key: cord-0257160-ga1fks7l
authors: Puhach, O.; Adea, K.; Hulo, N.; Sattonnet-Roche, P.; Genecand, C.; Iten, A.; Jacquerioz Bausch, F.; Kaiser, L.; Vetter, P.; Eckerle, I.; Meyer, B.
title: Infectious viral load in unvaccinated and vaccinated patients infected with SARS-CoV-2 WT, Delta and Omicron
date: 2022-01-11
journal: nan
DOI: 10.1101/2022.01.10.22269010
sha: 87243d13d75592dd36e74debf610dbd3388b8b5f
doc_id: 257160
cord_uid: ga1fks7l

Abstract Background Viral load (VL) is one determinant of secondary transmission of SARS-CoV-2. Emergence of variants of concerns (VOC) Alpha and Delta was ascribed, at least partly, to higher VL. Furthermore, with parts of the population vaccinated, knowledge on VL in vaccine breakthrough infections is crucial. As RNA VL is only a weak proxy for infectiousness, studies on infectious virus presence by cell culture isolation are of importance. Methods We assessed nasopharyngeal swabs of COVID-19 patients for quantitative infectious viral titres (IVT) by focus-forming assay and compared to overall virus isolation success and RNA genome copies. We assessed infectious viral titres during the first 5 symptomatic days in a total of 384 patients: unvaccinated individuals infected with pre-VOC SARS-CoV-2 (n= 118) or Delta (n= 127) and vaccine breakthrough infections with Delta (n= 121) or Omicron (n=18). Findings Correlation between RNA copy number and IVT was low for all groups. No correlation between IVTs and age or sex was seen. We observed higher RNA genome copies in pre-VOC SARS-CoV-2 compared to Delta, but significantly higher IVTs in Delta infected individuals. In vaccinated vs. unvaccinated Delta infected individuals, RNA genome copies were comparable but vaccinated individuals have significantly lower IVTs, and cleared virus faster. Vaccinated individuals with Omicron infection had comparable IVTs to Delta breakthrough infections. Interpretation Quantitative IVTs can give detailed insights into virus shedding kinetics. Vaccination was associated with lower infectious titres and faster clearance for Delta, showing that vaccination would also lower transmission risk. Omicron vaccine breakthrough infections did not show elevated IVTs compared to Delta, suggesting that other mechanisms than increase VL contribute to the high infectiousness of Omicron. Funding This work was supported by the Swiss National Science Foundation 196644, 196383, NRP (National Research Program) 78 Covid-19 Grant 198412, the Fondation Ancrage Bienfaisance du Groupe Pictet and the Fondation Privee des Hopitaux Universitaires de Geneve.

Background 29 Viral load (VL) is one determinant of secondary transmission of SARS-CoV-2. Emergence of variants of 30 concerns (VOC) Alpha and Delta was ascribed, at least partly, to higher VL. Furthermore, with parts of 31 the population vaccinated, knowledge on VL in vaccine breakthrough infections is crucial. As RNA VL 32 is only a weak proxy for infectiousness, studies on infectious virus presence by cell culture isolation 33 are of importance. 34

We assessed nasopharyngeal swabs of COVID-19 patients for quantitative infectious viral titres (IVT) 36 by focus-forming assay and compared to overall virus isolation success and RNA genome copies. We 37 assessed infectious viral titres during the first 5 symptomatic days in a total of 384 patients: 38 unvaccinated individuals infected with pre-VOC SARS-CoV-2 (n= 118) or Delta (n= 127) and vaccine 39 breakthrough infections with Delta (n= 121) or Omicron (n=18). 40

