Skip to main content Accessibility help

We use cookies to distinguish you from other users and to provide you with a better experience on our websites. Close this message to accept cookies or find out how to manage your cookie settings.

Close cookie message
×
Hostname: page-component-848d4c4894-75dct Total loading time: 0 Render date: 2024-05-14T09:23:20.330Z Has data issue: false hasContentIssue false

Chapter 9 - Importance of Timely Sequencing, Tracking, and Surveillance of Emergent Variants

Published online by Cambridge University Press:  06 January 2024

By
Jessica Lin ,
Morgan Greenleaf ,
Yang Lu ,
Leda Bassit ,
Cassandra Wesselman  and
Anne Piantadosi
Edited by
Steven C. Schachter  and
Wade E. Bolton
Steven C. Schachter
Affiliation:
Harvard Medical School
Wade E. Bolton
Affiliation:
VentureWell/Rapid Acceleration of Diagnostics (RADx)
Get access

Summary

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution has given rise to new variants: viruses with different sets of mutations, some of which have increased transmissibility and immune escape. Detecting and monitoring new variants was made possible by intensive, global genomic surveillance efforts, including sequencing over 1.2 million SARS-CoV-2 genomes in the first pandemic year. Crucial to these efforts was the Rapid Acceleration of Diagnostics (RADx®) Variant Task Force, which was established in 2021 to monitor variants and assess the efficacy of RADx technologies against new variants. Major accomplishments of the RADx Variant Task Force include the establishment of the ROSALIND Diagnostic Monitoring system to identify mutations, the creation of an extensive biobank of sequenced samples, laboratory testing of RADx technologies against new variants as they emerged, and epitope mapping to identify mutations likely to affect an assay’s performance. Key lessons learned include (1) the need for very early establishment of pathogen sequencing, analysis, and data sharing; (2) the importance of both in silico and wet laboratory assessment of diagnostic assays; and (3) the benefits of interdisciplinary collaboration of government, academia, and industry.

Keywords

variantssequencinggenomic surveillancemutationCOVID-19 evolutionbioinformatics platformin silico testingwet laboratory testing
Type
Chapter
Information
Accelerating Diagnostics in a Time of Crisis
The Response to COVID-19 and a Roadmap for Future Pandemics
 , pp. 166 - 193
Publisher: Cambridge University Press
Print publication year: 2024

