Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples
Open accessPublished version of a preprint
Abstract
Genome sequencing has become a powerful tool for studying emerging infectious diseases; however, genome sequencing directly from clinical samples (i.e., without isolation and culture) remains challenging for viruses such as Zika, for which metagenomic sequencing methods may generate insufficient numbers of viral reads. Here we present a protocol for generating coding-sequence-complete genomes, comprising an online primer design tool, a novel multiplex PCR enrichment protocol, optimized library preparation methods for the portable MinION sequencer (Oxford Nanopore Technologies) and the Illumina range of instruments, and a bioinformatics pipeline for generating consensus sequences. The MinION protocol does not require an Internet connection for analysis, making it suitable for field applications with limited connectivity. Our method relies on multiplex PCR for targeted enrichment of viral genomes from samples containing as few as 50 genome copies per reaction. Viral consensus sequences can be achieved in 1-2 d by starting with clinical samples and following a simple laboratory workflow. This method has been successfully used by several groups studying Zika virus evolution and is facilitating an understanding of the spread of the virus in the Americas. The protocol can be used to sequence other viral genomes using the online Primal Scheme primer designer software. It is suitable for sequencing either RNA or DNA viruses in the field during outbreaks or as an inexpensive, convenient method for use in the lab.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Primers tiled across a genome can enable PCR amplification and amplicon NGS to recover viral genomes directly from clinical samples.
“Another example of a targeted NGS approach is the design of primers tiled across the genome to facilitate PCR amplification and amplicon NGS for recovery of viral genomes directly from clinical samples43.”
From Clinical metagenomics (2019) · cites this paper as [43]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Trimmomatic: a flexible trimmer for Illumina sequence data
Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548 · see citing works
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M. V., Kulikov, A. S., Lesin, V. M., Nikolenko, S., Pham, S., Prjibelski, A. D., et al. (2012) · Journal of Computational Biology · doi:10.1089/cmb.2012.0021 · Cited by 25,691 · see citing works
Robinson, J. T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E. S., Getz, G., & Mesirov, J. P. (2011) · Nature Biotechnology · doi:10.1038/nbt.1754 · Cited by 15,390 · see citing works
Primer3 on the WWW for General Users and for Biologist Programmers
Rozen, S., & Skaletsky, H. (2003) · Humana Press eBooks · doi:10.1385/1-59259-192-2:365 · Cited by 14,952 · see citing works
Sequencing technologies – the next generation
Metzker, M. L. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2626 · Cited by 7,066 · see citing works
Coming of age: ten years of next-generation sequencing technologies
Goodwin, S., McPherson, J. D., & McCombie, W. R. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.49 · Cited by 4,352 · see citing works
Snakemake—a scalable bioinformatics workflow engine
Köster, J., & Rahmann, S. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts480 · Cited by 2,780 · see citing works
Real-time, portable genome sequencing for Ebola surveillance
