SARS-CoV-2 population dynamics in immunocompetent individuals in a closed transmission chain shows genomic diversity over the course of infection

{ 'indexed': {'date-parts': [[2024, 7, 17]], 'date-time': '2024-07-17T00:25:10Z', 'timestamp': 1721175910088}, 'reference-count': 85, 'publisher': 'Springer Science and Business Media LLC', 'issue': '1', 'license': [ { 'start': { 'date-parts': [[2024, 7, 16]], 'date-time': '2024-07-16T00:00:00Z', 'timestamp': 1721088000000}, 'content-version': 'tdm', 'delay-in-days': 0, 'URL': 'https://creativecommons.org/licenses/by/4.0'}, { 'start': { 'date-parts': [[2024, 7, 16]], 'date-time': '2024-07-16T00:00:00Z', 'timestamp': 1721088000000}, 'content-version': 'vor', 'delay-in-days': 0, 'URL': 'https://creativecommons.org/licenses/by/4.0'}], 'funder': [ { 'DOI': '10.13039/100000038', 'name': 'U.S. Food and Drug Administration', 'doi-asserted-by': 'publisher', 'award': ['75F40120C00085']}, { 'DOI': '10.13039/501100000265', 'name': 'Medical Research Council', 'doi-asserted-by': 'publisher', 'award': ['MR/W005611/1', 'MR/Y004205/1']}], 'content-domain': {'domain': ['link.springer.com'], 'crossmark-restriction': False}, 'abstract': '<jats:title>Abstract</jats:title><jats:sec>\n' ' <jats:title>Background</jats:title>\n' ' <jats:p>SARS-CoV-2 remains rapidly evolving, and many biologically important ' 'genomic substitutions/indels have characterised novel SARS-CoV-2 lineages, which have emerged ' 'during successive global waves of the pandemic. Worldwide genomic sequencing has been able to ' 'monitor these waves, track transmission clusters, and examine viral evolution in real time to ' 'help inform healthcare policy. One school of thought is that an apparent greater than average ' 'divergence in an emerging lineage from contemporary variants may require persistent ' 'infection, for example in an immunocompromised host. Due to the nature of the COVID-19 ' 'pandemic and sampling, there were few studies that examined the evolutionary trajectory of ' 'SARS-CoV-2 in healthy individuals.</jats:p>\n' ' </jats:sec><jats:sec>\n' ' <jats:title>Methods</jats:title>\n' ' <jats:p>We investigated viral evolutionary trends and participant ' 'symptomatology within a cluster of 16 SARS-CoV-2 infected, immunocompetent individuals with ' 'no co-morbidities in a closed transmission chain. Longitudinal nasopharyngeal swab sampling ' 'allowed characterisation of SARS-CoV-2 intra-host variation over time at both the dominant ' 'and minor genomic variant levels through Nimagen-Illumina sequencing.</jats:p>\n' ' </jats:sec><jats:sec>\n' ' <jats:title>Results</jats:title>\n' ' <jats:p>A change in viral lineage assignment was observed in individual ' 'infections; however, there was only one indel and no evidence of recombination over the ' 'period of an acute infection. Minor and dominant genomic modifications varied between ' 'participants, with some minor genomic modifications increasing in abundance to become the ' 'dominant viral sequence during infection.</jats:p>\n' ' </jats:sec><jats:sec>\n' ' <jats:title>Conclusions</jats:title>\n' ' <jats:p>Data from this cohort of SARS-CoV-2-infected participants ' 'demonstrated that long-term persistent infection in an immunocompromised host was not ' 'necessarily a prerequisite for generating a greater than average frequency of amino acid ' 'substitutions. Amino acid substitutions at both the dominant and minor genomic sequence level ' 'were observed in immunocompetent individuals during infection showing that viral lineage ' 'changes can occur generating viral diversity.