Hayward, A

Krutikov, M

Shallcross, L

English

UCL Discovery

C o r r e s p o n d e n c eT h e  n e w  e ngl a nd  j o u r na l  o f  m e dic i n en engl j med nejm.org  1Spread of a Variant SARS-CoV-2 in Long-Term  Care Facilities in EnglandTo the Editor: Severe acute respiratory syn-drome coronavirus 2 (SARS-CoV-2) infections and hospital admissions for coronavirus dis-ease 2019 (Covid-19) increased rapidly in the South East region of England in November and December 2020, despite lockdown mea-sures.1,2 More than half of these infections were associated with a distinct phylogenetic cluster that is estimated to be 40 to 70% more transmissible than previous variants and is driv-ing the growth of infections across England.3 Given the excess deaths seen in long-term care facilities during the pandemic, preventing fur-ther spread of this variant, known as B.1.1.7, to long-term care facilities is a public health priority.We investigated the proportion of SARS-CoV-2 infections caused by the variant in staff and residents of long-term care facilities in England between October 5 and December 17, 2020. Participants were tested for SARS-CoV-2 by reverse-transcriptase–polymerase-chain-reac-tion (RT-PCR) assay of nasopharyngeal swabs collected weekly from staff or monthly from residents.PCR cycle-threshold (Ct) values indicating viral load were obtained for each of three gene targets (S, N, and ORF1ab) (see the Supplemen-tary Appendix, available with the full text of this letter at NEJM.org). The B.1.1.7 variant was identified in samples with S gene target failure on PCR (i.e., only ORF1ab and N were detected). The absence of detectable S gene was a marker of the variant from mid-November 2020 onward.1 The PCR results were linked to demographic data, and the percentages of sam-ples that were positive for one, two, or three gene targets were plotted with corresponding median Ct values according to week, geographic region, and age group.Of 143,994 samples obtained from staff and residents of long-term care facilities through-out England, 4442 (3.1%) were positive for at least one gene target on PCR assay. Overall, the total number and proportion of positive samples with S gene target failure increased from 70 of 582 (12.0%) to 491 of 813 (60.4%) between November 16 and December 13; this increase was associated with a decrease in median Ct values (Table S1 in the Supplemen-tary Appendix). Over the same time period, the proportion of samples with S gene target failure increased in the South East and East of England regions and London (Fig. 1). For ex-ample, in the South East region, the propor-tion increased from 25.9% on November 16 to 79.8% on December 13. By December 7, a total of 372 of 656 samples (56.7%) obtained from adults younger than 65 years of age and 119 of 157 samples (75.8%) obtained from those 65 years of age or older had S gene target failure (Fig. S3). Sequencing data were available from only two samples from long-term care facili-ties, and both of the sequenced samples were B.1.1.7. In England during this period, 90 to 100% of sequenced samples with S gene target failure were B.1.1.7.The SARS-CoV-2 B.1.1.7 variant is now prev-alent in all regions of England,4 and it spread rapidly from the community into long-term care facilities in the South East and East of England regions and London in November and December 2020. Emerging data suggest the variant may be associated with an increase in mortality.5 Enforcement of disease-control mea-sures to prevent further spread of this highly The New England Journal of Medicine Downloaded from nejm.org on March 23, 2021. For personal use only. No other uses without permission.  