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

WHO, Classification of omicron (B.1.1.529): SARS-CoV-2 variant of concern (November 26, 2021). https://tinyurl.com/yc57rbme (accessed December 19, 2021).Google Scholar
Campbell, F., Archer, B., Laurenson-Schafer, H., et al., Increased transmissibility and global spread of SARS-CoV-2 variants of concern as of June 2021. Euro Surveill, 26, 24 (2021), 2100509.Google Scholar
Nyberg, T., Twohig, K. A., Harris, R. J., et al., Risk of hospital admission for patients with SARS-CoV-2 variant B.1.1.7: cohort analysis. BMJ, 373 (2021), n1412.CrossRefGoogle ScholarPubMed
WHO, Weekly epidemiological update on COVID-19 – 20 July 2021 (2021). https://tinyurl.com/bdd6f82t (accessed August 15, 2022).Google Scholar
Public Health England, Risk assessment for SARS-CoV-2 variant Delta (2021). https://tinyurl.com/yckpacmk (accessed July 25, 2021).Google Scholar
Public Health England, SARS-CoV-2 variants of concern and variants under investigation (2021). https://tinyurl.com/4jbzmt3h (accessed January 4, 2023).Google Scholar
Nyberg, T., Ferguson, N. M., Nash, S. G., et al., Comparative analysis of the risks of hospitalisation and death associated with SARS-CoV-2 Omicron (B.1.1.529) and Delta (B.1.617.2) variants in England: a cohort study. Lancet 399, 10332 (2022), 1303–1312.CrossRefGoogle ScholarPubMed
Amicone, M., Borges, V., Alves, M. J., et al., Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution. Evol Med Public Health, 10, 1 (2022), 142–155.CrossRefGoogle ScholarPubMed
Duchene, S., Featherstone, L., Haritopoulou-Sinanidou, M., et al., Temporal signal and the phylodynamic threshold of SARS-CoV-2. Virus Evol, 6, 2 (2020): veaa061.Google Scholar
WHO, Listings of WHO’s response to COVID-19 (2020). www.who.int/news/item/29-06-2020-covidtimeline/ (accessed June 21, 2022).Google Scholar
Cohen, J., Chinese researchers reveal draft genome of virus implicated in Wuhan pneumonia outbreak (January 11, 2020). https://tinyurl.com/4sjfhy76 (accessed June 21, 2022).Google Scholar
Holmes, E., Novel 2019 coronavirus genome – SARS-CoV-2 coronavirus (2020). https://virological.org/t/novel-2019-coronavirus-genome/319 (accessed June 21, 2022).Google Scholar
Paden, C. R., Tao, Y., Queen, K., et al., Rapid, sensitive, full-genome sequencing of severe acute respiratory syndrome coronavirus 2. Emerg Infect Dis, 26, 10 (2020), 2401–2405.Google Scholar
Wu, F., Zhao, S., Yu, B., et al., A new coronavirus associated with human respiratory disease in China. Nature, 579, 7798 (2020): 265–269.Google Scholar
Hadfield, J., Megill, C., Bell, S. M., et al., Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, 34, 23 (2018): 4121–4123.Google Scholar
Benson, D. A., Cavanaugh, M., Clark, K., et al., GenBank. Nucleic Acids Res, 41, D1 (2013), D36–42.CrossRefGoogle ScholarPubMed
NCBI, GenBank overview. www.ncbi.nlm.nih.gov/genbank/ (accessed July 6, 2022).Google Scholar
NCBI, NCBI SARS-CoV-2 resources. www.ncbi.nlm.nih.gov/sars-cov-2/ (accessed September 12, 2022).Google Scholar
Shu, Y. and McCauley, J., GISAID: Global initiative on sharing all influenza data – from vision to reality. Euro Surveill, 22, 13 (2017), 30494.Google Scholar
COG-UK, History of COG-UK (2021). www.cogconsortium.uk/about/about-us/history-of-cog-uk/ (accessed July 5, 2022).Google Scholar
UK Health Security Agency, UK completes over 2 million SARS-CoV-2 whole genome sequences (February 10, 2022). https://tinyurl.com/yky7u7u9 (accessed July 7, 2022).Google Scholar
Maxmen, A., One million coronavirus sequences: popular genome site hits mega milestone. Nature, 593, 7857 (2021), 21.Google Scholar
CDC, CDC launches national viral genomics consortium to better map SARS-CoV-2 transmission (May 1, 2020). https://tinyurl.com/yxpj93vw (accessed July 7, 2022).Google Scholar
CDC, SPHERES (April 9, 2021). www.cdc.gov/coronavirus/2019-ncov/variants/spheres.html (accessed June 21, 2023).Google Scholar
CDC, COVID Data Tracker (2020). https://covid.cdc.gov/covid-data-tracker (accessed September 12, 2022).Google Scholar