</jats:p>\n' ' </jats:sec>', 'DOI': '10.1186/s13073-024-01360-1', 'type': 'journal-article', 'created': {'date-parts': [[2024, 7, 16]], 'date-time': '2024-07-16T11:02:23Z', 'timestamp': 1721127743000}, 'update-policy': 'http://dx.doi.org/10.1007/springer_crossmark_policy', 'source': 'Crossref', 'is-referenced-by-count': 0, 'title': 'SARS-CoV-2 population dynamics in immunocompetent individuals in a closed transmission chain ' 'shows genomic diversity over the course of infection', 'prefix': '10.1186', 'volume': '16', 'author': [ {'given': 'Hannah', 'family': 'Goldswain', 'sequence': 'first', 'affiliation': []}, {'given': 'Rebekah', 'family': 'Penrice-Randal', 'sequence': 'additional', 'affiliation': []}, {'given': 'I’ah', 'family': 'Donovan-Banfield', 'sequence': 'additional', 'affiliation': []}, {'given': 'Craig W.', 'family': 'Duffy', 'sequence': 'additional', 'affiliation': []}, {'given': 'Xiaofeng', 'family': 'Dong', 'sequence': 'additional', 'affiliation': []}, {'given': 'Nadine', 'family': 'Randle', 'sequence': 'additional', 'affiliation': []}, {'given': 'Yan', 'family': 'Ryan', 'sequence': 'additional', 'affiliation': []}, {'given': 'Aleksandra M.', 'family': 'Rzeszutek', 'sequence': 'additional', 'affiliation': []}, {'given': 'Jack', 'family': 'Pilgrim', 'sequence': 'additional', 'affiliation': []}, {'given': 'Emma', 'family': 'Keyser', 'sequence': 'additional', 'affiliation': []}, {'given': 'Simon A.', 'family': 'Weller', 'sequence': 'additional', 'affiliation': []}, {'given': 'Emma J.', 'family': 'Hutley', 'sequence': 'additional', 'affiliation': []}, {'given': 'Catherine', 'family': 'Hartley', 'sequence': 'additional', 'affiliation': []}, {'given': 'Tessa', 'family': 'Prince', 'sequence': 'additional', 'affiliation': []}, {'given': 'Alistair C.', 'family': 'Darby', 'sequence': 'additional', 'affiliation': []}, {'given': 'Niall', 'family': 'Aye Maung', 'sequence': 'additional', 'affiliation': []}, {'given': 'Henry', 'family': 'Nwume', 'sequence': 'additional', 'affiliation': []}, { 'ORCID': 'http://orcid.org/0000-0002-6582-0275', 'authenticated-orcid': False, 'given': 'Julian A.', 'family': 'Hiscox', 'sequence': 'additional', 'affiliation': []}, {'given': 'Stevan R.', 'family': 'Emmett', 'sequence': 'additional', 'affiliation': []}], 'member': '297', 'published-online': {'date-parts': [[2024, 7, 16]]}, 'reference': [ { 'key': '1360_CR1', 'doi-asserted-by': 'publisher', 'first-page': '270', 'DOI': '10.1038/s41586-020-2012-7', 'volume': '579', 'author': 'P Zhou', 'year': '2020', 'unstructured': 'Zhou P, Yang X-L, Wang X-G, Hu B, Zhang L, Zhang W, Si H-R, Zhu Y, Li B, ' 'Huang C-L, et al. A pneumonia outbreak associated with a new coronavirus ' 'of probable bat origin. Nature. 2020;579:270–3.', 'journal-title': 'Nature'}, { 'key': '1360_CR2', 'volume-title': 'The Huanan market was the epicenter of SARS-CoV-2 emergence', 'author': 'M Worobey', 'year': '2022', 'unstructured': 'Worobey M, Levy JI, Malpica Serrano LM, Crits-Christoph A, Pekar JE, ' 'Goldstein SA, Rasmussen AL, Kraemer MUG, Newman C, Koopmans MPG, et al. ' 'The Huanan market was the epicenter of SARS-CoV-2 emergence. 2022.'}, { 'key': '1360_CR3', 'volume-title': 'SARS-CoV-2 emergence very likely resulted from at least two zoonotic ' 'events', 'author': 'JE Pekar', 'year': '2022', 'unstructured': 'Pekar JE, Magee A, Parker E, Moshiri N, Izhikevich K, Havens JL, ' 'Gangavarapu K, Malpica Serrano LM, Crits-Christoph A, Matteson NL, et ' 'al. SARS-CoV-2 emergence very likely resulted from at least two zoonotic ' 'events. 2022.'