First and second SARS-CoV-2 waves in inner London: A comparison of admission characteristics and the impact of the B.1.1.7 variant

Abstract

Introduction: A second wave of SARS-CoV-2 infection spread across the UK in 2020 linked with emergence of the more transmissible B.1.1.7 variant. The emergence of new variants, particularly during relaxation of social distancing policies and implementation of mass vaccination, highlights the need for real-time integration of detailed patient clinical data alongside pathogen genomic data. We linked clinical data with viral genome sequence data to compare patients admitted during the first and second waves of SARS-CoV-2 infection. Methods: Clinical, laboratory and demographic data from five electronic health record (EHR) systems was collected for all cases with a positive SARS-CoV-2 RNA test between March 13th 2020 and February 17th 2021. SARS-CoV-2 viral sequencing was performed using Oxford Nanopore Technology. Descriptive data are presented comparing cases between waves, and between cases of B.1.1.7 and non-B.1.1.7 variants. Results: There were 5810 SARS-CoV-2 RNA positive cases comprising inpatients (n=2341), healthcare workers (n=1549), outpatients (n=874), emergency department (ED) attenders not subsequently admitted (n=532), inter-hospital transfers (n=281) and nosocomial cases (n=233). There were two dominant waves of admissions starting from around March 13th and October 20th, both with a temporally aligned rise in nosocomial cases (n=96 in wave one, n=137 in wave two). 1470 SARS-CoV-2 isolates were successfully sequenced, including 216/838 (26%) admitted cases from wave one, 472/1503 (31%) admitted cases in wave two and 121/233 (52%) nosocomial cases. 400/472 (85%) of sequenced isolates from admitted cases in wave two were the B.1.1.7 variant. The first B.1.1.7 variant was identified on 15th November 2020 and increased rapidly to comprise almost all sequenced isolates in January 2021 (n=600/617, 97%). Females made up a larger proportion of admitted cases in wave two (47.2% vs 41.8%, p=0.012), and in those infected with the B.1.1.7 variant compared to non-B.1.1.7 variants (48.0% vs 41.8%, p=0.042). A diagnosis of frailty was less common in wave two (11.5% v 22.8%, p<0.001) and in the group infected with B.1.1.7 (14.5% v 22.4%, p=0.001). There was no difference in severity on admission between waves, as measured by hypoxia at admission (wave one: 64.3% vs wave two: 65.6%, p=0.658). However, a higher proportion of cases infected with the B.1.1.7 variant were hypoxic on admission compared to other variants (70.0% vs 62.5%, p=0.029). Conclusions: Automated EHR data extraction linked with SARS-CoV-2 genome sequence data provides valuable insight into the evolving characteristics of cases admitted to hospital with COVID-19. The proportion of cases with hypoxia on admission was greater in those infected with the B.1.1.7 variant, which supports evidence the B.1.1.7 variant is associated with more severe disease. The number of nosocomial cases was similar in both waves despite introduction of many infection control interventions before wave two, an observation requiring further investigation.

Relevance of prediction scores derived from the SARS-CoV-2 first wave, in the UK COVID-19 second wave, for early discharge, severity and mortality: a PREDICT COVID UK prospective observational cohort study

“…This started in early September 2020, peaking on the 1st of January 2021 and prior to any significant vaccination effort 18 . A younger (60y vs 62y), less frail (12.8% vs 22.8%), more obese (29.1% vs 24.6%), and more female (47.3% vs 41.8%) case population in the second wave was noted in a small London study 17 . Spain and Japan noted similar demographic changes with reduced mortality but without documented SARS-CoV-2 variants 11,13 .…”

“…The UK variant, B.1.1.7, accounted for 58% to 83% of all second wave UK hospitalised cases with increased infectivity but reduced mortality compared to the parent D614G 16,17 . This started in early September 2020, peaking on the 1st of January 2021 and prior to any significant vaccination effort 18 .…”

Public Health and Health Systems Impacts of SARS-CoV-2 Variants of Concern: A Rapid Scoping Review

“…Four studies scored 80% or higher, [24][25][26][27] indicating high quality. The majority (n=8) scored 50-80%, [28][29][30][31][32][33][34][35] suggesting medium quality, while four studies were considered low quality, scoring 10-44%. [36][37][38][39] Twelve of the 33 studies were pre-prints, meaning they had not yet been peer reviewed.…”

“…Overall, 13 studies related to health system impacts were eligible for critical appraisal. Two were appraised as low quality, 38,39 seven as medium, 28,[30][31][32][33][34][35] and four as high. [24][25][26][27] Question 2A: Adjusting capacity planning to accommodate changes in the risk of re-infection and the risk of severe disease (e.g., hospitalization, admission to ICU, and death).…”

Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques

“…As more epidemiological data on human cases of B.1.1.7 infection become available, it appears that this variant transmits more efficiently than the variants it displaced ( 2 – 6 ), possibly due to increased virus shedding ( 7 ). Whether there is an increased disease severity associated with B.1.1.7 infection remains unclear ( 4 , 8 – 11 ). Data on infection in humans with B.1.351 are not yet widely available, and although its rapid spread suggests increased transmissibility, there are no data to confirm this ( 12 – 14 ).…”