Correspondence
1 Spinelli MA, Glidden DV, Gennatas ED, et al. or definite HAI (as previously regularly thereafter, cohorting of
Importance of non-pharmaceutical
interventions in lowering the viral inoculum to
defined1), and 465 infected health- patients to green, amber, and red
reduce susceptibility to infection by SARS-CoV-2 care workers (HCWs) were identified wards, and a comprehensive staff
and potentially disease severity. Lancet Infect Dis via the staff screening programme.2 screening programme. Continued
2021; published online Feb 22. https://doi.
org/10.1016/s1473-3099(20)30982-8. Nanopore sequencing was attempted hospital-based transmission despite
2 Bielecki M, Züst R, Siegrist D, et al. Social for 513 (44%) of 1178 patients, these efforts emphasises how
distancing alters the clinical course of
COVID-19 in young adults: a comparative
prioritising those with hospital- challenging it is to limit SARS-CoV-2
cohort study. Clin Infect Dis 2021; 72: 598–603. onset infections, and 324 (70%) of transmission in hospitals with
3 Marks M, Millat-Martinez P, Ouchi D, et al. 465 HCWs; 252 (21%) of 1178 patients limited side-room capacity, given
Transmission of COVID-19 in 282 clusters in
Catalonia, Spain: a cohort study. Lancet Infect Dis and 317 (68%) of 465 HCWs had the high infectivity of SARS-CoV-2
2021; published online Feb 2. https://doi. SARS-CoV-2 genomes available after and potential for asymptomatic
org/10.1016/S1473-3099(20)30985-3.
quality control filtering (as previously transmission. Genomic data were
4 Munster VJ, Feldmann F, Williamson BN, et al.
Respiratory disease in rhesus macaques described 1). Patient coverage was presented at seven of 11 clinical HAI
inoculated with SARS-CoV-2. Nature 2020; lower than in our previous study1 review meetings and at infection-
585: 268–72.
and for HCWs, reflecting different control meetings, informing decision-
diagnostic testing methods and making. Staff vaccinations began in
limitations on sequencing capacity. January, 2021, and have already had
Applying prospective The frequency of the B.1.1.7 a substantial impact on reducing
PANGO-lineage3 increased from 8% COVID-19 incidence.4
Published Online
genomic surveillance to (nine of 109) in November, 2020, to Our experience from the first and
May 10, 2021
https://doi.org/10.1016/
support investigation of 83% (257 of 311) in January, 2021. second epidemic waves of COVID-19
S1473-3099(21)00251-6 hospital-onset As in the first wave, outbreaks of at CUH identified several challenges
hospital-onset COVID-19 occurred to applying prospective genomic
COVID-19 on wards intended for patients surveillance to infection control. First,
without COVID-19, termed green close and efficient working between
Here, we provide an update on our wards. Where genomics were clinical, infection-control, sequencing,
previous Article,1 which described available, cases on these wards were and bioinformatic-analysis teams
the use of rapid SARS-CoV-2 often phylogenetically clustered is crucial. Second, changes in
genome sequencing to investigate (virus genomes with zero to one SARS-CoV-2 diagnostic methods
hospital-acquired infections (HAIs) at single nucleotide polymorphism resulted in technical difficulties in
Cambridge University Hospitals NHS differences), consistent with ward- obtaining sufficient good-quality
Foundation Trust (CUH), Cambridge, based transmission.1 This transmission genetic material for sequencing.