Quick, J., Loman, N. J., Duraffour, S., Simpson, J. T., Severi, E., Cowley, L. A., Boré, J. A., Koundouno, F. R., Dudas, G., Mikhail, A. F. W., et al. (2016) · Nature · doi:10.1038/nature16996 · Cited by 1,450 · see citing works
Self-citationPerformance comparison of benchtop high-throughput sequencing platforms
Loman, N. J., Misra, R., Dallman, T. J., Constantinidou, C., Gharbia, S. E., Wain, J. R., & Pallen, M. J. (2012) · Nature Biotechnology · doi:10.1038/nbt.2198 · Cited by 1,334 · see citing works
Self-citationTarget-enrichment strategies for next-generation sequencing
Mamanova, L., Coffey, A. J., Scott, C. E., Kozarewa, I., Turner, E. H., Kumar, A., Howard, E. K., Shendure, J., & Turner, D. (2010) · Nature Methods · doi:10.1038/nmeth.1419 · Cited by 1,221 · see citing works
Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak
Gire, S., Goba, A., Andersen, K. G., Sealfon, R. S. G., Park, D. J., Kanneh, L., Jalloh, S. C., Momoh, M., Fullah, M., Dudas, G., et al. (2014) · Science · doi:10.1126/science.1259657 · Cited by 1,218 · see citing works
Self-citationHighly parallel direct RNA sequencing on an array of nanopores
Garalde, D. R., Snell, E. A., Jachimowicz, D., Sipos, B., Lloyd, J. H., Bruce, M., Pantic, N., Admassu, T., James, P. L., Warland, A., et al. (2018) · Nature Methods · doi:10.1038/nmeth.4577 · Cited by 1,094 · see citing works
Kwok, S., Kellogg, D. E., McKinney, N., Spasic, D., Goda, L., Levenson, C., & Sninsky, J. J. (1990) · Nucleic Acids Research · doi:10.1093/nar/18.4.999 · Cited by 1,032 · see citing works
Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing
Wilson, M. R., Naccache, S. N., Samayoa, E., Biagtan, M., Bashir, H., Yu, G., Salamat, S. M., Somasekar, S., Federman, S., Miller, S., et al. (2014) · New England Journal of Medicine · doi:10.1056/nejmoa1401268 · Cited by 977 · see citing works
A New Arenavirus in a Cluster of Fatal Transplant-Associated Diseases
Palacios, G. F., Druce, J. D., Du, L., Tran, T., Birch, C. J., Briese, T., Conlan, S., Quan, P., Hui, J., Marshall, J., et al. (2008) · New England Journal of Medicine · doi:10.1056/nejmoa073785 · Cited by 692 · see citing works
Tablet-next generation sequence assembly visualization.
Milne, I., Bayer, M., Cardle, L., Shaw, P., Stephen, G., Wright, F., & Marshall, D. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp666 · Cited by 666 · see citing works
Establishment and cryptic transmission of Zika virus in Brazil and the Americas
Faria, N. R., Quick, J., Claro, I. M., Thézé, J., de Jesus, J. G., Giovanetti, M., Kraemer, M. U. G., Hill, S. C., Black, A., da Costa, A. C., et al. (2017) · Nature · doi:10.1038/nature22401 · Cited by 616 · see citing works
Self-citationGreninger, A. L., Naccache, S. N., Federman, S., Yu, G., Mbala, P., Bres, V., Stryke, D., Bouquet, J., Somasekar, S., Linnen, J. M., et al. (2015) · Genome Medicine · doi:10.1186/s13073-015-0220-9 · Cited by 558 · see citing works
Virus genomes reveal factors that spread and sustained the Ebola epidemic
Dudas, G., Carvalho, L. M., Bedford, T., Tatem, A. J., Baele, G., Faria, N. R., Park, D. J., Ladner, J. T., Arias, A., Asogun, D., et al. (2017) · Nature · doi:10.1038/nature22040 · Cited by 400 · see citing works
Self-citationZika virus evolution and spread in the Americas
Metsky, H. C., Matranga, C. B., Wohl, S., Schaffner, S. F., Freije, C. A., Winnicki, S. M., West, K. L., Qu, J., Baniecki, M. L., Gladden, A. D., et al. (2017) · Nature · doi:10.1038/nature22402 · Cited by 393 · see citing works