Msomi, N., Mlisana, K., and de Oliveira, T., A genomics network established to respond rapidly to public health threats in South Africa. Lancet Microbe, 1, 6 (2020), e229–230.Google Scholar
Leite, J. A., Vicari, A., Perez, E., et al., Implementation of a COVID-19 Genomic Surveillance Regional Network for Latin America and Caribbean region. PloS One, 17, 3 (2022): e0252526.CrossRefGoogle Scholar
Pan American Health Organization, COVID-19 Genomic Surveillance Regional Network (2022). https://tinyurl.com/yc8akdnr (accessed July 7, 2022).Google Scholar
Elbe, S. and Buckland-Merrett, G., Data, disease and diplomacy: GISAID’s innovative contribution to global health. Glob Chall, 1, 1 (2017), 33–46.Google Scholar
Gangavarapu, K., Latif, A. A., Mullen, J. L., et al., Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations. medRxiv (2022). https://doi.org/10.1101/2022.01.27.22269965 (accessed September 12, 2022).CrossRefGoogle Scholar
van Dorp, L., Acman, M., Richard, D., et al., Emergence of genomic diversity and recurrent mutations in SARS-CoV-2. Infect Genet Evol, 83 (2020), 104351.CrossRefGoogle ScholarPubMed
Pybus, O., Rambaut, A., du Plessis, L., et al., Preliminary analysis of SARS-CoV-2 importation & establishment of UK transmission lineages (2020). https://tinyurl.com/4fhex3vn (accessed June 6, 2022).Google Scholar
Arons, M. M., Hatfield, K. M., Reddy, S. C., et al., Presymptomatic SARS-CoV-2 infections and transmission in a skilled nursing facility. N Engl J Med, 382, 22 (2020), 2081–2090.CrossRefGoogle Scholar
Müller, N. F., Wagner, C., Frazar, C. D., et al., Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State (2021). https://github.com/blab/ncov-wa-d614g (accessed July 1, 2022).Google Scholar
Candido, D. S., Claro, I. M., de Jesus, J. G., et al., Evolution and epidemic spread of SARS-CoV-2 in Brazil. Science, 369, 6508 (2020), 1255–1260.CrossRefGoogle ScholarPubMed
Korber, B., Fischer, W. M., Gnanakaran, S., et al., Tracking changes in SARS-CoV-2 spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell, 182, 4 (2020): 812–827.Google Scholar
Hodcroft, E. B., Zuber, M., Nadeau, S., et al., Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020. medRxiv (2021) https://doi.org/10.1101/2020.10.25.20219063.CrossRefGoogle Scholar
Volz, E., Hill, V., McCrone, J. T., et al., Evaluating the effects of SARS-CoV-2 spike mutation D614G on transmissibility and pathogenicity. Cell, 184, 1 (2021), 64–75.CrossRefGoogle ScholarPubMed
Zhang, L., Jackson, C. B., Mou, H., et al., SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. Nat Commun, 11, 1 (2020), 6013.CrossRefGoogle ScholarPubMed
Davies, N. G., Abbott, S., Barnard, R. C., et al., Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science, 372, 6538 (2021): eabg3055.CrossRefGoogle ScholarPubMed
Supasa, P., Zhou, D., Dejnirattisai, W., et al., Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera. Cell, 184, 8 (2021), 2201–2211.CrossRefGoogle ScholarPubMed
Wibmer, C. K., Ayres, F., Hermanus, T., et al., SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma. Nat Med, 27, 4 (2021), 622–625.CrossRefGoogle ScholarPubMed
Li, Q., Nie, J., Wu, J., et al., SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape. Cell, 184, 9 (2021), 2362–2371.CrossRefGoogle ScholarPubMed
Wang, P., Casner, R. G., Nair, M. S., et al., Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization. Cell Host Microbe, 29, 5 (2021), 747–751.Google Scholar
Planas, D., Bruel, T., Grzelak, L., et al., Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies. Nat Med, 27, 5 (2021), 917–924.CrossRefGoogle ScholarPubMed
Collier, D. A., De Marco, A., Ferreira, I. A. T. M., et al., Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. Nature, 593, 7857 (2021), 136–141.Google Scholar
FDA, Tests expected to fail to detect the SARS-CoV-2 omicron variant and sub-variants (2022). https://tinyurl.com/mrya77nm (accessed January 4, 2023).Google Scholar
