Vaccine effectiveness against SARS-CoV-2 infection, hospitalization, and death when combining a first dose ChAdOx1 vaccine with a subsequent mRNA vaccine in Denmark: A nationwide population-based cohort study.

BACKGROUND: The recommendations in several countries to stop using the ChAdOx1 vaccine has led to vaccine programs combining different Coronavirus Disease 2019 (COVID-19) vaccine types, which necessitates knowledge on vaccine effectiveness (VE) of heterologous vaccine schedules. The aim of this Danish nationwide population-based cohort study was therefore to estimate the VE against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection and COVID-19-related hospitalization and death following the first dose of the ChAdOx1 vaccine and the combination of the ChAdOx1/mRNA vaccines. METHODS AND
FINDINGS: All individuals alive in or immigrating to Denmark from 9 February 2021 to 23 June 2021 were identified in the Danish Civil Registration System. Information on exposure, outcomes, and covariates was obtained from Danish national registries. Poisson and Cox regression models were used to calculate crude and adjusted VE, respectively, along with 95% confidence intervals (CIs) against SARS-CoV-2 infection and COVID-19-related hospitalization or death comparing vaccinated versus unvaccinated individuals. The VE estimates were adjusted for calendar time as underlying time and for sex, age, comorbidity, country of origin, and hospital admission. The analyses included 5,542,079 individuals (97.6% of the total Danish population). A total of 144,360 individuals were vaccinated with the ChAdOx1 vaccine as the first dose, and of these, 136,551 individuals received an mRNA vaccine as the second dose. A total of 1,691,464 person-years and 83,034 SARS-CoV-2 infections were included. The individuals vaccinated with the first dose of the ChAdOx1 vaccine dose had a median age of 45 years. The study population was characterized by an equal distribution of males and females; 6.7% and 9.2% originated from high-income and other countries, respectively. The VE against SARS-CoV-2 infection when combining the ChAdOx1 and an mRNA vaccine was 88% (95% CI: 83; 92) 14 days after the second dose and onwards. There were no COVID-19-related hospitalizations or deaths among the individuals vaccinated with the combined vaccine schedule during the study period. Study limitations including unmeasured confounders such as risk behavior and increasing overall vaccine coverage in the general population creating herd immunity are important to take into consideration when interpreting the results.
CONCLUSIONS: In this study, we observed a large reduction in the risk of SARS-CoV-2 infection when combining the ChAdOx1 and an mRNA vaccine, compared with unvaccinated individuals.

Introduction

The Coronavirus Disease 2019 (COVID-19) pandemic caused by the outbreak of the novel coronavirus Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Wuhan, China, has caused major global public health concerns. As of 26 July 2021, more than 192 million cases and 4.1 million deaths have been reported worldwide [1]. In Denmark, the COVID-19 vaccination program started on 27 December 2020, with the BNT162b2 mRNA vaccine from Pfizer/BioNTech, also called Comirnaty. The mRNA-1273 vaccine (SpikeVax from Moderna) and the viral vector ChAdOx1 vaccine (Vaxzevria from Oxford/AstraZeneca) were introduced in the vaccination program on 14 January and 9 February 2021, respectively. The ChAdOx1 vaccine was primarily given to frontline personnel in healthcare, elderly care, and selected parts of the social sector who were at particular risk of infection with SARS-CoV-2 or who had been identified as performing critical functions in society (referred to as frontline personnel) [2]. On 11 March 2021, it was decided to pause the use of the ChAdOx1 vaccine in the Danish COVID-19 vaccination program due to a possible link between the vaccine and very rare cases of unusual blood clots, bleeding, and low blood platelet counts [3,4]. On 14 April 2021, it was decided not to continue with the use of the ChAdOx1 vaccine in the Danish vaccination program, due to the present epidemiological situation with a relatively low SARS-CoV-2 infection rate. The Danish Health Authority announced on 16 April 2021 that individuals who had only received the first dose of the ChAdOx1 vaccine should be offered a second dose of either the BNT162b2 mRNA or the mRNA-1273 vaccine (ChAdOx1/mRNA vaccine schedule) [4]. Studies from the UK have reported vaccine effectiveness (VE) estimates between 22% and 94% following the administration of 1 dose of ChAdOx1 [5-7]. Due to changing recommendations regarding the use of the ChAdOx1 vaccine [4] and to avoid vaccine shortages, some countries are combining vaccine types [8]. This creates a need for studies of VE for heterologous vaccination schedules [9]. Immunological data on a heterologous vaccination schedule indicate that the combination of the ChAdOx1/mRNA vaccines is at least as immunogenic and protective as homologous BNT162b2 vaccination [10,11]. However, to the best of our knowledge, no previous studies have reported VE of a ChAdOx1/mRNA vaccine schedule. This study aimed to estimate VE against SARS-CoV-2 infection and COVID-19–related hospitalization and death of (1) one dose of the ChAdOx1 vaccine and (2) the ChAdOx1/mRNA vaccine schedule both compared with unvaccinated individuals.

