August 15, 2022

Healty

Slick Healthy

Viral variant-resolved wastewater surveillance of SARS-CoV-2

  • Nicola, M. et al. The socio-economic implications of the coronavirus pandemic (COVID-19): a review. Int. J. Surg. 78, 185–193 (2020).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Josephson, A., Kilic, T. & Michler, J. D. Socioeconomic impacts of COVID-19 in low-income countries. Nat. Hum. Behav. 5, 557–565 (2021).

    PubMed 
    Article 

    Google Scholar 

  • Harvey, W. T. et al. SARS-CoV-2 variants, spike mutations and immune escape. Nat. Rev. Microbiol. 19, 409–424 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Callaway, E. Heavily mutated coronavirus variant puts scientists on alert. Nature 21, 600 (2021).

    Google Scholar 

  • Truong, T. T. et al. Increased viral variants in children and young adults with impaired humoral immunity and persistent SARS-CoV-2 infection: a consecutive case series. EBioMedicine 67, 103355 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Lucas, C. et al. Impact of circulating SARS-CoV-2 variants on mRNA vaccine-induced immunity. Nature 600, 523–529 (2021).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Chandler, J.C. et al. SARS-CoV-2 exposure in wild white-tailed deer (Odocoileus virginianus). Proc. Natl Acad. Sci. USA 118, e2114828118 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Plante, J. A. et al. The variant gambit: COVID-19’s next move. Cell Host Microbe 29, 508–515 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Gardy, J. L. & Loman, N. J. Towards a genomics-informed, real-time, global pathogen surveillance system. Nat. Rev. Genet. 19, 9–20 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Grubaugh, N. D. et al. Tracking virus outbreaks in the twenty-first century. Nat Microbiol. 4, 10–19 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Smith, G. J. D. et al. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza a epidemic. Nature 459, 1122–1125 (2009).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Inzaule, S. C., Tessema, S. K., Kebede, Y., Ogwell Ouma, A. E. & Nkengasong, J. N. Genomic-informed pathogen surveillance in Africa: opportunities and challenges. Lancet Infect. Dis. 21, e281–e289 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Woolhouse, M. E. J., Rambaut, A. & Kellam, P. Lessons from Ebola: improving infectious disease surveillance to inform outbreak management. Sci. Transl. Med. 7, 307rv5 (2015).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Furuse, Y. Genomic sequencing effort for SARS-CoV-2 by country during the pandemic. Int. J. Infect. Dis. 103, 305–307 (2021).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • The COVID-19 Genomics UK (COG-UK) consortium. An integrated national scale SARS-CoV-2 genomic surveillance network. Lancet Microbe 1, e99–e100 (2020).

    Article 

    Google Scholar 

  • Treibel, T. A. et al. COVID-19: PCR screening of asymptomatic health-care workers at London hospital. Lancet 395, 1608–1610 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Brito, A. F. et al. Global disparities in SARS-CoV-2 genomic surveillance. Preprint at medRxiv https://doi.org/10.1101/2021.08.21.21262393 (2021)..

  • Belman, S., Saha, S. & Beale, M. A. SARS-CoV-2 genomics as a springboard for future disease mitigation in LMICs. Nat. Rev. Microbiol. https://doi.org/10.1038/s41579-021-00664-y (2021).

    Article 
    PubMed Central 

    Google Scholar 

  • Majid, F., Omer, S. B. & Khwaja, A. I. Optimising SARS-CoV-2 pooled testing for low-resource settings. Lancet Microbe 1, e101–e102 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Larsen, D. A., Green, H., Collins, M. B. & Kmush, B. L. Wastewater monitoring, surveillance and epidemiology: a review of terminology for a common understanding. FEMS Microbes 2, xtab011 (2021).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Cavany, S. et al. Inferring SARS-CoV-2 RNA shedding into wastewater relative to the time of infection. Epidemiol Infect. 150, e21 (2022).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Bonanno Ferraro, G. et al. A state-of-the-art scoping review on SARS-CoV-2 in sewage focusing on the potential of wastewater surveillance for the monitoring of the COVID-19 pandemic. Food Environ. Virol. https://doi.org/10.1007/s12560-021-09498-6 (2021).