}, { 'key': '1360_CR4', 'doi-asserted-by': 'publisher', 'first-page': '54', 'DOI': '10.1186/s13073-023-01208-0', 'volume': '15', 'author': 'M Shuaib', 'year': '2023', 'unstructured': 'Shuaib M, Adroub S, Mourier T, Mfarrej S, Zhang H, Esau L, Alsomali A, ' 'Alofi FS, Ahmad AN, Shamsan A, et al. Impact of the SARS-CoV-2 ' 'nucleocapsid 203K/204R mutations on the inflammatory immune response in ' 'COVID-19 severity. Genome Med. 2023;15:54.', 'journal-title': 'Genome Med'}, { 'key': '1360_CR5', 'doi-asserted-by': 'publisher', 'first-page': '437', 'DOI': '10.1016/S0140-6736(22)00017-4', 'volume': '399', 'author': 'N Wolter', 'year': '2022', 'unstructured': 'Wolter N, Jassat W, Walaza S, Welch R, Moultrie H, Groome M, Amoako DG, ' 'Everatt J, Bhiman JN, Scheepers C, et al. Early assessment of the ' 'clinical severity of the SARS-CoV-2 omicron variant in South Africa: a ' 'data linkage study. Lancet. 2022;399:437–46.', 'journal-title': 'Lancet'}, { 'key': '1360_CR6', 'doi-asserted-by': 'publisher', 'first-page': '1618', 'DOI': '10.1016/S0140-6736(22)00327-0', 'volume': '399', 'author': 'C Menni', 'year': '2022', 'unstructured': 'Menni C, Valdes AM, Polidori L, Antonelli M, Penamakuri S, Nogal A, ' 'Louca P, May A, Figueiredo JC, Hu C, et al. Symptom prevalence, ' 'duration, and risk of hospital admission in individuals infected with ' 'SARS-CoV-2 during periods of omicron and delta variant dominance: a ' 'prospective observational study from the ZOE COVID Study. Lancet. ' '2022;399:1618–24.', 'journal-title': 'Lancet'}, { 'key': '1360_CR7', 'doi-asserted-by': 'publisher', 'first-page': 'e1128', 'DOI': '10.1093/cid/ciab721', 'volume': '75', 'author': 'SWX Ong', 'year': '2022', 'unstructured': 'Ong SWX, Chiew CJ, Ang LW, Mak TM, Cui L, Toh M, Lim YD, Lee PH, Lee TH, ' 'Chia PY, et al. Clinical and Virological Features of Severe Acute ' 'Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants of Concern: A ' 'Retrospective Cohort Study Comparing B.1.17 (Alpha), B.1.351 (Beta), and ' 'B.1.6172 (Delta). Clin Infect Dis. 2022;75:e1128–36.', 'journal-title': 'Clin Infect Dis'}, { 'key': '1360_CR8', 'doi-asserted-by': 'publisher', 'first-page': '270', 'DOI': '10.4161/rna.8.2.15013', 'volume': '8', 'author': 'MR Denison', 'year': '2011', 'unstructured': 'Denison MR, Graham RL, Donaldson EF, Eckerle LD, Baric RS. ' 'Coronaviruses: an RNA proofreading machine regulates replication ' 'fidelity and diversity. RNA Biol. 2011;8:270–9.', 'journal-title': 'RNA Biol'}, { 'key': '1360_CR9', 'doi-asserted-by': 'crossref', 'unstructured': 'Moeller NH, Shi K, Demir O, Belica C, Banerjee S, Yin L, Durfee C, Amaro ' 'RE, Aihara H: Structure and dynamics of SARS-CoV-2 proofreading ' 'exoribonuclease ExoN. Proc Natl Acad Sci U S A. 2022;119:e2106379119.', 'DOI': '10.1073/pnas.2106379119'}, { 'key': '1360_CR10', 'doi-asserted-by': 'publisher', 'first-page': 'e0091321', 'DOI': '10.1128/msphere.00913-21', 'volume': '7', 'author': 'T Prince', 'year': '2022', 'unstructured': 'Prince T, Dong X, Penrice-Randal R, Randle N, Hartley C, Goldswain H, ' 'Jones B, Semple MG, Baillie JK, Openshaw PJM, et al. Analysis of ' 'SARS-CoV-2 in Nasopharyngeal Samples from Patients with COVID-19 ' 'Illustrates Population Variation and Diverse Phenotypes, Placing the ' 'Growth Properties of Variants of Concern in Context with Other Lineages. ' 'mSphere. 