Methods

Study design and population

All residents in Denmark are registered in the Danish Civil Registration System (CRS) and assigned a unique personal identification number (CPR number), which is used in all national registries, enabling accurate individual-level linkages between registries [12]. The high quality of this registry is ensured by the ongoing correction of errors and the validation of information recorded [12]. In this nationwide retrospective population-based cohort study, individuals were included in the study population if they were residents in Denmark on 9 February 2021 or immigrated before the end of study on 23 June 2021. Individuals who had received a COVID-19 vaccine or had a reverse transcription polymerase chain reaction (RT-PCR) confirmed SARS-CoV-2 infection before the start of the study (2.4%) were excluded. The latter exclusion criteria was applied due to expected natural immunity from previous SARS-CoV-2 infection [13]. All study participants were followed from 9 February 2021 and until a SARS-CoV-2 infection, receiving the first dose of another COVID-19 vaccine than the ChAdOx1 vaccine, receiving the second dose of the ChAdox1 vaccine, emigration, death, or end of follow-up (23 June 2021), whichever came first. The study participants contributed with follow-up time to the first exposure when they received the first dose of the ChAdOx1 vaccine and to the second exposure when they received the second dose of an mRNA vaccine following the first dose of ChAdOx1 during the study period (Fig 1). Information on immigration, emigration, and vital status was retrieved from the CRS [12]. Information on the date of vaccination and type of vaccine was retrieved from the Danish Vaccination Registry, which includes data on all administered vaccines [14]. Information on the second dose is only included if a person has completed the vaccination schedule with the correct time window relevant for the specific type of vaccine. The study did not have a prespecified analysis plan. This study is reported as per the REporting of studies Conducted using Observational Routinely-collected health Data (RECORD) Statement (S1 Checklist).

Fig 1

Flow chart of the study population.

COVID-19, Coronavirus Disease 2019; COVID-19, Coronavirus Disease 2019.

Assessment of exposures

The exposures of interest were (1) a single dose of ChAdOx1 and (2) a second dose of either BNT162b2 mRNA or mRNA-1273 following the first dose of ChAdOx1. Unvaccinated individuals with no history of SARS-CoV-2 infection were used as reference. To examine the effect of 1 dose of ChAdOx1 on SARS-CoV-2 infection, time following vaccination was divided into 0 to 13 days (the run-in period), and 14 days and onward was divided into 7-day intervals until receiving the second dose. The effect of 1 dose of ChAdOx1 on COVID-19–related hospitalization and death was divided into 0 to 13 days (the run-in period) and 14 days and onwards until receiving the second dose of an mRNA vaccine. The effect of the combined vaccine schedule on all outcomes was divided into 0 to 13 days and 14 days and onwards.

Assessment of outcomes

The outcomes of interest were a SARS-CoV-2 infection, defined as a laboratory-confirmed RT-PCR SARS-CoV-2–positive test, and COVID-19–related hospitalization and death. Information on RT-PCR SARS-CoV-2–positive tests was retrieved from the Danish Microbiology Database (MiBa), which is a national database that automatically accumulates both positive and negative test results from all Danish departments of clinical microbiology [15]. Information about rapid antigen tests was not included due to moderate sensitivity in asymptomatic patients compared with RT-PCR [16]. A COVID-19–related hospitalization or death was defined as an admission within 14 days or death within 30 days after a positive SARS-CoV-2 test, respectively. Therefore, time at risk for the COVID-19–related outcomes were extended to 14 and 30 days after a confirmed SARS-CoV-2 infection, respectively. Hospital admissions and discharge dates were retrieved from the Danish National Patient Registry (DNPR) [17].

Covariates

The incidence of SARS-CoV-2 varied considerably throughout the study period. To control for this variation through the study period, calendar time was used as the underlying time. Further, age, sex, country of origin, and comorbidity were also included as covariates for the association between COVID-19 vaccination and SARS-CoV-2 infection, hospitalization, and death. Finally, hospital admission was included as a covariate for the association between COVID-19 vaccination and SARS-CoV-2 infection and death. Information on date of birth and sex (male/female) was retrieved from the CRS [12]. The presence of comorbidity (yes/no) within the previous 5 years (data retrieved at start of study) was identified based on diagnoses coded according to the International Classification of Diseases, 10th revision (ICD-10). Diagnoses included 1 primary and optional secondary diagnosis for each patient contact and were retrieved from the DNPR [17]. The ICD-10 codes included in the comorbidity covariate are provided in S1 Table. Information on country of origin (Denmark/high-income/other/unknown) was retrieved from the CRS (S2 Table) [12]. Only the country of origin variable contained missing observations (0.2%); these were included as unknown.

Statistical analysis

Characteristics of the included population were described using proportions. Crude VE estimates were calculated using a Poisson regression with overdispersion (quasi-Poisson) and time at risk as offset. Adjusted hazard ratios (HRs) were obtained using a Cox regression model with calendar time as underlying time due to varying incidence of SARS-CoV-2 during the study period. Sex, country of origin, and comorbidity were included as fixed covariates, being admitted to hospital as a time varying covariate, and age as a cubic spline. Time intervals after vaccination were included as a time varying covariate. The VE estimates were calculated as (1−HR)∙100%. The assumption of proportionality of hazards was assessed graphically and found to be valid.

A sensitivity analysis of the VE against SARS-CoV-2 infection following the ChAdOx1/BNT162b2 mRNA vaccine schedule and the ChAdOx1/mRNA-1273 vaccine schedule, respectively, was conducted to assess if there was any difference in VE between the BNT162b2 mRNA and the mRNA-1273 vaccine as the second dose.

Data were analyzed using R version 4.0.5 (R Foundation for Statistical Computing; https://www.R-project.org/).

Ethical considerations

The present study was based on existing administrative data and did not require ethical approval.