Self-citationClinical and biological insights from viral genome sequencing
Houldcroft, C. J., Beale, M. A., & Breuer, J. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2016.182 · Cited by 360 · see citing works
Genomic epidemiology reveals multiple introductions of Zika virus into the United States
Grubaugh, N. D., Ladner, J. T., Kraemer, M. U. G., Dudas, G., Tan, A. L., Gangavarapu, K., Wiley, M. R., White, S., Thézé, J., Magnani, D. M., et al. (2017) · Nature · doi:10.1038/nature22400 · Cited by 353 · see citing works
Self-citationThe evolution of Ebola virus: Insights from the 2013-2016 epidemic
Holmes, E. C., Dudas, G., Rambaut, A., & Andersen, K. G. (2016) · Nature · doi:10.1038/nature19790 · Cited by 314 · see citing works
Self-citationTemporal and spatial analysis of the 2014–2015 Ebola virus outbreak in West Africa
Carroll, M. W., Matthews, D. A., Hiscox, J. A., Elmore, M. J., Pollakis, G., Rambaut, A., Hewson, R., García-Dorival, I., Boré, J. A., Koundouno, F. R., et al. (2015) · Nature · doi:10.1038/nature14594 · Cited by 306 · see citing works
Self-citationClinical Sequencing Uncovers Origins and Evolution of Lassa Virus
Andersen, K. G., Shapiro, B. J., Matranga, C. B., Sealfon, R. S. G., Lin, A. E., Moses, L., Folarin, O. A., Goba, A., Odia, I., Ehiane, P. E., et al. (2015) · Cell · doi:10.1016/j.cell.2015.07.020 · Cited by 302 · see citing works
Self-citation5′ end cDNA amplification using classic RACE
Scotto–Lavino, E., Du, G., & Frohman, M. A. (2006) · Nature Protocols · doi:10.1038/nprot.2006.480 · Cited by 272 · see citing works
Nakamura, S., Yang, C.-S., Sakon, N., Ueda, M., Tougan, T., Yamashita, A., Goto, N., Takahashi, K., Yasunaga, T., Ikuta, K., et al. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004219 · Cited by 267 · see citing works
1970s and ‘Patient 0’ HIV-1 genomes illuminate early HIV/AIDS history in North America
Worobey, M., Watts, T. D., McKay, R. A., Suchard, M. A., Granade, T. C., Teuwen, D. E., Koblin, B. A., Heneine, W., Lemey, P., & Jaffe, H. W. (2016) · Nature · doi:10.1038/nature19827 · Cited by 221 · see citing works
Genome Analysis Linking Recent European and African Influenza (H5N1) Viruses
Salzberg, S. L., Kingsford, C., Cattoli, G., et al. (2007) · Emerging infectious diseases · doi:10.3201/eid1305.070013 · Cited by 220 · see citing works
Nanopore Sequencing as a Rapidly Deployable Ebola Outbreak Tool
Hoenen, T., Groseth, A., Rosenke, K., Fischer, R. J., Hoenen, A., Judson, S. D., Martellaro, C., Falzarano, D., Marzi, A., Squires, R. B., et al. (2015) · Emerging infectious diseases · doi:10.3201/eid2202.151796 · Cited by 218 · see citing works
Connor, T. R., Loman, N. J., Thompson, S., Smith, A. W., Southgate, J., Poplawski, R., Bull, M. J., Richardson, E. J., Ismail, M. A., Thompson, S. E., et al. (2016) · Microbial Genomics · doi:10.1099/mgen.0.000086 · Cited by 208 · see citing works
Self-citationMobile real-time surveillance of Zika virus in Brazil
Faria, N. R., Sabino, E. C., Nunes, M. R. T., Alcantara, L. C. J., Loman, N. J., & Pybus, O. G. (2016) · Genome Medicine · doi:10.1186/s13073-016-0356-2 · Cited by 195 · see citing works
Self-citationGuerbois, M., Fernández‐Salas, I., Azar, S. R., Danis‐Lozano, R., Alpuche-Aranda, C. M., Leal, G., Malo‐García, I. R., González, E. E. D., Casas‐Martínez, M., Rossi, S. L., et al. (2016) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiw302 · Cited by 186 · see citing works