Washington, N. L., White, S., Barrett, K. M. S., et al., S gene dropout patterns in SARS-CoV-2 tests suggest spread of the H69del/V70del mutation in the US. medRxiv (2020). https://doi.org/10.1101/2020.12.24.20248814 (accessed July 19, 2022).Google Scholar
Wollschläger, P., Todt, D., Gerlitz, N., et al., SARS-CoV-2 N gene dropout and N gene Ct value shift as indicator for the presence of B.1.1.7 lineage in a commercial multiplex PCR assay. Clin Microbiol Infect, 27, 9 (2021), 1353.e1–1353.e5.Google Scholar
Earnest, R., Uddin, R., Matluk, N., et al., Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA. Cell Rep Med, 3, 4 (2022), 100583.CrossRefGoogle ScholarPubMed
Sheikh, A., McMenamin, J., Taylor, B., and Robertson, C., SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness. Lancet, 397, 10293 (2021), 2461–2462.Google Scholar
Ong, S. W. X., Chiew, C. J., Ang, L. W., 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.1.1.7 (Alpha), B.1.351 (Beta), and B.1.617.2 (Delta). Clin Infect Dis, 75, 1 (2022), e1128–1136.Google Scholar
Jung, C., Kmiec, D., Koepke, L., et al., Omicron: what makes the latest SARS-CoV-2 variant of concern so concerning? J Virol, 96, 6 (2022), e02077–21.CrossRefGoogle ScholarPubMed
Hu, J., Peng, P., Cao, X., et al., Increased immune escape of the new SARS-CoV-2 variant of concern Omicron. Cell Mol Immunol, 19, 2 (2022): 293–295.CrossRefGoogle ScholarPubMed
Hui, K. P. Y., Ho, J. C. W., Cheung, M., et al., SARS-CoV-2 Omicron variant replication in human bronchus and lung ex vivo. Nature, 603, 7902 (2022), 715–720.Google Scholar
WHO, Severity of disease associated with Omicron variant as compared with Delta variant in hospitalized patients with suspected or confirmed SARS-CoV-2 infection (June 7, 2022). www.who.int/publications-detail-redirect/9789240051829 (accessed July 21, 2022).Google Scholar
Abdullah, F., Myers, J., Basu, D., et al., Decreased severity of disease during the first global Omicron variant covid-19 outbreak in a large hospital in Tshwane, South Africa. Int J Infect Dis, 116 (2022), 38–42.CrossRefGoogle Scholar
Liu, L., Iketani, S., Guo, Y., et al., Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2. Nature, 602, 7898 (2022), 676–681.Google Scholar
Planas, D., Saunders, N., Maes, P., et al., Considerable escape of SARS-CoV-2 Omicron to antibody neutralization. Nature, 602, 7898 (2022), 671–675.Google Scholar
Pulliam, J. R. C., van Schalkwyk, C., Govender, N., et al., Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa. Science, 376, 6593 (2022): eabn4947.Google Scholar
Marks, P., Coronavirus (COVID-19) update: FDA recommends inclusion of omicron BA.4/5 component for COVID-19 vaccine booster doses, FDA (June 30, 2022). https://tinyurl.com/2p7tnf7f (accessed July 21, 2022).Google Scholar
Pfizer, Pfizer and BioNTech announce omicron-adapted COVID-19 vaccine candidates demonstrate high immune response against omicron (June 25, 2022). https://tinyurl.com/muc8ftjp (accessed July 21, 2022).Google Scholar
Konings, F., Perkins, M. D., Kuhn, J. H., et al., SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse. Nat Microbiol, 6, 7 (2021), 821–823.CrossRefGoogle ScholarPubMed
GISAID, Clade and lineage nomenclature aids in genomic epidemiology studies of active hCoV-19 viruses (March 2, 2021). https://tinyurl.com/yhya9y3x (accessed June 28, 2022).Google Scholar
Hodcroft, E. B., Hadfield, J., Neher, R. A., and Bedford, T., Year-letter genetic clade naming for SARS-CoV-2 on Nextstrain.org (June 2, 2020). https://tinyurl.com/cnmws8f5 (accessed June 28, 2022).Google Scholar
Bedford, T., Hodcroft, E. B., and Neher, R. A., Updated Nextstrain SARS-CoV-2 clade naming strategy (January 6, 2021). https://tinyurl.com/53aeyjsu (accessed June 28, 2022).Google Scholar
Roemer, C., Hodcroft, E. B., Neher, R. A., and Bedford, T., SARS-CoV-2 clade naming strategy for 2022 (April 29, 2022). https://tinyurl.com/4bdkftz8 (accessed July 11, 2022).Google Scholar
Pango Network, What are Pango lineages? (2022). https://tinyurl.com/ycytjtbv (accessed June 28, 2022).Google Scholar
