Incidence of community acquired lower respiratory tract disease in Bristol, UK during the COVID-19 pandemic: A prospective cohort study

Abstract

Background: The emergence of COVID-19 and public health measures implemented to reduce SARS-CoV-2 infections have both affected acute lower respiratory tract disease (aLRTD) epidemiology and incidence trends. The severity of COVID-19 and non-SARS-CoV-2 aLRTD during this period have not been compared in detail.

Methods: We conducted a prospective cohort study of adults age ≥18 years admitted to either of two acute care hospitals in Bristol, UK, from August 2020 to November 2021. Patients were included if they presented with signs or symptoms of aLRTD (e.g., cough, pleurisy), or a clinical or radiological aLRTD diagnosis.

Findings: 12,557 adult aLRTD hospitalisations occurred: 10,087 were associated with infection (pneumonia or non-pneumonic lower respiratory tract infection [NP-LRTI]), 2161 with no infective cause, with 306 providing a minimal surveillance dataset. Confirmed SARS-CoV-2 infection accounted for 32% (3178/10,087) of respiratory infections. Annual incidences of overall, COVID-19, and non- SARS-CoV-2 pneumonia were 714.1, 264.2, and 449.9, and NP-LRTI were 346.2, 43.8, and 302.4 per 100,000 adults, respectively. Weekly incidence trends in COVID-19 aLRTD showed large surges (median 6.5 [IQR 0.7-10.2] admissions per 100,000 adults per week), while other infective aLRTD events were more stable (median 14.3 [IQR 12.8-16.4] admissions per 100,000 adults per week) as were non-infective aLRTD events (median 4.4 [IQR 3.5-5.5] admissions per 100,000 adults per week).

Interpretation: While COVID-19 disease was a large component of total aLRTD during this pandemic period, non- SARS-CoV-2 infection still caused the majority of respiratory infection hospitalisations. COVID-19 disease showed significant temporal fluctuations in frequency, which were less apparent in non-SARS-CoV-2 infection. Despite public health interventions to reduce respiratory infection, disease incidence remains high.

Funding: AvonCAP is an investigator-led project funded under a collaborative agreement by Pfizer.

Keywords: CAP, community acquired pneumonia; COPD, chronic obstructive pulmonary disease; COVID-19; COVID-19, Coronavirus disease 2019; CRDE, chronic respiratory disease exacerbation; Cardiac failure; HF, heart failure; Lower respiratory tract infection; NP-LRTI, non-pneumonic lower respiratory tract infection; Pneumonia; SARS-CoV-2; aLRTD, acute lower respiratory tract disease.

Figure 1

Summary of aLRTD incidence between 1st August 2020 and 15th November 2021. Panel A shows categories with combinations of having a single aLRTD phenotype (e.g., pneumonia alone), two phenotypes (e.g., pneumonia and CRDE), or three phenotypes (e.g., pneumonia, CRDE and HF); the numbers along the axes show counts for each phenotype, both singly and in combination, stratified by SARS-CoV-2 PCR status. 640/6661 (9.6%) cases of pneumonia were not radiologically confirmed [423/6661 (6.4%) with no consolidation/infiltrate and 217/6661 (3.3%) with no radiology performed]. Panel B shows the proportion of cases with each single aLRTD phenotype out of the total number of cases in each strata. Where cases have multiple phenotypes they are counted once for each phenotype, hence proportions do not add up to 100%. Panel C shows the proportion of cases with every combination of aLRTD phenotypes, stratified by SARS-CoV-2 status. In this panel each case is counted only once and hence proportions do add up to 100%. Panels E and F show boxplot summaries of the distributions for key patient indicators in each phenotype combination category: E) age, and F) CCI score, stratified by SARS-CoV-2 PCR status. Panels D and G indicate differences in these key indicators between SARS-CoV-2 PCR positive and negative patients for D) age, and G) CCI score, in tabular form. P-values are the result of 2 sided Kolmogorov–Smirnov significance tests. CCI, Charlson Comorbidity Index; CRDE, chronic respiratory disease exacerbation; HF, heart failure; NP-LRTI, non-pneumonic lower respiratory tract infection; Pn, pneumonia.

Figure 2

Hospitalisations with aLRTD, by primary clinical presentation (non-infective, SARS-CoV-2 infection and infection with no evidence of SARS-CoV-2) and age group. (A) The upper panel shows the weekly number of hospital admissions associated with positive SARS-CoV-2 PCR results taken at the time of admission, as a bar chart. For comparison the red line shows the weekly number of SARS-CoV-2 cases in the immediate locality of the study sites. In the second panel we show the remaining non-SARS-CoV-2 infection aLRTD admissions, stratified by primary clinical presentation, and in the 3^rd panel non-infective aLRTD admissions (including primary presentations with heart failure and/or exacerbation of chronic respiratory disease). Pneumonia cases are shown in yellow, and NP-LRTI in green. (B) Points represent weekly counts of aLRTD admissions. Estimates of the underlying incidence rates are shown as continuous lines, assuming the admissions follow a Poisson distribution with a time varying rate, using a locally fitted polynomial in time, using a maximum likelihood method. The earliest date that the COVID-19 vaccination program opened to any people in each age group is marked on each panel with a solid vertical line, and the date by which all people in the age group were eligible for vaccination by a dashed vertical line (where different) (Supplementary Table 5). Grey bars in the background indicate periods when non-pharmaceutical interventions were in place to control the spread of SARS-CoV-2. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Figure 3

Incidence per 100,000 population per week by age group for non-infective aLRTD, PCR positive SARS-CoV-2 aLRTD, and infection with no evidence of SARS-CoV-2. (A) As in Figure 3 estimates of the underlying incidence rates are shown as continuous lines. Grey bars in the background indicate periods when non-pharmaceutical interventions were in place to control the spread of SARS-CoV-2. (B) aLRTD cumulative hospital cases (per 100,000 people) in adults in Bristol, UK over 12 months (August 2020–July 2021). Additional data are located in Supplementary Table 4. aLRTD, acute lower respiratory tract disease; NP-LRTI, non-pneumonic lower respiratory tract infection; PCR, polymerase chain reaction.