A guide to the design and use of mismatched and degenerate primers.Preprint
Kwok, S., Chang, S. Y., Sninsky, J. J., & Wang, A. (1994) · Genome Research · doi:10.1101/gr.3.4.s39 · Cited by 154 · see citing works
Kilianski, A., Haas, J., Corriveau, E. J., Liem, A. T., Willis, K. L., Kadavy, D. R., Rosenzweig, C. N., & Minot, S. S. (2015) · GigaScience · doi:10.1186/s13742-015-0051-z · Cited by 152 · see citing works
Matranga, C. B., Andersen, K. G., Winnicki, S., Busby, M., Gladden, A. D., Tewhey, R., Stremlau, M. H., Berlin, A. M., Gire, S., England, E. M., et al. (2014) · Genome biology · doi:10.1186/s13059-014-0519-7 · Cited by 142 · see citing works
Self-citationHighly parallel direct RNA sequencing on an array of nanoporesPreprint
Garalde, D. R., Snell, E. A., Jachimowicz, D., et al. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/068809 · Cited by 134 · see citing works
Thomson, E. C., Ip, C. L. C., Badhan, A., et al. (2016) · Journal of Clinical Microbiology · doi:10.1128/jcm.00330-16 · Cited by 132 · see citing works
Arias, A., Watson, S. J., Asogun, D., Tobin, E. A., Lu, J. Q., Phan, M. V. T., Jah, U., Wadoum, R. E. G., Meredith, L. W., Thorne, L., et al. (2016) · Virus Evolution · doi:10.1093/ve/vew016 · Cited by 124 · see citing works
Self-citationMinION nanopore sequencing of an influenza genome
Wang, J. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00766 · Cited by 111 · see citing works
Real-time digital pathogen surveillance — the time is now
Gardy, J. L., Loman, N. J., & Rambaut, A. (2015) · Genome biology · doi:10.1186/s13059-015-0726-x · Cited by 109 · see citing works
Self-citationNorovirus Whole-Genome Sequencing by SureSelect Target Enrichment: a Robust and Sensitive Method
Brown, J. R., Roy, S., Ruis, C., Romero, E. Y., Shah, D., Williams, R. J., & Breuer, J. (2016) · Journal of Clinical Microbiology · doi:10.1128/jcm.01052-16 · Cited by 85 · see citing works
Carrillo, C., Lu, Z., Borca, M. V., Vagnozzi, A. E., Kutish, G. F., & Rock, D. L. (2007) · Journal of Virology · doi:10.1128/jvi.00930-07 · Cited by 77 · see citing works
A Modified RNA-Seq Approach for Whole Genome Sequencing of RNA Viruses from Faecal and Blood Samples
Batty, E. M., Wong, T. H. N., Trebes, A., Argoud, K., Attar, M., Buck, D., Ip, C. L. C., Golubchik, T., Cule, M., Bowden, R. J., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0066129 · Cited by 63 · see citing works
Yuste, E., López‐Galíndez, C., & Domingo, E. (2000) · Journal of Virology · doi:10.1128/jvi.74.20.9546-9552.2000 · Cited by 54 · see citing works
Hysom, D., Naraghi‐Arani, P., Elsheikh, M. M., Carrillo, A. C., Williams, P. L., & Gardner, S. N. (2012) · PLoS ONE · doi:10.1371/journal.pone.0034560 · Cited by 53 · see citing works
Enrichment by hybridisation of long DNA fragments for Nanopore sequencing
Eckert, S. E., Chan, J. Z.-M., Houniet, D. T., et al. (2016) · Microbial Genomics · doi:10.1099/mgen.0.000087 · Cited by 47 · see citing works
Distinct Zika Virus Lineage in Salvador, Bahia, Brazil
Naccache, S. N., Thézé, J., Sardi, S. I., Somasekar, S., Greninger, A. L., Bandeira, A. C., Campos, G. S., Tauro, L. B., Faria, N. R., Pybus, O. G., et al. (2016) · Emerging infectious diseases · doi:10.3201/eid2210.160663 · Cited by 45 · see citing works
Self-citationKilianski, A., Roth, P. A., Liem, A. T., et al. (2016) · Emerging infectious diseases · doi:10.3201/eid2208.160270 · Cited by 39 · see citing works