  • Hassard, F., Lundy, L., Singer, A. C., Grimsley, J. & di Cesare, M. Innovation in wastewater near-source tracking for rapid identification of COVID-19 in schools. Lancet Microbe 2, e4–e5 (2021).

    PubMed 
    Article 

    Google Scholar 

  • la Rosa, G. et al. SARS-CoV-2 has been circulating in northern Italy since December 2019: evidence from environmental monitoring. Sci. Total Environ. 750, 141711 (2021).

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • Martin, J. et al. Tracking SARS-CoV-2 in sewage: evidence of changes in virus variant predominance during COVID-19 pandemic. Viruses 12, 1144 (2020).

    CAS 
    PubMed Central 
    Article 

    Google Scholar 

  • Nemudryi, A. et al. Temporal Detection and Phylogenetic Assessment of SARS-CoV-2 in Municipal Wastewater. Cell Rep. Med. 1, 100098 (2020).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Wurtzer, S. et al. Monitoring the propagation of SARS CoV2 variants by tracking identified mutation in wastewater using specific RT–qPCR. Preprint at medRxiv https://doi.org/10.1101/2021.03.10.21253291 (2021).

  • Peccia, J. et al. Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics. Nat. Biotechnol. 38, 1164–1167 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Agrawal, S., Orschler, L. & Lackner, S. Long-term monitoring of SARS-CoV-2 RNA in wastewater of the Frankfurt metropolitan area in Southern Germany. Sci Rep. 11, 5372 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Daleiden, B. et al. Wastewater surveillance of SARS-CoV-2 in Austria: development, implementation, and operation of the Tyrolean wastewater monitoring program. J. Water Health 20, 314–328 (2022).

    Article 

    Google Scholar 

  • Radu, E. et al. Emergence of SARS-CoV-2 Alpha lineage and its correlation with quantitative wastewater-based epidemiology data. Water Res. 215, 118257 (2022).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Markt, R. et al. Detection and abundance of SARS-CoV-2 in wastewater in Liechtenstein, and the estimation of prevalence and impact of the B.1.1.7 variant. J. Water Health 20, 114–125 (2021).

    Article 

    Google Scholar 

  • Karthikeyan, S. et al. High-throughput wastewater SARS-CoV-2 detection enables forecasting of community infection dynamics in San Diego County. mSystems 6, e00045-21 (2021).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Crits-Christoph, A. et al. Genome sequencing of sewage detects regionally prevalent SARS-CoV-2 variants. mBio 12, 02703-20 (2021).

    Article 

    Google Scholar 

  • Izquierdo-Lara, R. et al. Monitoring SARS-CoV-2 circulation and diversity through community wastewater sequencing, the Netherlands and Belgium. Emerg. Infect. Dis. 27, 1405–1415 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Agrawal, S. et al. A pan-European study of SARS-CoV-2 variants in wastewater 2 under the EU Sewage Sentinel System. Preprint at medRxiv https://doi.org/10.1101/2021.06.11.21258756 (2021).

  • Bar-Or, I. et al. Detection of SARS-CoV-2 variants by genomic analysis of wastewater samples in Israel. Sci. Total Environ. 789, 148002 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Fontenele, S. et al. High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants. Water Res. 205, 117710 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Fuqua, J. L. et al. The rapid assessment of aggregated wastewater samples for genomic surveillance of SARS-CoV-2 on a city-wide scale. Pathogens 10, 1271 (2021).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Jahn, K. et al. Detection of SARS-CoV-2 variants in Switzerland by genomic analysis of wastewater samples. Preprint at medRxiv https://doi.org/10.1101/2021.01.08.21249379 (2021).

  • Pechlivanis, N. et al. Detecting SARS-CoV-2 lineages and mutational load in municipal wastewater and a use-case in the metropolitan area of Thessaloniki, Greece. Sci. Rep. 12, 2659 (2021).