Results

The study population included 5,542,079 individuals, among which 144,360 individuals (2.6%) received the ChAdOx1 vaccine as the first dose. Of these, 88,050 (61%) and 48,501 (33.6%) individuals received the BNT162b2 mRNA and the mRNA-1273 vaccine as the second dose, respectively. A total of 1,691,464 person-years and 83,034 SARS-CoV-2 infections were included. The individuals vaccinated with the first dose of the ChAdOx1 vaccine dose had a median age of 45 years. In the total study population, 25.6% had at least one of the comorbidities defined in S1 Table. The comorbidity category other diseases, cardiovascular diseases, and respiratory diseases were most prevalent. Furthermore, 6.7% and 9.2% originated from high-income and other countries, respectively, and there was an equal distribution of males and females (Table 1). However, the proportion of females were higher among the individuals who received the first dose of the ChAdOx1 vaccine (79.8%).

Table 1

Characteristics of the 5,542,079 individuals in the study population.

		N	%
Number of individuals included in the analyses		5,542,079	100%
Median age (years) at first dose of the ChAdOx1 vaccine (IQR)		45 (33; 55)
Median age (years) at second dose of an mRNA vaccine (IQR)		46 (34; 55)
Sex	Male	2,801,776	50.6
	Female	2,740,303	49.4
Presence of at least 1 comorbidity	Yes	1,416,332	25.6
	No	4,125,747	74.4
Country of origin	Denmark	4,653,808	84.0
	High-income countries	369,255	6.7
	Other countries	509,330	9.2
	Unknown	9,686	0.2
Coverage of 1 dose of the ChAdOx1 vaccine	Frontline personnel	143,231	2.6
	Other	1,129	0.02
Coverage of second dose of the BNT162b2 mRNA following a first dose ChAdOx1		88,050	1.6
Coverage of the second dose of the mRNA-1273 following a first dose ChAdOx1		48,501	0.9
Median follow-up days (min, IQR, max)		133 (1, 97, 135, 135)
Median number of days to the first dose (IQR)		18 (11, 24)
Median number of days from the first dose to the second dose (IQR)		82 (78, 85)

The incidence of SARS-CoV-2 infection decreased from 27 December 2020 where the vaccination program was initiated in Denmark (Fig 2). Most likely, the decrease was a result of the combination of the newly started vaccination program and the lockdown from 16 December 2020 until 1 March 2021. The partial reopening in March 2021 resulted in a slight increase in SARS-CoV-2 infections until 1 June 2021, where approximately 35% and 20% of the population had started or completed vaccination, respectively (Fig 2). As of 26 July 2021, 74.3% of all SARS-CoV-2 RT-PCR–positive tests registered in 2021 had been sequenced (Fig 2). Based on the available sequencing data, the B.1.1.7 variant (Alpha) was observed throughout the whole study and was dominant after mid-February. The B.1.617.2 variant first became prominent after the end of the present study (23 June 2021), and during the study period, only a small proportion of this variant was observed (Fig 2).

Fig 2

Percentage of population vaccinated and incidence of SARS-CoV-2 infection (7 days running mean).

SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus 2.

The adjusted VE estimates against SARS-CoV-2 infection between 14 and 83 days after 1 dose of the ChAdOx1 vaccine were relatively stable with overlapping confidence intervals (CIs) (Fig 3). These VE estimates ranged from 29% (95% CI: 12; 43) to 44% (95% CI: 32; 55) after 1 dose of the ChAdOx1 vaccine (Table 2). The VE estimates at 84 days and onwards were not statistically significant. However, the estimates are broadly similar throughout. The reason these VE estimates fail to meet the level of statistical significance is the increase in variability presumably related to the number of people remaining at risk at those time points. For the ChAdOx1/mRNA vaccine schedule, statistically significant adjusted VE estimates of 66% (95% CI: 59; 72) and 88% (95% CI: 83; 92) were observed at 0 to 13 days and from 14 days and onwards after the second dose, respectively (Table 2). The sensitivity analysis examining the VE against SARS-CoV-2 infection following the ChAdOx1/BNT162b2 mRNA and the ChAdOx1/mRNA-1273 vaccine schedules showed similar results (S3 Table).

Fig 3

Adjusted VE estimates against RT-PCR SARS-CoV-2 infection of the first dose of the ChAdOx1 vaccine and the ChAdOx1/mRNA vaccine schedule.

Each dot illustrates the estimated VE and the bars show the accompanying 95% CI. CI, confidence interval; RT-PCR, reverse transcription polymerase chain reaction; SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus 2; VE, vaccine effectiveness.

Table 2

Unadjusted and adjusted VE estimates against RT-PCR SARS-CoV-2 infection of 1 dose of the ChAdOx1 vaccine and the ChAdOx1/mRNA vaccine schedule.