Rambaut, A., Holmes, E. C., O’Toole, Á, et al., A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol, 5, 11 (2020), 1403–1407.CrossRefGoogle ScholarPubMed
WHO, WHO announces simple, easy-to-say labels for SARS-CoV-2 variants of interest and concern (May 31, 2021). https://tinyurl.com/y2umf75f (accessed June 28, 2022).Google Scholar
WHO, COVID-19 weekly epidemiological update (February 25, 2021). https://tinyurl.com/55vm2fnk (accessed July 12, 2022).Google Scholar
WHO, Tracking SARS-CoV-2 variants (2021). www.who.int/en/activities/tracking-SARS-CoV-2-variants/ (accessed December 27, 2021).Google Scholar
CDC, SARS-CoV-2 variant classifications and definitions (2022). https://tinyurl.com/5n6srche (accessed June 6, 2022).Google Scholar
FDA, Policy for evaluating impact of viral mutations on COVID-19 tests (2021). https://tinyurl.com/5atty76z (accessed January 4, 2023).Google Scholar
FDA, SARS-CoV-2 viral mutations: impact on COVID-19 tests (2022). https://tinyurl.com/2upu8w6s (accessed July 25, 2022).Google Scholar
Holland, S. C., Bains, A., Holland, L. A., et al., SARS-CoV-2 Delta variant N gene mutations reduce sensitivity to the TaqPath COVID-19 multiplex molecular diagnostic assay. Viruses, 14, 6 (2022), 1316.Google Scholar
Bourassa, L., Perchetti, G. A., Phung, Q., et al., A SARS-CoV-2 nucleocapsid variant that affects antigen test performance. J Clin Virol, 141 (2021), 104900.Google Scholar
Mahase, E., Covid-19: What do we know about Omicron sublineages? BMJ, 376 (2022), o358.CrossRefGoogle ScholarPubMed
Wise, J., Covid-19: Omicron sub variants driving new wave of infections in UK. BMJ, 377 (2022), o1506.Google Scholar
Wang, Q., Guo, Y., Iketani, S., et al., Antibody evasion by SARS-CoV-2 Omicron subvariants BA.2.12.1, BA.4, & BA.5. Nature, 608, 7923 (2022), 603–608.Google Scholar
Xia, S., Wang, L., Zhu, Y., Lu, L., and Jiang, S., Origin, virological features, immune evasion and intervention of SARS-CoV-2 Omicron sublineages. Signal Transduct Target Ther, 7, 1 (2022), 1–7.Google ScholarPubMed
Cao, Y., Yisimayi, A., Jian, F., et al., BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection. Nature, 608, 7923 (2022), 593–602.Google Scholar
WHO, TAG-VE statement on Omicron sublineages BQ.1 and XBB (October 27, 2022). https://tinyurl.com/wz24x74m (accessed December 8, 2022).Google Scholar
Arora, P., Kempf, A., Nehlmeier, I., et al., Omicron sublineage BQ.1.1 resistance to monoclonal antibodies. Lancet Infect Dis, 23, 1 (2023), 22–23.CrossRefGoogle ScholarPubMed
Planas, D., Bruel, T., Staropoli, I., et al., Resistance of Omicron subvariants BA.2.75.2, BA.4.6 and BQ.1.1 to neutralizing antibodies, bioRxiv (2022). https://doi.org/10.1101/2022.11.17.516888 (accessed December 9, 2022).Google Scholar
Qu, P., Evans, J. P., Faraone, J., et al., Distinct neutralizing antibody escape of SARS-CoV-2 omicron subvariants BQ.1, BQ.1.1, BA.4.6, BF.7 and BA.2.75.2, bioRxiv (2022). https://doi.org/10.1101/2022.10.19.512891 (accessed December 8, 2022).Google Scholar
Zou, J., Kurhade, C., Patel, S., et al., Improved neutralization of Omicron BA.4/5, BA.4.6, BA.2.75.2, BQ.1.1, and XBB.1 with bivalent BA.4/5 vaccine, bioRxiv (2022). https://doi.org/10.1101/2022.11.17.516898 (accessed December 9, 2022).CrossRefGoogle Scholar
Pfizer, Pfizer and BioNTech announce updated clinical data for omicron BA.4/BA.5-adapted bivalent booster demonstrating substantially higher immune response in adults compared to the original COVID-19 vaccine (November 4, 2022). https://tinyurl.com/bdhekpzz (accessed December 9, 2022).Google Scholar
Link-Gelles, R., Effectiveness of bivalent mRNA vaccines in preventing symptomatic SARS-CoV-2 infection – increasing community access to testing program, United States, September–November 2022. MMWR Morb Mortal Wkly Rep, 71, 48 (2022), 1526–1530.CrossRefGoogle ScholarPubMed
Harris, R. S., Improved Pairwise Alignment of Genomic DNA, Thesis (2007). www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf (accessed September 21, 2022).Google Scholar