2022;7:e0091321.', 'journal-title': 'mSphere'}, { 'key': '1360_CR11', 'doi-asserted-by': 'publisher', 'first-page': '47', 'DOI': '10.1186/s13059-023-02881-5', 'volume': '24', 'author': 'H Goldswain', 'year': '2023', 'unstructured': 'Goldswain H, Dong X, Penrice-Randal R, Alruwaili M, Shawli GT, Prince T, ' 'Williamson MK, Raghwani J, Randle N, Jones B, et al. The P323L ' 'substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective ' 'advantage during infection. Genome Biol. 2023;24:47.', 'journal-title': 'Genome Biol'}, { 'key': '1360_CR12', 'doi-asserted-by': 'publisher', 'first-page': '18721', 'DOI': '10.1038/s41598-022-22060-z', 'volume': '12', 'author': 'P Dudouet', 'year': '2022', 'unstructured': 'Dudouet P, Colson P, Aherfi S, Levasseur A, Beye M, Delerce J, Burel E, ' 'Lavrard P, Bader W, Lagier JC, et al. SARS-CoV-2 quasi-species analysis ' 'from patients with persistent nasopharyngeal shedding. Sci Rep. ' '2022;12:18721.', 'journal-title': 'Sci Rep'}, { 'key': '1360_CR13', 'doi-asserted-by': 'publisher', 'first-page': '1560 e1561', 'DOI': '10.1016/j.cmi.2020.07.032', 'volume': '26', 'author': 'A Jary', 'year': '2020', 'unstructured': 'Jary A, Leducq V, Malet I, Marot S, Klement-Frutos E, Teyssou E, Soulie ' 'C, Abdi B, Wirden M, Pourcher V, et al. Evolution of viral quasispecies ' 'during SARS-CoV-2 infection. Clin Microbiol Infect. 2020;26:1560 ' 'e1561–1560 e1564.', 'journal-title': 'Clin Microbiol Infect'}, { 'key': '1360_CR14', 'doi-asserted-by': 'crossref', 'unstructured': "Volz E, Hill V, McCrone JT, Price A, Jorgensen D, O'Toole Á, Southgate " 'J, Johnson R, Jackson B, Nascimento FF, et al. Evaluating the Effects of ' 'SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. ' 'Cell. 2021;184:64–75.', 'DOI': '10.1101/2020.07.31.20166082'}, { 'key': '1360_CR15', 'doi-asserted-by': 'crossref', 'unstructured': 'Yurkovetskiy L, Wang X, Pascal KE, Tomkins-Tinch C, Nyalile TP, Wang Y, ' 'Baum A, Diehl WE, Dauphin A, Carbone C, et al. Structural and Functional ' 'Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Cell. ' '2020;83:739–51.', 'DOI': '10.1016/j.cell.2020.09.032'}, { 'key': '1360_CR16', 'doi-asserted-by': 'crossref', 'unstructured': 'Lythgoe KA, Hall M, Ferretti L, de Cesare M, MacIntyre-Cockett G, Trebes ' 'A, Andersson M, Otecko N, Wise EL, Moore N, et al. SARS-CoV-2 ' 'within-host diversity and transmission. Science. 2021;372:eabg0281.', 'DOI': '10.1126/science.abg0821'}, { 'key': '1360_CR17', 'doi-asserted-by': 'publisher', 'first-page': '713', 'DOI': '10.1093/cid/ciaa203', 'volume': '71', 'author': 'Z Shen', 'year': '2020', 'unstructured': 'Shen Z, Xiao Y, Kang L, Ma W, Shi L, Zhang L, Zhou Z, Yang J, Zhong J, ' 'Yang D, et al. Genomic Diversity of Severe Acute Respiratory ' 'Syndrome-Coronavirus 2 in Patients With Coronavirus Disease 2019. Clin ' 'Infect Dis. 2020;71:713–20.', 'journal-title': 'Clin Infect Dis'}, { 'key': '1360_CR18', 'doi-asserted-by': 'publisher', 'first-page': 'e0100321', 'DOI': '10.1128/Spectrum.01003-21', 'volume': '9', 'author': 'EN Gallichotte', 'year': '2021', 'unstructured': 'Gallichotte EN, Quicke KM, Sexton NR, Fitzmeyer E, Young MC, Janich AJ, ' 'Dobos K, Pabilonia KL, Gahm G, Carlton EJ, et al. Early Adoption of ' 'Longitudinal Surveillance for SARS-CoV-2 among Staff in Long-Term Care ' 'Facilities: Prevalence. Virologic and Sequence Analysis Microbiol ' 'Spectr. 2021;9:e0100321.', 'journal-title': 'Virologic and Sequence Analysis Microbiol Spectr'}, { 'key': '1360_CR19', 'doi-asserted-by': 'publisher', 'first-page': '1343', 'DOI': '10.1001/jamainternmed.2021.4686', 'volume': '181', 'author': 'Y Ge', 'year': '2021', 'unstructured': 'Ge Y, Martinez L, Sun S, Chen Z, Zhang F, Li F, Sun W, Chen E, Pan J, Li ' 'C, et al. COVID-19 Transmission Dynamics Among Close Contacts of Index ' 'Patients With COVID-19: A Population-Based Cohort Study in Zhejiang ' 'Province. China JAMA Intern Med. 2021;181:1343–50.', 'journal-title': 'China JAMA Intern Med'}, { 'key': '1360_CR20', 