					Unadjusted		Adjusted*
Vaccine type	Time interval (days)	No. of events	Person-years	Incidence rate	VE, %	95% CI	VE, %	95% CI
Unvaccinated		81,755	1,645,793	0.0497	Reference		Reference
One dose of the ChAdOx1 vaccine	0–13	197	5,528	0.0356	28	8; 44	0	−15; 14
	14–20	69	2,759	0.0250	50	23; 67	39	23; 52
	21–27	66	2,758	0.0239	52	26; 69	44	29; 56
	28–34	85	2,744	0.0310	38	8; 58	29	12; 43
	35–41	81	2,741	0.0296	41	12; 60	35	19; 48
	42–48	106	2,737	0.0387	22	−10; 45	17	−1; 31
	49–55	96	2,733	0.0351	29	−1; 51	29	3; 42
	56–62	98	2,728	0.0359	28	−3; 49	36	21; 47
	63–69	99	2,660	0.0372	25	−7; 47	41	28; 51
	70–76	91	2,429	0.0375	25	−9; 48	44	32; 55
	77–83	83	1,723	0.0482	3	−43; 34	31	14; 44
	84–90	46	615	0.0748	−51	−154; 11	−3	−37; 23
	91–97	12	237	0.0506	−2	−183; 63	23	−36; 56
	98–104	5	146	0.0342	31	−235; 86	29	−71; 70
	≥105	7	161	0.0436	12	−234; 77	−47	−208; 30
The ChAdOx1/mRNA vaccine schedule	0–13	109	5,197	0.0210	58	41; 70	66	59; 72
	≥14	29	7,775	0.0037	92	86; 96	88	83; 92

*Adjusted for calendar time, age, sex, country of origin, hospital admission, and comorbidity.

CI, confidence interval; RT-PCR, reverse transcription polymerase chain reaction; SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus 2; VE, vaccine effectiveness.

A statistically significant adjusted VE of 93% (95% CI: 80; 98) against COVID-19–related hospitalization was observed from 14 days after the first dose ChAdOx1 and until receiving a second dose of an mRNA vaccine. No COVID-19–related hospitalizations occurred after the ChAdOx1/mRNA vaccine schedule. Therefore, it was not possible to estimate VE estimates against COVID-19–related hospitalization for the ChAdOx1/mRNA vaccine schedule (Table 3). Also, no COVID-19–related deaths were observed in the period after receiving the first dose of the ChAdOx1 or in the time period following the ChAdOx1/mRNA vaccine schedule (Table 3).

Table 3

Unadjusted and adjusted VE estimates against COVID-19–related hospitalization and death of 1 dose of the ChAdOx1 vaccine and the ChAdOx1/mRNA vaccine schedule.

		COVID-19–related hospitalization							COVID-19–related death
					Unadjusted		Adjusted*					Unadjusted		Adjusted**
Vaccine type	Time interval (days)	No. of events	Person-years	Incidence rate	VE, %	95% CI	VE, %	95% CI	No. of events	Person-years	Incidence rate	VE, %	95% CI	VE, %	95% CI
Unvaccinated		1,821	1,646,552	0.0011	Reference		Reference		122	1,652,106	0.0001	Reference		Reference
One dose of the ChAdOx1 vaccine	0–13	6	5,529	0.0011	19	−3,020; 97	6	−110; 58	0	5,532	0	-	-	-	-
	≥14	3	27,195	0.0001	90	−1,220; 100	93	80; 98	0	27,260	0	-	-	-	-
The ChAdOx1/mRNA vaccine schedule	0–13	0	5,197	0	-	-	-	-	0	5,201	0	-	-	-	-
	≥14	0	7,772	0	-	-	-	-	0	7,782	0	-	-	-	-

*Adjusted for calendar time, age, sex, country of origin and comorbidity.

**Adjusted for calendar time, age, sex, country of origin, comorbidity and hospital admission.

CI, confidence interval; COVID-19, Coronavirus Disease 2019; VE, vaccine effectiveness.

Discussion

This nationwide population-based cohort study showed a significant reduction in the risk of SARS-CoV-2 infection 14 days after the second dose with a VE of 88% (95% CI: 83; 92) when combining the viral vector vaccine ChAdOx1 and an mRNA vaccine. No COVID-19–related hospitalizations or deaths occurred among individuals who received the ChAdOx1/mRNA vaccine schedule during the studied period indicating that a combined ChAdOx1 /mRNA vaccine schedule protects against severe outcomes. However, studies with longer follow-up time are needed to confirm these findings, especially because death is a rare outcome in the population of working-age.

The VE of the ChAdOx1/mRNA vaccine schedule is similar to the VE estimates of 80% (95% CI: 77; 83) and 90% (95% CI: 82; 95) reported in 2 previous Danish studies of frontline personnel (healthcare workers) who received 2 doses of the BNT162b2 mRNA vaccine [18,19]. Immunological studies also indicate that the ChAdOx1/BNT162b2 vaccine schedule is associated with stronger humoral immune responses and stronger anti-SARS-CoV-2 spike T cell responses compared with 2 doses of the ChAdOx1 vaccine [20]. Also, a 14-day robust humoral and cellular immune response after the second dose of BNT162b2 was observed in individuals primed with ChAdOx1 8 to 12 weeks earlier [21]. Heterologous vaccination schedules studies are important, as several countries want to implement a combined vaccination program with the ChAdOx1 vaccine and an mRNA vaccine to avoid restarting the vaccination schedule with 2 mRNA vaccines [8]. This is due to both changes in recommendations regarding the use of the ChAdOx1 vaccine and to avoid vaccine shortage. Additionally, some countries may need to combine viral vector vaccines with mRNA vaccines to boost immunity.

