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

Genomic epidemiology of early SARS-CoV-2 transmission dynamics in Bangladesh | medRxiv /* */ /* */ <!-- <!-- /*! * yepnope1.5.4 * (c) WTFPL, GPLv2 */ (function(a,b,c){function d(a){return"[object Function]"==o.call(a)}function e(a){return"string"==typeof a}function f(){}function g(a){return!a||"loaded"==a||"complete"==a||"uninitialized"==a}function h(){var a=p.shift();q=1,a?a.t?m(function(){("c"==a.t?B.injectCss:B.injectJs)(a.s,0,a.a,a.x,a.e,1)},0):(a(),h()):q=0}function i(a,c,d,e,f,i,j){function k(b){if(!o&&g(l.readyState)&&(u.r=o=1,!q&&h(),l.onload=l.onreadystatechange=null,b)){"img"!=a&&m(function(){t.removeChild(l)},50);for(var d in y[c])y[c].hasOwnProperty(d)&&y[c][d].onload()}}var j=j||B.errorTimeout,l=b.createElement(a),o=0,r=0,u={t:d,s:c,e:f,a:i,x:j};1===y[c]&&(r=1,y[c]=[]),"object"==a?l.data=c:(l.src=c,l.type=a),l.width=l.height="0",l.onerror=l.onload=l.onreadystatechange=function(){k.call(this,r)},p.splice(e,0,u),"img"!=a&&(r||2===y[c]?(t.insertBefore(l,s?null:n),m(k,j)):y[c].push(l))}function j(a,b,c,d,f){return q=0,b=b||"j",e(a)?i("c"==b?v:u,a,b,this.i++,c,d,f):(p.splice(this.i++,0,a),1==p.length&&h()),this}function k(){var a=B;return a.loader={load:j,i:0},a}var l=b.documentElement,m=a.setTimeout,n=b.getElementsByTagName("script")[0],o={}.toString,p=[],q=0,r="MozAppearance"in l.style,s=r&&!!b.createRange().compareNode,t=s?l:n.parentNode,l=a.opera&&"[object Opera]"==o.call(a.opera),l=!!b.attachEvent&&!l,u=r?"object":l?"script":"img",v=l?"script":u,w=Array.isArray||function(a){return"[object Array]"==o.call(a)},x=[],y={},z={timeout:function(a,b){return b.length&&(a.timeout=b[0]),a}},A,B;B=function(a){function b(a){var a=a.split("!"),b=x.length,c=a.pop(),d=a.length,c={url:c,origUrl:c,prefixes:a},e,f,g;for(f=0;f<d;f++)g=a[f].split("="),(e=z[g.shift()])&&(c=e(c,g));for(f=0;f<b;f++)c=x[f](c);return c}function g(a,e,f,g,h){var i=b(a),j=i.autoCallback;i.url.split(".").pop().split("?").shift(),i.bypass||(e&&(e=d(e)?e:e[a]||e[g]||e[a.split("/").pop().split("?")[0]]),i.instead?i.instead(a,e,f,g,h):(y[i.url]?i.noexec=!0:y[i.url]=1,f.load(i.url,i.forceCSS||!i.forceJS&&"css"==i.url.split(".").pop().split("?").shift()?"c":c,i.noexec,i.attrs,i.timeout),(d(e)||d(j))&&f.load(function(){k(),e&&e(i.origUrl,h,g),j&&j(i.origUrl,h,g),y[i.url]=2})))}function h(a,b){function c(a,c){if(a){if(e(a))c||(j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}),g(a,j,b,0,h);else if(Object(a)===a)for(n in m=function(){var b=0,c;for(c in a)a.hasOwnProperty(c)&&b++;return b}(),a)a.hasOwnProperty(n)&&(!c&&!--m&&(d(j)?j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}:j[n]=function(a){return function(){var b=[].slice.call(arguments);a&&a.apply(this,b),l()}}(k[n])),g(a[n],j,b,n,h))}else!c&&l()}var h=!!a.test,i=a.load||a.both,j=a.callback||f,k=j,l=a.complete||f,m,n;c(h?a.yep:a.nope,!!i),i&&c(i)}var i,j,l=this.yepnope.loader;if(e(a))g(a,0,l,0);else if(w(a))for(i=0;i (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0];var j=d.createElement(s);var dl=l!='dataLayer'?'&l='+l:'';j.src='//www.googletagmanager.com/gtm.js?id='+i+dl;j.type='text/javascript';j.async=true;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-P4HH5NV'); Skip to main content Home About Submit ALERTS / RSS Search for this keyword Advanced Search Genomic epidemiology of early SARS-CoV-2 transmission dynamics in Bangladesh Lorcan Carnegie , John McCrone , Louis Du Plessis , Mahmudul Hasan , Md Zulfekar Ali , Ruhena Begum , M Z Hassan , Sharif Islam , Md Habibur Rahman , ASM Uddin , Md Samun Sarker , Tridip Das , Muhamad Maqsud Hossain , Mala Khan , Mamudul Hasan Razu , Arifa Akram , Sunzida Arina , Md Ehsanul Hoque , Md. Maruf Ahmed Molla , Tasnim Nafisa , Pawan Angra , Andrew Rambaut , Steven Pullan , Karen Osman , Md. Ahasanul Hoque , Paritosh Biswas , Meerjady Sabrina Flora , Jayna Raghwani , Guillaume Fournie , Md Abdus Samad , Sarah C Hill doi: https://doi.org/10.1101/2024.05.07.24306987 Lorcan Carnegie 1 Royal Veterinary College; Find this author on Google Scholar Find this author on PubMed Search for this author on this site For correspondence: lcarnegie20{at}rvc.ac.uk John McCrone 2 The University of Edinburgh, Institute of Ecology and Evolution; Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Louis Du Plessis 3 ETH Zurich, Department of Biosystems Science and Engineering; Swiss Institute of Bioinformatics; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Mahmudul Hasan 4 Bangladesh Livestock Research Institute; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Md Zulfekar Ali 4 Bangladesh Livestock Research Institute; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Ruhena Begum 4 Bangladesh Livestock Research Institute; Find this author on Google Scholar Find this author on PubMed Search for this author on this site M Z Hassan 4 Bangladesh Livestock Research Institute; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Sharif Islam 5 Bangladesh Livestock Research Institute; Virginia Tech, Global Change Center; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Md Habibur Rahman 4 Bangladesh Livestock Research Institute; Find this author on Google Scholar Find this author on PubMed Search for this author on this site ASM Uddin 4 Bangladesh Livestock Research Institute; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Md Samun Sarker 4 Bangladesh Livestock Research Institute; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Tridip Das 6 Chattogram Veterinary and Animal Sciences University; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Muhamad Maqsud Hossain 7 North South University, NSU Genome Research Institute (NGRI); North South University, Department of Biochemistry and Microbiology; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Mala Khan 8 Bangladesh Reference Institute for Chemical Measurements; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Mamudul Hasan Razu 8 Bangladesh Reference Institute for Chemical Measurements; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Arifa Akram 9 National Institute of Laboratory Medicine & Referral Centre; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Sunzida Arina 9 National Institute of Laboratory Medicine & Referral Centre; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Md Ehsanul Hoque 9 National Institute of Laboratory Medicine & Referral Centre; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Md. Maruf Ahmed Molla 9 National Institute of Laboratory Medicine & Referral Centre; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Tasnim Nafisa 9 National Institute of Laboratory Medicine & Referral Centre; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Pawan Angra 10 Centers for Disease Control and Prevention; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Andrew Rambaut 11 The University of Edinburgh, Institute of Ecology and Evolution; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Steven Pullan 12 UK Health Security Agency; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Karen Osman 12 UK Health Security Agency; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Md. Ahasanul Hoque 6 Chattogram Veterinary and Animal Sciences University; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Paritosh Biswas 6 Chattogram Veterinary and Animal Sciences University; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Meerjady Sabrina Flora 13 Government of the People's Republic of Bangladesh Ministry of Health and Family Welfare, National Institute of Preventive and Social Medicine; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Jayna