Li, K. W., Shrivastava, S., Brownley, A., et al. (2012) · Virology Journal · doi:10.1186/1743-422x-9-261 · Cited by 36 · see citing works
Baylis, S. A., Hanschmann, K.-M. O., Schnierle, B. S., Trösemeier, J., Blümel, J., & Zika Virus Collaborative Study Group (2017) · Transfusion · doi:10.1111/trf.14026 · Cited by 32 · see citing works
Self-citationTrösemeier, J., Musso, D., Blümel, J., et al. (2016) · Genome Announcements · doi:10.1128/genomea.00917-16 · Cited by 22 · see citing works
Misencik, M. J., Grubaugh, N. D., Andreadis, T. G., Ebel, G. D., & Armstrong, P. M. (2016) · Vector-Borne and Zoonotic Diseases · doi:10.1089/vbz.2015.1889 · Cited by 17 · see citing works
Self-citationMultiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes
Gardner, S. N., Jaing, C. J., Elsheikh, M. M., et al. (2014) · Advances in Bioinformatics · doi:10.1155/2014/101894 · Cited by 15 · see citing works
Thomson, E. C., Ip, C. L. C., Badhan, A., et al. (2016) · Journal of Hepatology · doi:10.1016/s0168-8278(16)00666-8 · Cited by 14 · see citing works
Complete Genome Sequence of Zika Virus Isolated from Semen
Atkinson, B., Graham, V., Miles, R. W., et al. (2016) · Genome Announcements · doi:10.1128/genomea.01116-16 · Cited by 14 · see citing works
PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes
Yu, Q., Ryan, E. M., Allen, T. M., et al. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq624 · Cited by 12 · see citing works
First Complete Genome Sequences of Zika Virus Isolated from Febrile Patient Sera in Ecuador
Márquez, S., Montoya, J. C., Pullan, S. T., et al. (2017) · Genome Announcements · doi:10.1128/genomea.01673-16 · Cited by 5 · see citing works
Self-citationA Novel System Control for Quality Control of Diagnostic Tests Based on Next-Generation Sequencing
Chan, M. K. L., Smirnov, A., Mulawadi, F. H., et al. (2016) · The Journal of Applied Laboratory Medicine · doi:10.1373/jalm.2016.020131 · Cited by 4 · see citing works
Brown, J. R., Ruis, C., Tutill, H. J., et al. (2015) · Journal of Clinical Virology · doi:10.1016/j.jcv.2015.07.037 · Cited by 1 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- [41]Brown JR Norovirus whole-genome sequencing by SureSelect target enrichment: a robust and sensitive method J Clin Microbiol 54 2530 2537 2016 27487952 PMC5035417
Cited by
Sorted by citations
Nanopore sequencing and assembly of a human genome with ultra-long reads
Jain, M., Koren, S., Miga, K. H., Quick, J., Rand, A. C., Sasani, T. A., Tyson, J. R., Beggs, A. D., Dilthey, A. T., Fiddes, I. T., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4060 · Cited by 1,892 · see citing works
Self-citationNeuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity
Cantuti-Castelvetri, L., Ojha, R., Pedro, L. D., Djannatian, M., Franz, J., Kuivanen, S., van der Meer, F., Kallio, K., Kaya, T., Anastasina, M., et al. (2020) · Science · doi:10.1126/science.abd2985 · Cited by 1,925 · see citing works
Chiu, C. Y., & Miller, S. A. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0113-7 · Cited by 1,620 · see citing works
Establishment and cryptic transmission of Zika virus in Brazil and the Americas
Faria, N. R., Quick, J., Claro, I. M., Thézé, J., de Jesus, J. G., Giovanetti, M., Kraemer, M. U. G., Hill, S. C., Black, A., da Costa, A. C., et al. (2017) · Nature · doi:10.1038/nature22401 · Cited by 616 · see citing works
Self-citationEvolution and epidemic spread of SARS-CoV-2 in Brazil