Due to the decision to withdraw the ChAdOx1 vaccine from the Danish vaccination program, the second vaccine dose was postponed, and it was therefore possible to evaluate the VE of 1 dose of the ChAdOx1 vaccine over a longer time. The VE estimates ranged from 29% (95% CI: 12; 43) to 44% (95% CI: 32; 55) between 14 to 83 days after 1 dose of the ChAdOx1 vaccine. No effectiveness against SARS-CoV-2 infection and COVID-19–related hospital admission during the first 0 to 13 days after 1 dose of the ChAdOx1 vaccine was observed. This was expected due to the run-in period before immunity is anticipated to occur. A test-negative case–control study from England including adults aged 70 years and older showed a VE against symptomatic PCR confirmed SARS-CoV-2 infection, of 22% (95% CI: 11; 32) from 14 to 20 days, reaching a VE of 73% (95% CI: 27; 90) at 35 days and onwards after 1 dose of the ChAdOx1 vaccine [6]. Additional protection against hospital admission was observed, showing a VE against emergency hospital admission of 80% [6]. Another cohort study from England, including long-term care facility residents aged 65 years and older, showed adjusted HR against SARS-CoV-2 infection immediately after the first dose translated to VE estimates of 49% (95% CI: 01; 74) at 0 to 6 days, 42% (95% CI: 04; 65) at 7 to 13 days, 67% (95% CI: 32; 84) at 28 to 34 days, and 68% (95% CI: 34; 85) at 35 to 48 days [7]. A national prospective cohort study from Scotland reported VE estimates against hospital admission ranging between 68% (95% CI: 61; 73) and 97% (95% CI: 63; 100) at 0 to 41 days after the first dose of the ChAdOx1 vaccine [5]. The differences in the VE estimates between these studies [5-7] and the present study may be explained by differences in the study populations. As of 30 June 2021, Denmark has the highest testing rate for SARS-CoV-2 per 100,000 individuals among European countries [22]. As a result of the high testing rate, we may have detected more SARS-CoV-2 infections in Denmark than in England and Scotland and therefore observing a lower VE of 1 dose of the ChAdOx1 vaccine. Furthermore, differences in SARS-CoV-2 variants and the background risk of COVID-19 during the study period may also affect the VE estimates. Our results indicate that the ChAdOx1/mRNA vaccine schedule are effective against the Alpha variant, which became the dominating variant during the study period.

The strengths of this study are the high-quality registers and the possibility to use the unique personal identifier to link data on all residents in Denmark. The national testing strategy during the study period, including unlimited access to free-of-charge RT-PCR tests nationwide, led to a high proportion of the population being tested, which enabled us to capture data on both asymptomatic and symptomatic infections. Another strength was the access to national data on all laboratory-confirmed RT-PCR SARS-CoV-2 infections. Also, a high sensitivity (97.1%) and specificity (99.98%) was observed for the RT-PCR test [23], ensuring a low risk of misclassification. An effort was made to ensure that all individuals had equal opportunities to receive the COVID-19 vaccines. This was done through an online booking system, special campaigns, offering vaccination in some workplaces, translating the material to other languages than Danish and English, and arranging transport for those who were not able to reach the vaccination clinics on their own.

The study also has some limitations. Since we were not able to discriminate between asymptomatic and symptomatic infections, it was not possible to assess the severity of a COVID-19 infection after vaccination based on symptoms. We used a positive SARS-CoV-2 test prior to hospitalization and death (i.e., COVID-19–related hospitalization and death) as a proxy for the severity of COVID-19, although this definition might be subject to uncertainty since COVID-19 may not be the cause of these outcomes. Another limitation is that differences in test behavior related to vaccination status may exist, which may result in capturing less asymptomatic infections in vaccinated individuals, thereby leading to elevated VE estimates. The Cox regression models were adjusted for potential confounders including calendar time, age, sex, country of origin, hospital admission, and comorbidity. However, we cannot eliminate differences in health-seeking behavior or test activity as well as residual confounding related to the dichotomous classification of the comorbidity covariate. This classification does not allow for the exclusion of differences in individual comorbidities across vaccination status, such as vaccinated individuals being more or less burdened by comorbid conditions than unvaccinated individuals. It was mainly frontline personnel who received the ChAdOx1 vaccine (99.3%). Therefore, we cannot eliminate confounding by indication, assuming that frontline personnel are more exposed to SARS-CoV-2 than the general population [24,25], which could result in a lower VE in this group. However, frontline personnel are also better trained to use personal protective equipment than the general population, which would moderate the increased risk from their occupational setting. The results may not be generalizable to other settings with a circulation of more transmissible SARS-CoV-2 variants such as the Delta variant. Through the study period, many individuals received COVID-19 vaccines other than ChAdOx1/mRNA vaccines, thus increasing the overall vaccine coverage in the general population and thereby creating indirect protective herd immunity.

In conclusion, a high protection against SARS-CoV-2 infection was observed with the ChAdOx1/mRNA vaccine schedule. No COVID-19–related hospitalizations were observed with the combined ChAdOx1/mRNA vaccine schedule. Furthermore, no COVID-19–related deaths were observed after neither the first dose of the ChAdOx1 vaccine nor the ChAdOx1/mRNA vaccine schedule. However, studies with longer follow-up time are needed to confirm these findings, especially because death is a rare outcome in the population of working-age.

The RECORD statement—checklist of items, extended from the STROBE statement, which should be reported in observational studies using routinely collected health data.

(DOCX)

Click here for additional data file.

Overview of the International Classification of Diseases, 10th revision (ICD-10) codes included in the comorbidity covariate.

(DOCX)

Click here for additional data file.

Definition of country of origin.

(DOCX)

Click here for additional data file.