'doi-asserted-by': 'crossref', 'unstructured': 'Khanh NC, Thai PQ, Quach HL, Thi NH, Dinh PC, Duong TN, Mai LTQ, Nghia ' 'ND, Tu TA, Quang N, et al. Transmission of SARS-CoV 2 During Long-Haul ' 'Flight. Emerg Infect Dis. 2020;26:2617–24.', 'DOI': '10.3201/eid2611.203299'}, { 'key': '1360_CR21', 'doi-asserted-by': 'crossref', 'unstructured': 'Letizia AG, Ramos I, Obla A, Goforth C, Weir DL, Ge Y, Bamman MM, Dutta ' 'J, Ellis E, Estrella L, et al. SARS-CoV-2 Transmission among Marine ' 'Recruits during Quarantine. The New Engl J Med. 2020;383:2407–16.', 'DOI': '10.1056/NEJMoa2029717'}, { 'key': '1360_CR22', 'doi-asserted-by': 'publisher', 'first-page': '679', 'DOI': '10.1038/s41586-022-04411-y', 'volume': '603', 'author': 'R Viana', 'year': '2022', 'unstructured': 'Viana R, Moyo S, Amoako DG, Tegally H, Scheepers C, Althaus CL, Anyaneji ' 'UJ, Bester PA, Boni MF, Chand M, et al. Rapid epidemic expansion of the ' 'SARS-CoV-2 Omicron variant in southern Africa. Nature. 2022;603:679–86.', 'journal-title': 'Nature'}, { 'key': '1360_CR23', 'doi-asserted-by': 'publisher', 'first-page': '277', 'DOI': '10.1038/s41586-021-03291-y', 'volume': '592', 'author': 'SA Kemp', 'year': '2021', 'unstructured': 'Kemp SA, Collier DA, Datir RP, Ferreira I, Gayed S, Jahun A, Hosmillo M, ' 'Rees-Spear C, Mlcochova P, Lumb IU, et al. SARS-CoV-2 evolution during ' 'treatment of chronic infection. Nature. 2021;592:277–82.', 'journal-title': 'Nature'}, { 'key': '1360_CR24', 'volume-title': 'The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the ' 'UK', 'author': 'V Hill', 'year': '2022', 'unstructured': 'Hill V, Du Plessis L, Peacock TP, Aggarwal D, Colquhoun R, Carabelli AM, ' 'Ellaby N, Gallagher E, Groves N, Jackson B, et al. The origins and ' 'molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK. 2022.'}, { 'key': '1360_CR25', 'doi-asserted-by': 'publisher', 'first-page': '760', 'DOI': '10.1086/500465', 'volume': '193', 'author': 'MG Ison', 'year': '2006', 'unstructured': 'Ison MG, Gubareva LV, Atmar RL, Treanor J, Hayden FG. Recovery of ' 'drug-resistant influenza virus from immunocompromised patients: a case ' 'series. J Infect Dis. 2006;193:760–4.', 'journal-title': 'J Infect Dis'}, { 'key': '1360_CR26', 'doi-asserted-by': 'publisher', 'first-page': 'ofad001', 'DOI': '10.1093/ofid/ofad001', 'volume': '10', 'author': 'KS Walter', 'year': '2023', 'unstructured': 'Walter KS, Kim E, Verma R, Altamirano J, Leary S, Carrington YJ, ' 'Jagannathan P, Singh U, Holubar M, Subramanian A, et al. Challenges in ' 'Harnessing Shared Within-Host Severe Acute Respiratory Syndrome ' 'Coronavirus 2 Variation for Transmission Inference. Open Forum Infect ' 'Dis. 2023;10:ofad001.', 'journal-title': 'Open Forum Infect Dis'}, { 'key': '1360_CR27', 'doi-asserted-by': 'publisher', 'first-page': '107', 'DOI': '10.1016/j.jhin.2021.02.022', 'volume': '111', 'author': 'AH Lovestad', 'year': '2021', 'unstructured': 'Lovestad AH, Jorgensen SB, Handal N, Ambur OH, Aamot HV. Investigation ' 'of intra-hospital SARS-CoV-2 transmission using nanopore whole-genome ' 'sequencing. J Hosp Infect. 