Candido, D. S., Claro, I. M., de Jesus, J. G., Souza, W. M., Moreira, F. R. R., Dellicour, S., Mellan, T. A., du Plessis, L., Pereira, R. H. M., Sales, F. C. S., et al. (2020) · Science · doi:10.1126/science.abd2161 · Cited by 573 · see citing works
Self-citationTransmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant
Deng, X., Garcia-Knight, M. A., Khalid, M. M., Servellita, V., Wang, C., Morris, M. K., Sotomayor-González, A., Glasner, D. R., Reyes, K. R., Gliwa, A. S., et al. (2021) · Cell · doi:10.1016/j.cell.2021.04.025 · Cited by 651 · see citing works
Genomic epidemiology reveals multiple introductions of Zika virus into the United States
Grubaugh, N. D., Ladner, J. T., Kraemer, M. U. G., Dudas, G., Tan, A. L., Gangavarapu, K., Wiley, M. R., White, S., Thézé, J., Magnani, D. M., et al. (2017) · Nature · doi:10.1038/nature22400 · Cited by 353 · see citing works
Self-citationOude Munnink, B. B., Nieuwenhuijse, D. F., Stein, M., O’Toole, Á., Haverkate, M., Mollers, M., Kamga, S. K., Schapendonk, C., Pronk, M., Lexmond, P., et al. (2020) · Nature Medicine · doi:10.1038/s41591-020-0997-y · Cited by 306 · see citing works
Tyler, A. D., Mataseje, L., Urfano, C. J., Schmidt, L., Antonation, K. S., Mulvey, M. R., & Corbett, C. R. (2018) · Scientific Reports · doi:10.1038/s41598-018-29334-5 · Cited by 294 · see citing works
Deng, X., Garcia-Knight, M. A., Khalid, M. M., Servellita, V., Wang, C., Morris, M. K., Sotomayor-González, A., Glasner, D. R., Reyes, K. R., Gliwa, A. S., et al. (2021) · doi:10.1101/2021.03.07.21252647 · Cited by 651 · see citing works
Thézé, J., Li, T., du Plessis, L., Bouquet, J., Kraemer, M. U. G., Somasekar, S., Yu, G., de Cesare, M., Balmaseda, A., Kuan, G., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.04.017 · Cited by 106 · see citing works
Self-citationHigh Throughput Sequencing for Detection of Foodborne Pathogens
Sekse, C., Holst-Jensen, A., Dobrindt, U., Johannessen, G. S., Li, W., Spilsberg, B., & Shi, J. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.02029 · Cited by 98 · see citing works
Bovine Respiratory Disease Diagnosis
Pardon, B., & Buczinski, S. (2020) · Veterinary Clinics of North America: Food Animal Practice · doi:10.1016/j.cvfa.2020.03.005 · Cited by 97 · see citing works
A Unique Clade of SARS-CoV-2 Viruses is Associated with Lower Viral Loads in Patient Upper Airways
Lorenzo-Redondo, R., Nam, H. H., Roberts, S. C., Simons, L. M., Jennings, L. J., Qi, C., Achenbach, C. J., Hauser, A. R., Ison, M. G., Hultquist, J. F., et al. (2020) · doi:10.1101/2020.05.19.20107144 · Cited by 111 · see citing works
Peng, J., Liu, J., Mann, S. A., Mitchell, A. M., Laurie, M. T., Sunshine, S., Pilarowski, G., Ayscue, P., Kistler, A., Vanaerschot, M., et al. (2022) · Clinical Infectious Diseases · doi:10.1093/cid/ciab283 · Cited by 41 · see citing works
Coincident rapid expansion of two SARS-CoV-2 lineages with enhanced infectivity in Nigeria
Ozer, E. A., Simons, L. M., Adewumi, O. M., Fowotade, A. A., Omoruyi, E. C., Adeniji, J. A., Dean, T. J., Zayas, J., Bhimalli, P. P., Ash, M. K., et al. (2021) · doi:10.1101/2021.04.09.21255206 · Cited by 34 · see citing works
- Authors
- Quick, J., Grubaugh, N. D., Pullan, S. T., Claro, I. M., Smith, A. D., Gangavarapu, K., Oliveira, G., Robles-Sikisaka, R., Rogers, T. F., Beutler, N. A., Burton, D. R., Lewis-Ximenez, L. L., de Jesus, J. G., Giovanetti, M., Hill, S. C., Black, A., Bedford, T., Carroll, M. W., Nunes, M., Alcantara, L. C., Sabino, E. C., Baylis, S. A., Faria, N. R., Loose, M., Simpson, J. T., Pybus, O. G., Andersen, K. G., & Loman, N. J.