Unadjusted and adjusted vaccine effectiveness (VE) estimates against RT-PCR SARS-CoV-2 infection of 1 dose of the ChAdOx1 vaccine and the ChAdOx1/BNT162b2 mRNA or ChAdOx1/mRNA-1273 vaccine schedule, respectively.

(DOCX)

Click here for additional data file.

27 Jul 2021

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Please ensure that the paper adheres to the PLOS Data Availability Policy (see http://journals.plos.org/plosmedicine/s/data-availability), which requires that all data underlying the study's findings be provided in a repository or as Supporting Information. For data residing with a third party, authors are required to provide instructions with contact information for obtaining the data. PLOS journals do not allow statements supported by "data not shown" or "unpublished results." For such statements, authors must provide supporting data or cite public sources that include it.

We look forward to receiving your revised manuscript.

Sincerely,

Louise Gaynor-Brook, MBBS PhD

Associate Editor

PLOS Medicine

plosmedicine.org

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Comments from the Academic Editor:

There is a lot unclear about the methods and statistical analysis of the study. Who was included, what was the vaccination status of the rest of the population, were there people with 2 mRNA vaccinations, would it make sense to compare these to the ones included in the study? Also, the statistical analysis is described only very briefly, without any justification for underlying assumptions. How do the estimated HRs and incidences compare to the observed incidence at the time of observation?

I am sure that the authors have a very good and complete data set, so it would be worthwhile extracting more complete information, adding new analyses and substantially improving presentation of the methods.

Requests from the editors:

General comments:

Throughout the paper, please adapt reference call-outs to the following style: "... low blood platelet counts [3,4]." (noting the absence of spaces within the square brackets).

Data availability:

PLOS Medicine requires that the de-identified data underlying the specific results in a published article be made available, without restrictions on access, in a public repository or as Supporting Information at the time of article publication, provided it is legal and ethical to do so. If the data are not freely available, please describe briefly the ethical, legal, or contractual restriction that prevents you from sharing it. Please state the owner of the data set and contact information for data requests (web or email address). Note that a study author cannot be the contact person for the data.

Title: Please revise your title according to PLOS Medicine's style. Please place the study design in the subtitle (ie, after a colon). We suggest “Vaccine effectiveness against SARS-CoV-2 infection, hospitalization and death when combining a first-dose ChAdOx1 vaccine with a subsequent mRNA vaccine in Denmark: a nationwide population-based cohort study” or similar

Abstract:

Please structure your abstract using the PLOS Medicine headings (Background, Methods and Findings, Conclusions).

Abstract Background: Please expand upon the context of why the study is important. The final sentence should clearly state the study question.

Abstract Methods and Findings:

Please provide brief demographic details of the study population (e.g. sex, age, ethnicity, etc)

Please include the dates during which the study took place and length of follow up.

In the last sentence of the Abstract Methods and Findings section, please describe 2-3 of the main limitations of the study's methodology

Abstract Conclusions:

Please begin your Abstract Conclusions with "In this study, we observed ..." or similar, to summarize the main findings from your study without overstating your conclusions.

Author Summary:

At this stage, we ask that you include a short, non-technical Author Summary of your research to make findings accessible to a wide audience that includes both scientists and non-scientists. The Author Summary should immediately follow the Abstract in your revised manuscript. This text is subject to editorial change and should be distinct from the scientific abstract. Please see our author guidelines for more information: https://journals.plos.org/plosmedicine/s/revising-your-manuscript#loc-author-summary

In the final bullet point of ‘What Do These Findings Mean?’, please describe the main limitations of the study in non-technical language.

Introduction:

Line 66 - please temper assertions of primacy by adding ‘to the best of our knowledge’ or similar.

Methods:

Did your study have a prospective protocol or analysis plan? Please state this (either way) early in the Methods section. If a prospective analysis plan (from your funding proposal, IRB or other ethics committee submission, study protocol, or other planning document written before analyzing the data) was used in designing the study, please include the relevant prospectively written document with your revised manuscript as a Supporting Information file to be published alongside your study, and cite it in the Methods section. A legend for this file should be included at the end of your manuscript. If no such document exists, please make sure that the Methods section transparently describes when analyses were planned, and if/when reported analyses differed from those that were planned. Changes in the analysis-- including those made in response to peer review comments-- should be identified as such in the Methods section of the paper, with rationale. If a reported analysis was performed based on an interesting but unanticipated pattern in the data, please be clear that the analysis was data-driven.

Please ensure that the study is reported according to the RECORD guideline, and include the completed RECORD checklist as Supporting Information. Please add the following statement, or similar, to the Methods: "This study is reported as per the REporting of studies Conducted using Observational Routinely-collected health Data (RECORD) Statement (S1 Checklist)." The RECORD guideline can be found here: https://www.equator-network.org/reporting-guidelines/record/ When completing the checklist, please use section and paragraph numbers, rather than page numbers which will likely no longer correspond to the appropriate sections after copy-editing.

Please provide an ethics statement in your Methods section.

Results:

Line 143 - please provide a reference to Table S1 in which details of comorbidities are provided, and provide a few examples of these comorbidities in the main text

Lines 156-178 - please clarify what is meant by ' Significant adjusted VE estimates’ and ‘VE estimates were not significant’

Discussion:

Please present and organize the Discussion as follows: a short, clear summary of the article's findings; what the study adds to existing research and where and why the results may differ from previous research; strengths and limitations of the study; implications and next steps for research, clinical practice, and/or public policy; one-paragraph conclusion.