Copyright © 2021 Massachusetts Medical Society. All rights reserved. T h e  n e w  e ngl a nd  j o u r na l  o f  m e dic i n en engl j med nejm.org  228449115428311901583351003543545176933671771263302234284201254446281538822391012214474542551043852115911369454231601114Percent of Positive Samples1008090706040301050200B East of England RegionA South East Region2 31 4October2 31 4Week of TestNovember2 31DecemberPercent of Positive Samples10080907060403010502002 31 4October2 31 4Week of TestNovember2 31DecemberC LondonPercent of Positive Samples10080907060403010502002 31 4October2 31 4Week of TestNovember2 31DecemberDetected (S gene target failure)Not detectedORF1ab and N Gene TargetsThe New England Journal of Medicine Downloaded from nejm.org on March 23, 2021. For personal use only. No other uses without permission.  Copyright © 2021 Massachusetts Medical Society. All rights reserved. Correspondencen engl j med nejm.org  3transmissible variant is needed, particularly in long-term care facilities.Maria Krutikov, M.R.C.P. Andrew Hayward, M.D. Laura Shallcross, Ph.D.University College London London, United Kingdom l . shallcross@ ucl . ac . ukThe views expressed in this letter are those of the authors and not necessarily those of the U.K. National Health Service or the Department of Health and Social Care.Supported by funding from the Department of Health and So-cial Care through the VIVALDI (Covid-19 in care homes) study.Disclosure forms provided by the authors are available with the full text of this letter at NEJM.org.This letter was published on March 16, 2021, at NEJM.org.1. Public Health England. Investigation of novel SARS-COV-2 variant: variant of concern 202012/01. 2020 (https://assets . publishing . service . gov . uk/ government/ uploads/ system/ uploads/  attachment_data/ file/ 947048/ Technical_Briefing_VOC_SH_NJL2 _SH2 . pdf).2. COG-UK. COG-UK report on SARS-CoV-2 spike mutations of interest in the UK. 2021 (https://www . cogconsortium . uk/  wp - content/ uploads/ 2021/ 01/ Report - 2_COG - UK_SARS - CoV - 2 - Mutations . pdf).3. New and Emerging Respiratory Virus Threats Advisory Group. NERVTAG/SPI-M extraordinary meeting on SARS-CoV-2 variant of concern 202012/01 (variant B.1.1.7). Note of meeting. 2020 (https://assets . publishing . service . gov . uk/ government/ uploads/  system/ uploads/ attachment_data/ file/ 954945/ s0993 - nervtag - spi - m - voc - meeting . pdf).4. Public Health England. Investigation of novel SARS-CoV-2 variant: variant of concern 202012/01. Technical briefing 4. 2021 (https://assets . publishing . service . gov . uk/ government/ uploads/  system/ uploads/ attachment_data/ file/ 952490/ Variant_of_Concern _VOC_202012_01_Technical_Briefing_4_England . pdf).5. Horby P, Huntley C, Davies N, et al. NERVTAG paper on COVID-19 variant of concern B.1.1.7. 2021 (https://assets . publishing . service . gov . uk/ government/ uploads/ system/ uploads/  attachment_data/ file/ 955239/ NERVTAG_paper_on_variant_of _concern__VOC__B . 1 . 1 . 7 . pdf).DOI: 10.1056/NEJMc2035906Correspondence Copyright © 2021 Massachusetts Medical Society.Figure 1 (facing page). SARS-CoV-2–Positive Samples with S Gene Target Failure, According to Week and Geographic Region in England.Samples were obtained from staff and residents of long-term care facilities. The numbers of samples that were posi-tive for SARS-CoV-2 on polymerase-chain-reaction assay per week from October 5 through December 17, 2020, in the South East region (Panel A), the East of England region (Panel B), and London (Panel C) are shown. Samples with  S gene target failure were those in which only the ORF1ab and N gene targets were detected. Since mid-November, 2020, S gene target failure has been shown to be a reliable marker of variant B.1.1.7. Data collection was incomplete in the final week, so a decrease in the total number of samples is shown.The New England Journal of Medicine Downloaded from nejm.org on March 23, 2021. For personal use only. No other uses without permission.  Copyright © 2021 Massachusetts Medical Society. All rights reserved. 

Spread of a Variant SARS-CoV-2 in Long-Term Care Facilities in England

https://discovery.ucl.ac.uk/10124720/1/Krutikov_NEJM2021.pdf

Spread of a Variant SARS-CoV-2 in Long-Term Care Facilities in England

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