Raghwani 14 The Royal Veterinary College; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Guillaume Fournie 15 The Royal Veterinary College; INRAE Find this author on Google Scholar Find this author on PubMed Search for this author on this site Md Abdus Samad 4 Bangladesh Livestock Research Institute; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Sarah C Hill 14 The Royal Veterinary College; Find this author on Google Scholar Find this author on PubMed Search for this author on this site Abstract Info/History Metrics Supplementary material Data/Code Preview PDF 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 worlds least developed countries (LDCs). Methods: To begin to address this disparity, we studied the transmission dynamics of the virus in Bangladesh during the countrys 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. Competing Interest Statement The authors have declared no competing interest. Funding Statement L.C. is supported by a Biotechnology and Biological Sciences Research Council (BBSRC) London Interdisciplinary Biosciences Consortium (LIDo) studentship [grant number BB/T008709/1]. S.C.H. is supported by a Sir Henry Wellcome Postdoctoral Fellowship from the Wellcome Trust [220414/Z/20/Z] (https://wellcome.org/). J.R., M.H. and G.F. are supported by the UKRI GCRF One Health Poultry Hub (Grant No. BB/S011269/1), one of twelve interdisciplinary research hubs funded under the UK governments Grand Challenge Research Fund Interdisciplinary Research Hub initiative. G.F. was supported by the French National Research Agency and the French Ministry of Higher Education and Research. M.A.S. is supported by Zoonosis and Transboundary Animal Diseases Prevention and Control project [Grant No.223038200], MoFL, Bangladesh. S.I., R.B., and M.S.S. are supported by the Combating the threats of antimicrobial resistance and zoonotic diseases to achieve the GHSA in Bangladesh [Grant no. NU2GGH002077]. Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study was carried out under the ethical approval from the ethical approval committee of Bangladesh Livestock Research Institute, Bangladesh with the reference number BLRI/EA/2020102/2022, and with informed consent from tested individuals. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Footnotes The manuscript has been revised to correct a small number of colour errors that were introduced during the PDF converting process. This has been corrected in the revision. Data Availability The datasets and BEAST XML files supporting the conclusions of this article are available in the Github repository. The dataset for the newly reported genetic sequence data supporting the conclusions of this article are available in GISAID EpiFlu database (https://gisaid.org) under the accession numbers included within the additional files of this article [Table S6]. https://github.com/lorcancarnegie/SARS_CoV_2_Bangladesh Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. View the discussion thread. Back to top Previous Next Posted May 08, 2024. Download PDF Supplementary Material Data/Code Email Thank you for your interest in spreading the word about medRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. You are going to email the following Genomic epidemiology of early SARS-CoV-2 transmission dynamics in Bangladesh Message Subject (Your Name) has forwarded a page to you from medRxiv Message Body (Your Name) thought you would like to see this page from the medRxiv website. Your Personal Message CAPTCHA This question is for testing whether or not you are a human visitor and to prevent automated spam submissions. Share Genomic epidemiology of early SARS-CoV-2 transmission dynamics in Bangladesh Lorcan Carnegie , John McCrone , Louis Du Plessis , Mahmudul