Please remove all subheadings within your Discussion e.g. Strengths and limitations

Figures:

Please provide titles and legends for all figures (including those in Supporting Information files).

Please indicate in the figure caption the meaning of the bars [and whiskers] in Figure 2.

Tables:

Please present numerators and denominators in your tables.

Please specify the variables controlled for in Tables 2, 3 and 4.

References:

Please ensure that journal name abbreviations match those found in the National Center for Biotechnology Information (NCBI) databases, and are appropriately formatted and capitalised.

Please also see https://journals.plos.org/plosmedicine/s/submission-guidelines#loc-references for further details on reference formatting.

Supplementary files:

Please provide titles and legends for each individual table in the Supporting Information.

Comments from the reviewers:

Reviewer #1: This is a very nice and important study that utilizes the power of the Danish health informatics system, and the decision to suspend the use of ChAdOx1, to assess the efficacy of the ChAdOx1/mRNA combination.

The results are important and valuable for global vaccine policy.

Points

- two different mRNA vaccines were used. Is there sufficient statistical power to assess if there is any difference between these ? They have different doses and there is a suggestion that Moderna may be more potent.

- the time interval between first and second dose if important for immune response. This appears to vary and I wonder if a plot of 'time between doses', with median and range, may be a useful addition?

- very minor corrections of English - eg use of double negative in last sentence.

Reviewer #2: This paper describes the effectiveness of a single dose of ChAdOx1 vaccination as well as ChAdOx1 followed by a mRNA vaccination. The findings from this study are important as countries are considering differing vaccination schedules and ways to conserve and share doses. Strengths of the study include its population based, large sample size, and near-complete capture of key data on infections, healthcare utilization, and vaccinations.

Specific comments for the authors:

Background - lines 56-57: "due to the present epidemiological situation" - not sure what this means? Because of the blood clot data - or because of patterns of SARS-CoV-2 circulation?

Assessment of exposure - lines 89-91: Individuals who exclusively received one or two doses of mRNA vaccines were excluded from analysis, correct?

Not sure what is meant by "western" and "non-western" heritage. Please explain further.

Results - lines 138-140: Is it correct that 7,809 individuals received one ChAdOx1 vaccine but did not go on to receive a second dose of any product? Or did some of these individuals receive a second dose of ChAdOx1? Were these individuals excluded from the analysis, or did they contribute to the one ChAdOx1 dose VE estimate? How many people in the population were unvaccinated or exclusively received mRNA vaccines? I think it's important to report the size of the unvaccinated sample since they are used as the comparison group.

Line 168: typographical error: "receptively" should be "respectively"

All-cause mortality: This seems a little problematic as an outcome in this VE analysis because it is a very non-specific outcome. Could the authors provide a little more explanation about why they chose to investigate this outcome? Did the authors believe that COVID-related deaths would be missed with their case definition (even though they report that testing was common in Denmark)? All-cause hospitalization also seems like a non-specific outcome.

COVID-19 hospitalizations and deaths based on positive PCR results prior to events - the authors note this as a limitation. Could diagnosis codes or cause of death have been incorporated to improve the specificity of the case definition?

In Table 1, it appears the authors are able to distinguish front-line personnel from other vaccine recipients. The authors note that front-line personnel may have different SARS-CoV-2 exposures and PPE use behaviors that might have impacted VE. Did the authors consider a sensitivity analysis limiting to front-line workers to see if that impacted their findings?

Table 1 - "median number of days to the first dose" - not sure what this means? Wasn't follow up time started at the date of the first dose?

Reviewer #3: See attachment

Any attachments provided with reviews can be seen via the following link:

[LINK]

Submitted filename: gram.pdf

Click here for additional data file.

7 Oct 2021

Submitted filename: Requests.docx

Click here for additional data file.

16 Nov 2021

Dear Dr. Gram,

Thank you very much for re-submitting your manuscript "Vaccine effectiveness against SARS-CoV-2 infection, hospitalization and death when combining a first dose ChAdOx1 vaccine with a subsequent mRNA vaccine in Denmark: a nationwide population-based cohort study" (PMEDICINE-D-21-03254R2) for consideration at PLOS Medicine.

I have discussed the paper with our academic editor and it was also seen again by one reviewer. I am pleased to tell you that, provided the remaining editorial and production issues are fully dealt with, we expect to be able to accept the paper for publication in the journal.

The remaining issues that need to be addressed are listed at the end of this email. Any accompanying reviewer attachments can be seen via the link below. Please take these into account before resubmitting your manuscript:

[LINK]

***Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out.***

In revising the manuscript for further consideration here, please ensure you address the specific points made by each reviewer and the editors. In your rebuttal letter you should indicate your response to the reviewers' and editors' comments and the changes you have made in the manuscript. Please submit a clean version of the paper as the main article file. A version with changes marked must also be uploaded as a marked up manuscript file.

Please also check the guidelines for revised papers at http://journals.plos.org/plosmedicine/s/revising-your-manuscript for any that apply to your paper. If you haven't already, we ask that you provide a short, non-technical Author Summary of your research to make findings accessible to a wide audience that includes both scientists and non-scientists. The Author Summary should immediately follow the Abstract in your revised manuscript. This text is subject to editorial change and should be distinct from the scientific abstract.

We hope to receive your revised manuscript within 1 week. Please email us (plosmedicine@plos.org) if you have any questions or concerns.