    Article 
    CAS 

    Google Scholar 

  • Smyth, D.S., Trujillo, M., Gregory, D.A. et al. Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. Nat Commun 13, 635 (2022). https://doi.org/10.1038/s41467-022-28246-3

  • la Rosa, G. et al. Rapid screening for SARS-CoV-2 variants of concern in clinical and environmental samples using nested RT-PCR assays targeting key mutations of the spike protein. Water Res. 197, 117104 (2021).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Prado, T. et al. Wastewater-based epidemiology as a useful tool to track SARS-CoV-2 and support public health policies at municipal level in Brazil. Water Res. 191, 116810 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Rimoldi, S. G. et al. Presence and infectivity of SARS-CoV-2 virus in wastewaters and rivers. Sci. Total Environ. 744, 140911 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Agrawal, S., Orschler, L. & Lackner, S. Metatranscriptomic analysis reveals SARS-CoV-2 mutations in wastewater of the Frankfurt metropolitan area in Southern Germany. Microbiol. Resour. Announc. 10, e00280-21 (2021).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Huisman, J. S. et al. Wastewater-based estimation of the effective reproductive number of SARS-CoV-2. Environ. Health Perspect. 130, 057011 (2022).

    PubMed Central 
    Article 

    Google Scholar 

  • Jahn, K. et al. Detection and surveillance of SARS-CoV-2 genomic variants in wastewater. Preprint at medRxiv https://doi.org/10.1101/2021.01.08.21249379 (2021)..

  • O’Toole, Á. et al. Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evol. 7, veab064 (2021).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Özkan, E. et al. High-throughput mutational surveillance of the SARS-CoV-2 spike gene. Preprint at medRxiv https://doi.org/10.1101/2021.07.22.21259587 (2021).

  • Paetzold, J. et al. Impacts of rapid mass vaccination against SARS-CoV2 in an early variant of concern hotspot. Nat. Commun. 13, 612 (2022).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Hasell, J. et al. A cross-country database of COVID-19 testing. Sci. Data 7, 345 (2020).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Progress on household drinking water, sanitation and hygiene 2000-2020: five years into the SDGs. (WHO and UNICEF, 2021).

  • Popa, A. et al. Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2. Sci. Transl. Med. 12, eabe2555 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Elbe, S. & Buckland-Merrett, G. Data, disease and diplomacy: GISAID’s innovative contribution to global health. Global Challenges 1, 33–46 (2017).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Shu, Y. & McCauley, J. GISAID: global initiative on sharing all influenza data—from vision to reality. Eurosurveillance 22, 30494 (2017).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Cragg, J. G. Some statistical models for limited dependent variables with application to the demand for durable goods. Econometrica 39, 829–844 (1971).

    Article 

    Google Scholar 

  • van Poelvoorde, L. A. et al. Strategy and performance evaluation of low-frequency variant calling for SARS-CoV-2 using targeted deep Illumina sequencing. Front. Microbiol. 12, 747458 (2021).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Itokawa, K., Sekizuka, T., Hashino, M., Tanaka, R. & Kuroda, M. Disentangling primer interactions improves SARS-CoV-2 genome sequencing by multiplex tiling PCR. PLoS One 15, e0239403 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Nei, M. & Li, W.-H. Mathematical model for studying genetic variation in terms of restriction endonucleases (molecular evolution/mitochondrial DNA/nucleotide diversity). Genetics 76, 5269–5273 (1979).

    CAS 

    Google Scholar 

  • Been, F. et al. Population normalization with ammonium in wastewater-based epidemiology: application to illicit drug monitoring. Environ. Sci. Technol. 48, 8162–8169 (2014).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Cori, A., Ferguson, N. M., Fraser, C. & Cauchemez, S. A new framework and software to estimate time-varying reproduction numbers during epidemics. Am. J. Epidemiology 178, 1505–1512 (2013).

    Article 

    Google Scholar 

  • Campbell, F. et al. Increased transmissibility and global spread of SARSCoV- 2 variants of concern as at June 2021. Eurosurveillance 26, 1–6 (2021).