Hasan , Md Zulfekar Ali , Ruhena Begum , M Z Hassan , Sharif Islam , Md Habibur Rahman , ASM Uddin , Md Samun Sarker , Tridip Das , Muhamad Maqsud Hossain , Mala Khan , Mamudul Hasan Razu , Arifa Akram , Sunzida Arina , Md Ehsanul Hoque , Md. Maruf Ahmed Molla , Tasnim Nafisa , Pawan Angra , Andrew Rambaut , Steven Pullan , Karen Osman , Md. Ahasanul Hoque , Paritosh Biswas , Meerjady Sabrina Flora , Jayna Raghwani , Guillaume Fournie , Md Abdus Samad , Sarah C Hill medRxiv 2024.05.07.24306987; doi: https://doi.org/10.1101/2024.05.07.24306987 Share This Article: Copy Citation Tools Genomic epidemiology of early SARS-CoV-2 transmission dynamics in Bangladesh Lorcan Carnegie , John McCrone , Louis Du Plessis , Mahmudul Hasan , Md Zulfekar Ali , Ruhena Begum , M Z Hassan , Sharif Islam , Md Habibur Rahman , ASM Uddin , Md Samun Sarker , Tridip Das , Muhamad Maqsud Hossain , Mala Khan , Mamudul Hasan Razu , Arifa Akram , Sunzida Arina , Md Ehsanul Hoque , Md. Maruf Ahmed Molla , Tasnim Nafisa , Pawan Angra , Andrew Rambaut , Steven Pullan , Karen Osman , Md. Ahasanul Hoque , Paritosh Biswas , Meerjady Sabrina Flora , Jayna Raghwani , Guillaume Fournie , Md Abdus Samad , Sarah C Hill medRxiv 2024.05.07.24306987; doi: https://doi.org/10.1101/2024.05.07.24306987 Citation Manager Formats BibTeX Bookends EasyBib EndNote (tagged) EndNote 8 (xml) Medlars Mendeley Papers RefWorks Tagged Ref Manager RIS Zotero Tweet Widget Facebook Like Google Plus One Subject Area Public and Global Health Subject Areas All Articles Addiction Medicine (573) Allergy and Immunology (865) Anesthesia (303) Cardiovascular Medicine (4457) Dentistry and Oral Medicine (445) Dermatology (383) Emergency Medicine (610) Endocrinology (including Diabetes Mellitus and Metabolic Disease) (1517) Epidemiology (15244) Forensic Medicine (30) Gastroenterology (1132) Genetic and Genomic Medicine (6620) Geriatric Medicine (669) Health Economics (1002) Health Informatics (4557) Health Policy (1372) Health Systems and Quality Improvement (1615) Hematology (543) HIV/AIDS (1272) Infectious Diseases (except HIV/AIDS) (15936) Intensive Care and Critical Care Medicine (1106) Medical Education (624) Medical Ethics (147) Nephrology (670) Neurology (6634) Nursing (346) Nutrition (999) Obstetrics and Gynecology (1148) Occupational and Environmental Health (957) Oncology (3348) Ophthalmology (980) Orthopedics (369) Otolaryngology (421) Pain Medicine (436) Palliative Medicine (130) Pathology (665) Pediatrics (1696) Pharmacology and Therapeutics (693) Primary Care Research (714) Psychiatry and Clinical Psychology (5463) Public and Global Health (9257) Radiology and Imaging (2210) Rehabilitation Medicine and Physical Therapy (1371) Respiratory Medicine (1198) Rheumatology (598) Sexual and Reproductive Health (716) Sports Medicine (532) Surgery (714) Toxicology (99) Transplantation (289) Urology (265) (function(){function c(){var b=a.contentDocument||a.contentWindow.document;if(b){var d=b.createElement('script');d.innerHTML="window.__CF$cv$params={r:'a03475dfc86573bd',t:'MTc4MDA0NjgxNw=='};var a=document.createElement('script');a.src='/cdn-cgi/challenge-platform/scripts/jsd/main.js';document.getElementsByTagName('head')[0].appendChild(a);";b.getElementsByTagName('head')[0].appendChild(d)}}if(document.body){var a=document.createElement('iframe');a.height=1;a.width=1;a.style.position='absolute';a.style.top=0;a.style.left=0;a.style.border='none';a.style.visibility='hidden';document.body.appendChild(a);if('loading'!==document.readyState)c();else if(window.addEventListener)document.addEventListener('DOMContentLoaded',c);else{var e=document.onreadystatechange||function(){};document.onreadystatechange=function(b){e(b);'loading'!==document.readyState&&(document.onreadystatechange=e,c())}}}})();