Obenchain, V., Lawrence, M., Carey, V., et al., VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants. Bioinformatics, 30, 14 (2014), 2076–2078.CrossRefGoogle ScholarPubMed
Lefever, S., Pattyn, F., Hellemans, J., and Vandesompele, J., Single-nucleotide polymorphisms and other mismatches reduce performance of quantitative PCR assays. Clin Chem, 59, 10 (2013), 1470–1480.CrossRefGoogle ScholarPubMed
Yampolsky, L. Y. and Stoltzfus, A., The exchangeability of amino acids in proteins. Genetics, 170, 4 (2005), 1459–1472.Google Scholar
Fraczkiewicz, R. and Braun, W., Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules. J Comput Chem, 19, 3 (1998), 319–333.3.0.CO;2-W>CrossRefGoogle Scholar
Nehl, E. J., Heilman, S. S., Ku, D., et al., The RADx tech test verification core and the ACME POCT in the evaluation of COVID-19 testing devices: a model for progress and change. IEEE Open J Eng Med Biol, 2 (2021), 142–151.CrossRefGoogle Scholar
George, P. E., Stokes, C. L., Bassit, L. C., et al., Covid-19 will not “magically disappear”: why access to widespread testing is paramount. Am J Hematol, 96, 2 (2021), 174–178.Google Scholar
Roback, J. D., Tyburski, E. A., Alter, D., et al., The need for new test verification and regulatory support for innovative diagnostics. Nat Biotechnol, 39, 9 (2021), 1060–1062.Google Scholar
Frediani, J. K., Levy, J. M., Rao, A., et al., Multidisciplinary assessment of the Abbott BinaxNOW SARS-CoV-2 point-of-care antigen test in the context of emerging viral variants and self-administration. Sci Rep, 11, 1 (2021), 14604.Google Scholar
Rao, A., Bassit, L., Lin, J., et al., Assessment of the Abbott BinaxNOW SARS-CoV-2 rapid antigen test against viral variants of concern. iScience, 25, 3 (2022), 103968.CrossRefGoogle ScholarPubMed
Frank, F., Keen, M. M., Rao, A., et al., Deep mutational scanning identifies SARS-CoV-2 Nucleocapsid escape mutations of currently available rapid antigen tests. Cell, 185, 19 (2022), 3603–3616.CrossRefGoogle ScholarPubMed
Choi, B., Choudhary, M. C., Regan, J., et al., Persistence and evolution of SARS-CoV-2 in an immunocompromised host. N Engl J Med, 383, 23 (2020), 2291–2293.Google Scholar
Borges, V., Isidro, J., Cunha, M., et al., Long-term evolution of SARS-CoV-2 in an immunocompromised patient with non-Hodgkin lymphoma. mSphere, 6, 4 (2021), e00244-21.CrossRefGoogle Scholar
Kemp, S. A., Collier, D. A., Datir, R. P., et al., SARS-CoV-2 evolution during treatment of chronic infection. Nature, 592, 7853 (2021), 277–282.CrossRefGoogle ScholarPubMed
Oude Munnink, B. B., Sikkema, R. S., Nieuwenhuijse, D. F., et al., Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans. Science, 371, 6525 (2021), 172–177.CrossRefGoogle ScholarPubMed
Sila, T., Sunghan, J., Laochareonsuk, W., et al., Suspected cat-to-human transmission of SARS-CoV-2, Thailand, July–September 2021. Emerg Infect Dis, 28, 7 (2022), 1485–1488.CrossRefGoogle ScholarPubMed
Martins, M., Boggiatto, P. M., Buckley, A., et al., From deer-to-deer: SARS-CoV-2 is efficiently transmitted and presents broad tissue tropism and replication sites in white-tailed deer. PLoS Pathog, 18, 3 (2022), e1010197.Google Scholar
Kuchipudi, S. V., Surendran-Nair, M., Ruden, R. M., et al., Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer. Proc Natl Acad Sci, 119, 6 (2022), e2121644119.CrossRefGoogle ScholarPubMed
Eguia, R. T., Crawford, K. H. D., Stevens-Ayers, T., et al., A human coronavirus evolves antigenically to escape antibody immunity. PLoS Pathog, 17, 4 (2021), e1009453.Google Scholar
Kistler, K. E. and Bedford, T., Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229e. eLife, 10 (2021), e64509.CrossRefGoogle ScholarPubMed
Petrova, V. N. and Russell, C. A., The evolution of seasonal influenza viruses. Nat Rev Microbiol, 16, 1 (2018), 47–60.CrossRefGoogle ScholarPubMed

Save book to Kindle

To save this book to your Kindle, first ensure coreplatform@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×