angra, P, Rambaut, A, Pullan, ST, Osman, KL, Hoque, MA, Biswas, P, Flora, MS, Raghwani, J, Fournié, G, Samad, MA & Hill, SC 2024, 'Genomic epidemiology of early SARS-CoV-2 transmission dynamics in Bangladesh', Virology Journal, vol. 21, no. 1, 291. https://doi.org/10.1186/s12985-024-02560-2

TY - JOUR

T1 - Genomic epidemiology of early SARS-CoV-2 transmission dynamics in Bangladesh

AU - Carnegie, L.

AU - McCrone, J. T.

AU - du Plessis, L.

AU - Hasan, M.

AU - Ali, M.Z.

AU - Begum, R.

AU - Hassan, M.Z.

AU - Islam, S.

AU - Rahman, M.H.

AU - Uddin, A.S.M.

AU - Sarker, M.S.

AU - Das, T.

AU - Hossain, M.

AU - Khan, M.

AU - Razu, M.H.

AU - Akram, A.

AU - Arina, S.

AU - Hoque, E.

AU - Molla, M.M.A.

AU - Nafisaa, T.

AU - Angra, P.

AU - Rambaut, A.

AU - Pullan, S.T.

AU - Osman, K.L.

AU - Hoque, M.A.

AU - Biswas, P.

AU - Flora, M.S.

AU - Raghwani, J.

AU - Fournié, G.

AU - Samad, M.A.

AU - Hill, S.C.

N1 - We thank the Child Health Research Foundation (CHRF), Bangladesh, for allowing us to use their data on the GISAID EpiCoV database (accession numbers in Table S7-S8). We also acknowledge the use of additional sequences from the GISAID EpiCoV database for the global dataset used in our lineage analyses and provide accession numbers and acknowledgements in the supplementary electronic material (Table S7-S8). We thank the Directorate General of Health Services (DGHS) and Institute of Epidemiology Disease Control and Research (IEDCR) Bangladesh, DGHS, Ministry of Health and Family Welfare for sharing COVID-19 samples and data.

PY - 2024/11/13

Y1 - 2024/11/13

N2 - Background Genomic epidemiology has helped reconstruct the global and regional movement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, there is still a lack of understanding of SARS-CoV-2 spread in some of the world’s least developed countries (LDCs). Methods To begin to address this disparity, we studied the transmission dynamics of the virus in Bangladesh during the country’s first COVID-19 wave by analysing case reports and whole-genome sequences from all eight divisions of the country. Results We detected>50 virus introductions to the country during the period, including during a period of national lockdown. Additionally, through discrete phylogeographic analyses, we identified that geographical distance and population -density and/or -size influenced virus spatial dispersal in Bangladesh. Conclusions Overall, this study expands our knowledge of SARS-CoV-2 genomic epidemiology in Bangladesh, shedding light on crucial transmission characteristics within the country, while also acknowledging resemblances and differences to patterns observed in other nations.

AB - Background Genomic epidemiology has helped reconstruct the global and regional movement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, there is still a lack of understanding of SARS-CoV-2 spread in some of the world’s least developed countries (LDCs). Methods To begin to address this disparity, we studied the transmission dynamics of the virus in Bangladesh during the country’s first COVID-19 wave by analysing case reports and whole-genome sequences from all eight divisions of the country. Results We detected>50 virus introductions to the country during the period, including during a period of national lockdown. Additionally, through discrete phylogeographic analyses, we identified that geographical distance and population -density and/or -size influenced virus spatial dispersal in Bangladesh. Conclusions Overall, this study expands our knowledge of SARS-CoV-2 genomic epidemiology in Bangladesh, shedding light on crucial transmission characteristics within the country, while also acknowledging resemblances and differences to patterns observed in other nations.

KW - SARS-CoV-2

KW - Phylodynamics

KW - Bangladesh

KW - Genomic epidemiology

UR - https://github.com/lorcancarnegie/SARS_CoV_2_Bangladesh

UR - https://gisaid.org/

UR - https://static-content.springer.com/esm/art%3A10.1186%2Fs12985-024-02560-2/MediaObjects/12985_2024_2560_MOESM1_ESM.docx

U2 - 10.1186/s12985-024-02560-2

DO - 10.1186/s12985-024-02560-2

M3 - Article

SN - 1743-422X

VL - 21

JO - Virology Journal

JF - Virology Journal

IS - 1

M1 - 291

ER -

Genomic epidemiology of early SARS-CoV-2 transmission dynamics in Bangladesh

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