- Affiliations
- University of Birmingham (GB)
- Scripps Research Institute (US)
- Public Health England (GB)
- Universidade de São Paulo (BR)
- University of Rome Tor Vergata (IT)
- University of Oxford (GB)
- University of Washington (US)
- Fred Hutch Cancer Center (US)
- Paul Ehrlich Institut (DE)
- University of Nottingham (GB)
- Ontario Institute for Cancer Research (CA)
- Corresponding author
- Loman, Nicholas J
- ORCID
- Quick, Joshua
- Grubaugh, Nathan D
- Pullan, Steven T
- Claro, Ingra M
- Smith, Andrew D
- Gangavarapu, Karthik
- Oliveira, Glenn
- Rogers, Thomas F
- Beutler, Nathan A
- Burton, Dennis R
- Giovanetti, Marta
- Hill, Sarah C
- Black, Allison
- Bedford, Trevor
- Carroll, Miles W
- Alcantara, Luiz Carlos
- Baylis, Sally A
- Faria, Nuno R
- Loose, Matthew
- Simpson, Jared T
- Pybus, Oliver G
- Andersen, Kristian G
- Loman, Nicholas J
- Venue
- Nature Protocols
- Published
- 2017-05-24
- Volume
- 12
- Issue
- 6
- Pages
- 1261-1276
- ISSN
- 1750-2799 (ISSN-L)
- 1754-2189
- PMC
- PMC5902022
- OpenAlex
- W2616925143
- Cited by
- 1,190
- References
- 61
- Citations by year
- 2026: 95 · 2025: 129 · 2024: 160 · 2023: 150 · 2022: 139 · 2021: 207 · 2020: 158 · 2019: 72 · 2018: 52 · 2017: 26 · 2012: 1
- FWCI
- 79.48
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature Protocols (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- University of Birmingham Research Portal (University of Birmingham) (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Arca - Repositório Institucional da Fiocruz (submittedVersion, other-oa)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion, other-oa)
- Funders
- National Science Foundation (1256082, UL1TR001114)
- United States Agency for International Development (AIDOAAA1400102, PREDICT-2)
- Wellcome Trust (204311, 204311/Z/16/Z)
- Ministério da Saúde
- National Institutes of Health (UL1TR001114, HHSN272201400048C, DGE-1256082, GM111274)
- Medical Research Council (204311/Z/16/Z, MR/M501621/1, ZK/16-078, MR/L015080/1, MC_PC_15100)
- National Institute of General Medical Sciences (U54GM111274, R35GM119774)
- National Institute of Allergy and Infectious Diseases (T32AI007244, HHSN272201400048C)
- National Center for Advancing Translational Sciences
- Topics
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Mosquito-borne diseases and control
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Health Sciences › Medicine › Infectious Diseases › Viral Infections and Outbreaks Research
- Keywords
- Zika virus, multiplex PCR, viral genome sequencing, Oxford Nanopore MinION, Oxford Nanopore sequencing, Illumina sequencing, target enrichment, clinical samples, primer design, consensus sequence, viral evolution, RNA viruses, DNA viruses, outbreak response
- MeSH terms
- DNA Viruses, RNA Viruses, Genome, Viral, Sequence Analysis, DNA, Molecular Epidemiology, Multiplex Polymerase Chain Reaction
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