We ask every co-author listed on the manuscript to fill in a contributing author statement. If any of the co-authors have not filled in the statement, we will remind them to do so when the paper is revised. If all statements are not completed in a timely fashion this could hold up the re-review process. Should there be a problem getting one of your co-authors to fill in a statement we will be in contact. YOU MUST NOT ADD OR REMOVE AUTHORS UNLESS YOU HAVE ALERTED THE EDITOR HANDLING THE MANUSCRIPT TO THE CHANGE AND THEY SPECIFICALLY HAVE AGREED TO IT.

Please ensure that the paper adheres to the PLOS Data Availability Policy (see http://journals.plos.org/plosmedicine/s/data-availability), which requires that all data underlying the study's findings be provided in a repository or as Supporting Information. For data residing with a third party, authors are required to provide instructions with contact information for obtaining the data. PLOS journals do not allow statements supported by "data not shown" or "unpublished results." For such statements, authors must provide supporting data or cite public sources that include it.

To enhance the reproducibility of your results, we recommend that you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. Additionally, PLOS ONE offers an option to publish peer-reviewed clinical study protocols. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript.

Please note, when your manuscript is accepted, an uncorrected proof of your manuscript will be published online ahead of the final version, unless you've already opted out via the online submission form. If, for any reason, you do not want an earlier version of your manuscript published online or are unsure if you have already indicated as such, please let the journal staff know immediately at plosmedicine@plos.org.

Please let me know if you have any questions, and we look forward to receiving the revised manuscript.

Sincerely,

Richard Turner PhD, for Louise Gaynor-Brook, MBBS PhD

Senior Editor, PLOS Medicine

rturner@plos.org

------------------------------------------------------------

Requests from Editors:

To your data statement (submission form), please add a web address, for example, for those wishing to inquire about access to study data.

At line 37 and any other instances in the paper, please rephrase "heritage", "Western" and "non-Western" to avoid potential stigmatization. Are you able to substitute "Danes", "European migrants", "non-European migrants" and "others", for example?

At line 41, please adapt the final sentence of the "Methods and findings" subsection of your abstract to begin "Study limitations include ..." or similar.

At line 43, please remove the comma after "observed" and make that "large" rather than "high" (reduction).

At line 58 (author summary) please make that "... associated with estimated protection ...".

At line 68, please use the notation "... 4.1 million".

Please state explicitly in the Methods section (main text) that "The study did not have a prespecified analysis plan." or similar, assuming this is the case.

Please remove the statement on Data Availability from the Methods section (main text). In the event of publication, this information will appear in the article metadata, via entries in the submission form.

Throughout the text, please style reference call-outs as follows: "... platelet counts [3,4]." (noting the absence of spaces within the square brackets).

For reference 5 and other citations to the journal, "Lancet" will suffice as the journal name.

Please add "[Preprint]" to reference 6 and any other preprints that are cited, unless you are able to substitute the corresponding peer-reviewed publications.

Noting reference 7, please ensure that all references have full access details.

Thank you for including a completed RECORD checklist. Please break this out into a separate attachment, labelled "S1_RECORD_Checklist" or similar and referred to as such in your Methods section (main text).

Comments from Reviewers:

*** Reviewer #3:

The authors have addressed all my points and the study is much clearer now.

Michael Dewey

***

Any attachments provided with reviews can be seen via the following link:

[LINK]

18 Nov 2021

Submitted filename: Response to Editors.docx

Click here for additional data file.

24 Nov 2021

Dear Dr Gram,

On behalf of my colleagues and the Academic Editor, Dr Kretzschmar, I am pleased to inform you that we have agreed to publish your manuscript "Vaccine effectiveness against SARS-CoV-2 infection, hospitalization and death when combining a first dose ChAdOx1 vaccine with a subsequent mRNA vaccine in Denmark: a nationwide population-based cohort study" (PMEDICINE-D-21-03254R3) in PLOS Medicine.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. Please be aware that it may take several days for you to receive this email; during this time no action is required by you. Once you have received these formatting requests, please note that your manuscript will not be scheduled for publication until you have made the required changes.

Prior to final acceptance, please make the following minor changes:

At line 41 (abstract), we suggest adapting the text to "Study limitations including unmeasured ...";

The first paragraph of the Discussion (main text) should summarize the findings, and we therefore suggest incorporating a paragraph break at line 238 prior to "The VE of ...";

Reference 13 appears to be a preprint, and if so please add "[preprint]"; and

Noting reference 20, please ensure that all references have full access details.

In the meantime, please log into Editorial Manager at http://www.editorialmanager.com/pmedicine/, click the "Update My Information" link at the top of the page, and update your user information to ensure an efficient production process.

PRESS

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We also ask that you take this opportunity to read our Embargo Policy regarding the discussion, promotion and media coverage of work that is yet to be published by PLOS. As your manuscript is not yet published, it is bound by the conditions of our Embargo Policy. Please be aware that this policy is in place both to ensure that any press coverage of your article is fully substantiated and to provide a direct link between such coverage and the published work. For full details of our Embargo Policy, please visit http://www.plos.org/about/media-inquiries/embargo-policy/.

To enhance the reproducibility of your results, we recommend that you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. Additionally, PLOS ONE offers an option to publish peer-reviewed clinical study protocols. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols

Thank you again for submitting to PLOS Medicine. We look forward to publishing your paper.

Sincerely,

Richard Turner PhD, for Louise Gaynor-Brook, MBBS PhD

Senior Editor, PLOS Medicine

rturner@plos.org