    Article 

    Google Scholar 

  • Davies, N. G. et al. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science 372, eabg3055 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Washington, N. L. et al. Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States. Cell 184, 2587–2594.e7 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Ito, K., Piantham, C. & Nishiura, H. Relative instantaneous reproduction number of Omicron SARS-CoV-2 variant with respect to the Delta variant in Denmark. J. Med. Virol. 94, 2265–2268 (2021).

    Article 
    CAS 

    Google Scholar 

  • Baaijens, J. A. et al. Variant abundance estimation for SARS-CoV-2 in 1 wastewater using RNA-Seq quantification 2. Preprint at medRxiv https://doi.org/10.1101/2021.08.31.21262938 (2021).

  • Pipes, L., Chen, Z., Afanaseva, S. & Nielsen, R. Estimating the relative proportions of SARS-CoV-2 strains from 2 wastewater samples. Preprint at medRxiv https://doi.org/10.1101/2022.01.13.22269236 (2021).

  • Sapoval, N. et al. Enhanced Detection of Recently Emerged SARS-CoV-2 Variants of Concern in Wastewater. Preprint at medRxiv https://doi.org/10.1101/2021.09.08.21263279 (2021).

  • Wade, M. J. et al. Understanding and managing uncertainty and variability for wastewater monitoring beyond the pandemic: lessons learned from the United Kingdom national COVID-19 surveillance programmes. J. Hazard. Mater. 424, 127456 (2022).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Karthikeyan, S. et al. Rapid, large-scale wastewater surveillance and automated reporting system enable early detection of nearly 85% of COVID-19 cases on a university campus. mSystems 6, 793–814 (2021).

    Google Scholar 

  • Calderón-Franco, D., Orschler, L., Lackner, S., Agrawal, S. & Weissbrodt, D. G. Monitoring SARS-CoV-2 in sewage: toward sentinels with analytical accuracy. Sci. Total Environ. 804, 150244 (2022).

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • Shrestha, S. et al. Wastewater-based epidemiology for cost-effective mass surveillance of covid-19 in low-and middle-income countries: challenges and opportunities. Water 13, 2897 (2021).

    CAS 
    Article 

    Google Scholar 

  • Hong, P. Y. et al. Estimating the minimum number of SARS-CoV-2 infected cases needed to detect viral RNA in wastewater: to what extent of the outbreak can surveillance of wastewater tell us? Environ. Res. 195, 110748 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Basu, P. et al. Surveillance of SARS-CoV-2 RNA in open-water sewage canals contaminated with untreated wastewater in resource-constrained regions. Access Microbiol. 4, 000318 (2022).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Chan, M. C. W. et al. Seasonal influenza a virus in feces of hospitalized adults. Emerg. Infect. Dis. 17, 2038–2042 (2011).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Pogka, V. et al. Laboratory surveillance of polio and other enteroviruses in high-risk populations and environmental samples. Appl. Environ. Microbiol. 83, e02872-16 (2017).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Wolfe, M. K. et al. Wastewater-based detection of an influenza outbreak. Preprint at medRxiv https://doi.org/10.1101/2022.02.15.22271027 (2022).

  • Lynch, M., Bost, D., Wilson, S., Maruki, T. & Harrison, S. Population-genetic inference from pooled-sequencing data. Genome Biol. Evol. 6, 1210–1218 (2014).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Suratekar, R. et al. High diversity in Delta variant across countries revealed by genome‐wide analysis of SARS‐CoV‐2 beyond the Spike protein. Mol. Syst. Biol. 18, e10673 (2022).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Stern, A. et al. The unique evolutionary dynamics of the SARS-CoV-2 Delta variant-2 sequencing. Preprint at medRxiv https://doi.org/10.1101/2021.08.05.21261642 (2021).

  • Yuan, S. et al. Pathogenicity, transmissibility, and fitness of SARS-CoV-2 Omicron in Syrian hamsters. Science. 0, eabn8939. 10.1126/science.abn8939 (2022).