2021;111:107–16.', 'journal-title': 'J Hosp Infect'}, { 'key': '1360_CR28', 'doi-asserted-by': 'publisher', 'first-page': '436', 'DOI': '10.1016/j.jmii.2021.07.006', 'volume': '55', 'author': 'PY Huang', 'year': '2022', 'unstructured': 'Huang PY, Wu TS, Cheng CW, Chen CJ, Huang CG, Tsao KC, Lin CS, Chung TY, ' 'Lai CC, Yang CT, et al. A hospital cluster of COVID-19 associated with a ' 'SARS-CoV-2 superspreading event. J Microbiol Immunol Infect. ' '2022;55:436–44.', 'journal-title': 'J Microbiol Immunol Infect'}, { 'key': '1360_CR29', 'doi-asserted-by': 'publisher', 'first-page': 'e0277754', 'DOI': '10.1371/journal.pone.0277754', 'volume': '17', 'author': 'M Mele-Casas', 'year': '2022', 'unstructured': 'Mele-Casas M, Launes C, de Sevilla MF, Hernandez-Garcia M, Pons-Tomas G, ' 'Bassat Q, Fumado V, Fortuny C, Garcia-Miquel A, Bonet-Carne E, et al. ' 'Low transmission of SARS-CoV-2 derived from children in family clusters: ' 'An observational study of family households in the Barcelona ' 'Metropolitan Area. Spain PLoS One. 2022;17:e0277754.', 'journal-title': 'Spain PLoS One'}, { 'key': '1360_CR30', 'doi-asserted-by': 'publisher', 'first-page': '1626', 'DOI': '10.3201/eid2607.200718', 'volume': '26', 'author': 'C Li', 'year': '2020', 'unstructured': 'Li C, Ji F, Wang L, Wang L, Hao J, Dai M, Liu Y, Pan X, Fu J, Li L, et ' 'al. Asymptomatic and Human-to-Human Transmission of SARS-CoV-2 in a ' '2-Family Cluster, Xuzhou. China Emerg Infect Dis. 2020;26:1626–8.', 'journal-title': 'China Emerg Infect Dis'}, { 'key': '1360_CR31', 'doi-asserted-by': 'publisher', 'first-page': 'e0040022', 'DOI': '10.1128/msphere.00400-22', 'volume': '7', 'author': 'EE Bendall', 'year': '2022', 'unstructured': 'Bendall EE, Paz-Bailey G, Santiago GA, Porucznik CA, Stanford JB, ' 'Stockwell MS, Duque J, Jeddy Z, Veguilla V, Major C, et al. SARS-CoV-2 ' 'Genomic Diversity in Households Highlights the Challenges of ' 'Sequence-Based Transmission Inference. mSphere. 2022;7:e0040022.', 'journal-title': 'mSphere'}, { 'key': '1360_CR32', 'doi-asserted-by': 'publisher', 'first-page': '000252', 'DOI': '10.1099/acmi.0.000252', 'volume': '3', 'author': 'D Hare', 'year': '2021', 'unstructured': 'Hare D, Gonzalez G, Dean J, McDonnell K, Carr MJ, De Gascun CF. Genomic ' 'epidemiological analysis of SARS-CoV-2 household transmission. Access ' 'Microbiol. 2021;3:000252.', 'journal-title': 'Access Microbiol'}, { 'key': '1360_CR33', 'doi-asserted-by': 'publisher', 'first-page': '105253', 'DOI': '10.1016/j.meegid.2022.105253', 'volume': '99', 'author': 'C De Marco', 'year': '2022', 'unstructured': 'De Marco C, Marascio N, Veneziano C, Biamonte F, Trecarichi EM, ' 'Santamaria G, Leviyang S, Liberto MC, Mazzitelli M, Quirino A, et al. ' 'Whole-genome analysis of SARS-CoV-2 in a 2020 infection cluster in a ' 'nursing home of Southern Italy. Infect Genet Evol. 2022;99:105253.', 'journal-title': 'Infect Genet Evol'}, { 'key': '1360_CR34', 'doi-asserted-by': 'publisher', 'first-page': 'veac052', 'DOI': '10.1093/ve/veac052', 'volume': '8', 'author': 'WW Hannon', 'year': '2022', 'unstructured': 'Hannon WW, Roychoudhury P, Xie H, Shrestha L, Addetia A, Jerome KR, ' 'Greninger AL, Bloom JD. Narrow transmission bottlenecks and limited ' 'within-host viral diversity during a SARS-CoV-2 outbreak on a fishing ' 'boat. Virus Evol. 2022;8:veac052.', 'journal-title': 'Virus Evol.'}, { 'key': '1360_CR35', 'doi-asserted-by': 'publisher', 'first-page': '104993', 'DOI': '10.1016/j.jcv.2021.104993', 'volume': '144', 'author': 'JPM Coolen', 'year': '2021', 'unstructured': 'Coolen JPM, Wolters F, Tostmann A, van Groningen LFJ, Bleeker-Rovers CP, ' 'Tan E, van der Geest-Blankert N, Hautvast JLA, Hopman J, Wertheim HFL, ' 'et al. SARS-CoV-2 whole-genome sequencing using reverse complement PCR: ' 'For easy, fast and accurate outbreak and variant analysis. J Clin Virol. ' '2021;144:104993.', 'journal-title': 'J Clin Virol'}, { 'key': '1360_CR36', 'doi-asserted-by': 'publisher', 'first-page': '7284', 'DOI': '10.1038/s41467-022-34839-9', 'volume': '13', 'author': 'I Donovan-Banfield', 'year': '2022', 'unstructured': 'Donovan-Banfield I, Penrice-Randal R, Goldswain H, Rzeszutek AM, Pilgrim ' 'J, Bullock K, Saunders G, Northey J, Dong X, Ryan Y, et al. ' 'Characterisation of SARS-CoV-2 genomic variation in response to ' 'molnupiravir treatment in the AGILE Phase IIa clinical trial. Nat ' 'Commun. 