UK. CUH experienced a substantial occurred despite substantial Third, the speed from sampling to
second wave of COVID-19 (figure). efforts to reduce HAIs, including sequencing to analysis is crucial; for
Between Nov 2, 2020, and Feb 7, 2021, universal surgical mask wearing by maximum impact, genomic data
162 (14%) of 1178 patients with staff, SARS-CoV-2 screening of all should be available to inform real-time
COVID-19 at CUH had a suspected patients at hospital admission and decision-making. Finally, sustained
funding and human resource capacity
300 Classification are essential for consistent service
Community onset, community associated delivery. Nevertheless, we have shown
250 Community onset, health-care associated
Hospital acquired, indeterminate that introducing rapid genomic
200
sequencing and data analysis into
Case number
Hospital acquired, suspected
Hospital acquired, definite
150
Health-care worker
hospital outbreak investigations
100 Other is both feasible and beneficial; the
challenge is to translate this from
50
an emergency response into routine
0
clinical practice.
v2
v9
c7
11
18
25
b1
c2
v2
v3
c1
v1
c2
Jan
CJRI, CJ, and DDA report funding to their institution
De
Jan
No
Fe
Jan
No
Jan
De
De
No
De
No
No
from MRC. MPW reports grants from Wellcome.
Week commencing
SJP reports receiving consulting fees for
participating on the Pfizer Coronavirus External
Figure: Hospital-acquired SARS-CoV-2 infections in Cambridge University Hospitals during the Advisory Board and honoraria from SVB Leerink.
second wave IG reports grants from Wellcome and MRC.
Epidemic curve showing weekly case numbers for new diagnoses of COVID-19 at Cambridge University MET reports grants from Academy of Medical
Hospitals (positive SARS-CoV-2 PCR tests) from Nov 2, 2020, to Feb 7, 2021, coloured by infection Sciences and The Health Foundation, non-financial
See Online for appendix classification (appendix).
916 www.thelancet.com/infection Vol 21 July 2021
Correspondence
support from the NIHR Cambridge Biomedical †Contributed equally 1 Meredith LW, Hamilton WL, Warne B, et al. Rapid
Research Centre, book royalties from Oxford implementation of SARS-CoV-2 sequencing to
‡Members listed in the appendix investigate cases of health-care associated
University Press, and honoraria from Wellcome
Department of Medicine (WLH, TF, BW, BB, MPW, COVID-19: a prospective genomic surveillance
Sanger Institute and University of Cambridge.
study. Lancet Infect Dis 2020; 20: 1263–71.
All other authors declare no competing interests. SJP, MET), Division of Virology, Department of
Pathology (AJ, IG), and Medical Research Council 2 Rivett L, Sridhar S, Sparkes D, et al. Screening of
*William L Hamilton†, Tom Fieldman†, Biostatistics Unit (CJRI, CJ, DDA), University of
healthcare workers for SARS-CoV-2 highlights
the role of asymptomatic carriage in COVID-19
Aminu Jahun†, Ben Warne, Cambridge, Cambridge CB2 0QQ, UK; Cambridge transmission. elife 2020; 9: 1–20.
Christopher J R Illingworth, University Hospitals National Health Service
3 Rambaut A, Holmes EC, O’Toole Á, et al.
Foundation Trust, Cambridge, UK (WLH, TF, BW, EM,
Chris Jackson, Beth Blane, MPW, TG, MET); Cambridge Institute of Therapeutic
A dynamic nomenclature proposal for
SARS-CoV-2 lineages to assist genomic
Elinor Moore, Michael P Weekes, Immunology and Infectious Disease, Jeffrey Cheah epidemiology. Nat Microbiol 2020; 5: 1403–07.
Sharon J Peacock, Daniela De Angelis, Biomedical Centre, Cambridge, UK (MPW); National 4 Jones NK, Rivett L, Seaman S, et al.
Ian Goodfellow, Theodore Gouliouris, Infection Service, Public Health England, London, Single-dose BNT162b2 vaccine protects
UK (SJP, DDA); Clinical Microbiology and Public against asymptomatic SARS-CoV-2 infection.
M Estée Török, on behalf of the Health Laboratory, Public Health England, eLife 2021; published online April 8.
Cambridge COVID-19 group‡ Cambridge, UK (TG) https://doi.org/10.7554/elife.68808.
[email protected]
www.thelancet.com/infection Vol 21 July 2021 917