  • Safford, H. R., Shapiro, K. & Bischel, H. N. Wastewater analysis can be a powerful public health tool—if it’s done sensibly. Proc. Natl Acad. Sci. USA 119, e2119600119 (2022).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Water quality—determination of the chemical oxygen demand index (ST-COD)—small-scale sealed-tube method. DS/ISO 15705:2002(E) (International Standards Organisation, 2002).

  • Water quality—determination of nitrogen—part 1: method using oxidative digestion with peroxodisulfate. ISO 11905-1:1997 (International Standards Organisation, 1997).

  • Water quality—determination of ammonium nitrogen—method by flow analysis (CFA and FIA) and spectrometric detection. ISO 11732:2005. (International Standards Organisation, 2005).

  • Ye, Y., Ellenberg, R. M., Graham, K. E. & Wigginton, K. R. Survivability, partitioning, and recovery of enveloped viruses in untreated municipal wastewater. Environ. Sci. Technol. 50, 5077–5085 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Wu, F. et al. SARS-CoV-2 titers in wastewater are higher than expected from clinically confirmed cases. mSystems 5, e00614-20 (2020).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Bushnell, B., Rood, J. & Singer, E. BBMerge – Accurate paired shotgun read merging via overlap. PLoS One 12, e0185056 (2017).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Grubaugh, N. D. et al. An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar. Genome Biol. 20, 8 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Wilm, A. et al. LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res. 40, 11189–11201 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987–2993 (2011).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6, 80–92 (2012).

    CAS 
    Article 

    Google Scholar 

  • Cingolani, P. et al. Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift. Front. Genet. 3, 35 (2012).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Smithson, M. & Verkuilen, J. A better lemon squeezer? Maximum-likelihood regression with beta-distributed dependent variables. Psychol. Methods 11, 54–71 (2006).

    PubMed 
    Article 

    Google Scholar 

  • Rigby, R. A. & Stasinopoulos, D. M. Generalized additive models for location, scale and shape. J. R. Stat. Soc. C Appl. Stat. 54, 507–554 (2005).

    Article 

    Google Scholar 

  • Barndorff-Nielsen, E. & Jorgensen, B. Some Parametric Models on the Simplex. J.Multivar. Anal. 39, 106–116 (1991).

    Article 

    Google Scholar 

  • Lee, S., Wolberg, G. & Shin, S. Y. Scattered data interpolation with multilevel B-splines. IEEE Trans. Vis. Comput. Graph. 3, 228–244 (1997).

    Article 

    Google Scholar 

  • Thompson, R. N. et al. Improved inference of time-varying reproduction numbers during infectious disease outbreaks. Epidemics 29, 100356 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Hart, W. et al. Inference of the SARS-CoV-2 generation time using UK household data. eLife 11, e70767 (2022).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Hart, W. S. et al. Generation time of the alpha and delta SARS-CoV-2 variants: an epidemiological analysis. Lancet Infect. Dis. 22, 603–610 (2022).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Abbott, S., Sherratt, K., Moritz, G. & Funk, S. Estimation of the test to test distribution as a proxy for generation interval distribution for the Omicron variant in England. Preprint at medRxiv https://doi.org/10.1101/2022.01.08.22268920 (2022).

  • Rousseeuw, P. J. Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J. Comput. Appl. Math. 20, 53–65 (1987).

    Article 

    Google Scholar 

  • Nelson, C. W., Moncla, L. H. & Hughes, A. L. SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data. Bioinformatics 31, 3709–3711 (2015).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Heiler, G. et al. Country-wide mobility changes observed using mobile phone data during COVID-19 pandemic. In 2020 IEEE International Conference on Big Data (Big Data) 3123–3132 (IEEE, 2020).

  • Triska, P., Amman, F., Endler, L. & Bergthaler, A. WAVES (Web-based tool for Analysis and Visualization of Environmental Samples) – a web application for visualization of wastewater pathogen sequencing results. Preprint at medRxiv https://doi.org/10.1101/2022.05.31.22275831 (2022).