2022;13:7284.', 'journal-title': 'Nat Commun'}, { 'key': '1360_CR37', 'doi-asserted-by': 'crossref', 'unstructured': 'Martin M: Cutadapt Removes Adapter Sequences From High-Throughput ' 'Sequencing Reads. EMBnet. 2011;17:1.', 'DOI': '10.14806/ej.17.1.200'}, { 'key': '1360_CR38', 'doi-asserted-by': 'publisher', 'first-page': 'i884', 'DOI': '10.1093/bioinformatics/bty560', 'volume': '34', 'author': 'S Chen', 'year': '2018', 'unstructured': 'Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ ' 'preprocessor. Bioinformatics. 2018;34:i884–90.', 'journal-title': 'Bioinformatics'}, { 'key': '1360_CR39', 'doi-asserted-by': 'publisher', 'first-page': '1754', 'DOI': '10.1093/bioinformatics/btp324', 'volume': '25', 'author': 'H Li', 'year': '2009', 'unstructured': 'Li H, Durbin R. 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SARS-CoV-2 Pandemic Tracing in Italy Highlights Lineages ' 'with Mutational Burden in Growing Subsets. Int J Mol Sci. 2022;23:4155.', 'DOI': '10.3390/ijms23084155'}, { 'key': '1360_CR72', 'doi-asserted-by': 'publisher', 'first-page': '1397', 'DOI': '10.1056/NEJMoa2118542', 'volume': '386', 'author': 'J Hammond', 'year': '2022', 'unstructured': 'Hammond J, Leister-Tebbe H, Gardner A, Abreu P, Bao W, Wisemandle W, ' 'Baniecki M, Hendrick VM, Damle B, Simon-Campos A, et al. Oral ' 'Nirmatrelvir for High-Risk, Nonhospitalized Adults with Covid-19. N Engl ' 'J Med. 2022;386:1397–408.', 'journal-title': 'N Engl J Med'}, { 'key': '1360_CR73', 'doi-asserted-by': 'publisher', 'first-page': 'e2317851121', 'DOI': '10.1073/pnas.2317851121', 'volume': '121', 'author': 'S Delgado', 'year': '2024', 'unstructured': 'Delgado S, Somovilla P, Ferrer-Orta C, Martinez-Gonzalez B, ' 'Vazquez-Monteagudo S, Munoz-Flores J, Soria ME, Garcia-Crespo C, de ' 'Avila AI, Duran-Pastor A, et al. Incipient functional SARS-CoV-2 ' 'diversification identified through neural network haplotype maps. Proc ' 'Natl Acad Sci U S A. 2024;121:e2317851121.', 'journal-title': 'Proc Natl Acad Sci U S A'}, { 'key': '1360_CR74', 'doi-asserted-by': 'publisher', 'first-page': '3235', 'DOI': '10.1038/s41467-023-38867-x', 'volume': '14', 'author': 'AS Gonzalez-Reiche', 'year': '2023', 'unstructured': 'Gonzalez-Reiche AS, Alshammary H, Schaefer S, Patel G, Polanco J, ' 'Carreno JM, Amoako AA, Rooker A, Cognigni C, Floda D, et al. Sequential ' 'intrahost evolution and onward transmission of SARS-CoV-2 variants. Nat ' 'Commun. 2023;14:3235.', 'journal-title': 'Nat Commun'}, { 'key': '1360_CR75', 'doi-asserted-by': 'crossref', 'unstructured': 'Klinakis A, Cournia Z, Rampias T. N-terminal domain mutations of the ' 'spike protein are structurally implicated in epitope recognition in ' 'emerging SARS-CoV-2 strains. Comput Struct Biotechnol J. 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' '2022;12:5856.', 'journal-title': 'Sci Rep'}, { 'key': '1360_CR84', 'doi-asserted-by': 'publisher', 'first-page': '238', 'DOI': '10.1186/s13059-020-02148-3', 'volume': '21', 'author': 'X Dong', 'year': '2020', 'unstructured': 'Dong X, Munoz-Basagoiti J, Rickett NY, Pollakis G, Paxton WA, Gunther S, ' 'Kerber R, Ng LFP, Elmore MJ, Magassouba N, et al. Variation around the ' 'dominant viral genome sequence contributes to viral load and outcome in ' 'patients with Ebola virus disease. Genome Biol. 2020;21:238.', 'journal-title': 'Genome Biol'}, { 'key': '1360_CR85', 'unstructured': 'Goldswain H, Penrice-Randal R, Donovan-Banfield I, Duffy CW, Dong X, ' 'Randle N, Ryan Y, Rzeszutek AM, Pilgrim J, Keyser E, et al. Longitudinal ' 'sequencing of SARS-CoV-2 in immunocompetent individuals raw sequence ' 'reads. Sequence Read Archive. 2024. ' 'https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1012698.'}], 'container-title': 'Genome Medicine', 'original-title': [], 'language': 'en', 'link': [ { 'URL': 'https://link.springer.com/content/pdf/10.1186/s13073-024-01360-1.pdf', 'content-type': 'application/pdf', 'content-version': 'vor', 'intended-application': 'text-mining'}, { 'URL': 'https://link.springer.com/article/10.1186/s13073-024-01360-1/fulltext.html', 'content-type': 'text/html', 'content-version': 'vor', 'intended-application': 'text-mining'}, { 'URL': 'https://link.springer.com/content/pdf/10.1186/s13073-024-01360-1.pdf', 'content-type': 'application/pdf', 'content-version': 'vor', 'intended-application': 'similarity-checking'}], 'deposited': { 'date-parts': [[2024, 7, 16]], 'date-time': '2024-07-16T11:10:35Z', 'timestamp': 1721128235000}, 'score': 1, 'resource': { 'primary': { 'URL': 'https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-024-01360-1'}}, 'subtitle': [], 'short-title': [], 'issued': {'date-parts': [[2024, 7, 16]]}, 'references-count': 85, 'journal-issue': {'issue': '1', 'published-online': {'date-parts': [[2024, 12]]}}, 'alternative-id': ['1360'], 'URL': 'http://dx.doi.org/10.1186/s13073-024-01360-1', 'relation': {}, 'ISSN': ['1756-994X'], 'subject': [], 'container-title-short': 'Genome Med', 'published': {'date-parts': [[2024, 7, 16]]}, 'assertion': [ { 'value': '23 September 2023', 'order': 1, 'name': 'received', 'label': 'Received', 'group': {'name': 'ArticleHistory', 'label': 'Article History'}}, { 'value': '4 July 2024', 'order': 2, 'name': 'accepted', 'label': 'Accepted', 'group': {'name': 'ArticleHistory', 'label': 'Article History'}}, { 'value': '16 July 2024', 'order': 3, 'name': 'first_online', 'label': 'First Online', 'group': {'name': 'ArticleHistory', 'label': 'Article History'}}, {'order': 1, 'name': 'Ethics', 'group': {'name': 'EthicsHeading', 'label': 'Declarations'}}, { 'value': 'During the early phase of the COVID-19 pandemic emergency public health and ' 'workforce protection measures were in place, so health surveillance was ' 'undertaken to prevent and manage transmission risk and morbidity. As part of ' 'these health surveillance measures, subjects consented to routine ' 'nasopharyngeal swab COVID-19 analysis and regular self-report of symptoms and ' 'signs such that disease outbreak could be prevented or controlled. In the UK, ' 'such public health surveillance measures do not require Research Ethics ' 'Committee review (UK Health Research Agency Guidance\xa0' '(hra-decisiontools.org.uk)). The Senior Medical Advisor is the sample database ' 'owner; all samples and clinical data were fully anonymised to the research ' 'team. All samples and data were GDPR compliant and the study conformed to the ' 'principles defined in the Declaration of Helsinki as adopted at the 64th WMA ' 'General Assembly at Fortaleza, Brazil in October 2013.', 'order': 2, 'name': 'Ethics', 'group': {'name': 'EthicsHeading', 'label': 'Ethics approval and consent to participate'}}, { 'value': 'Not applicable.', 'order': 3, 'name': 'Ethics', 'group': {'name': 'EthicsHeading', 'label': 'Consent for publication'}}, { 'value': 'The authors declare that they have no competing interests.', 'order': 4, 'name': 'Ethics', 'group': {'name': 'EthicsHeading', 'label': 'Competing interests'}}], 'article-number': '89'}