Correlation between RNA copy number and IVT was low for all groups. No correlation between IVTs 42 and age or sex was seen. We observed higher RNA genome copies in pre-VOC SARS-CoV-2 compared 43

to Delta, but significantly higher IVTs in Delta infected individuals. In vaccinated vs. unvaccinated Delta 44 infected individuals, RNA genome copies were comparable but vaccinated individuals have 45 significantly lower IVTs, and cleared virus faster. Vaccinated individuals with Omicron infection had 46

comparable IVTs to Delta breakthrough infections. 47 Introduction 60 As of 2 January 2021, the coronavirus disease 2019 (COVID-19) pandemic led to a total of nearly 289 61 million cases and just over 5.4 million deaths globally (1). Severe acute respiratory coronavirus 2 62 (SARS-CoV-2), the causative agent of COVID-19, primarily infects the cells of the upper respiratory 63 tract (URT) where it leads to an increasing viral load (VL) during the course of infection(2). 64

The two key parameters when assessing VL are either RNA genome copies, often expressed in cycle 65 threshold (Ct) values, or infectious virus that can only be assessed by virus isolation in cell culture. 66

Although the process of human-to-human transmission is complex, VL can serve as a proxy, with 67

higher VL posing a greater risk for onward transmission. In several epidemiological studies, higher viral 68 load expressed as viral RNA was associated with an increased secondary transmission in household 69

settings (3, 4) . Shedding of infectious SARS-CoV-2 in the URT starts on average two days prior to the 70 beginning of symptoms and gradually declines up to 8 days post onset of symptoms. Even though viral 71

RNA could be detected afterwards, in most studies infectious virus was not detected in respiratory 72 samples collected from immunocompetent individuals later than 8 days post onset of symptoms (5-73 9). Moreover, the detection of viral RNA does not correlate with infectiousness in an animal model 74 (10) . Instead, success of virus isolation in cell culture was found to be a proxy for detection of 75 infectious virus from respiratory specimens and the ability to shed and transmit fully competent viral 76 particles (8, 11, 12) . Virus isolation success can only give information about the presence or absence 77 of infectious virus, but is not able to quantify the infectious viral titre in samples of the URT (13). 78

Since the start of the pandemic, SARS-CoV-2 is constantly evolving, leading to the emergence of new 79

variants. While most variants vanished quickly, other such as D614G, and the designated variants of 80 concern (VOCs) Alpha, Beta, Gamma, Delta and Omicron harbour an apparent selection advantage 81 and manage to replace other existing variants locally or even globally. These VOCs exhibit various 82 mutations and amino acid alterations in viral proteins (14) is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted January 11, 2022. ; https://doi.org/10.1101 https://doi.org/10. /2022 of RNA viral loads was reported in vaccinated COVID-19 patients (BNT162b2 mRNA vaccine or  103 ChAdOx1 nCoV-19 (AZD1222) adenoviral vector vaccine), but no difference was observed at 6 months 104 post vaccination (26, 27) . Another study found reduced RNA viral load early after complete vaccination 105 when the Alpha VOC was prevalent, but no difference at later time points when the Delta VOC was 106 dominant (28). In addition, a study that investigated the kinetics of RNA viral load in COVID-19 patients 107 did not find a difference during the first 5 days post symptom onset, i.e. when most human-to-human 108 transmissions occur, but showed a faster decline of RNA viral load in vaccinated patients (29). 109

Similarly, a lower probability of virus isolation success was found in vaccinated vs unvaccinated 19 patients at the same RNA viral load indicating that vaccines can reduce the infectious viral load 111 (30). However, no study quantified infectious virus titres of different VOCs in URT samples of 112 vaccinated and unvaccinated COVID-19 patients. 113

Dynamics of infectious viral shedding in vaccinated and unvaccinated patients infected with relevant 114 SARS-CoV-2 variants of concern requires detailed investigation. Understanding of the SARS-CoV-2 viral 115

shedding in patients would help the implication of public health decisions to limit the transmission of 116 the virus in the community (31). Here we compare RNA and infectious viral load between pre-VOC 117 strains and Delta VOC in unvaccinated patients as well as in vaccination breakthrough infections due 118

to Delta and Omicron. Respiratory samples from mildly symptomatic patients of different age and sex, 119 sampled in the first five days post onset of symptoms were used for this study. By quantifying 120 infectious viral titres from URT specimens, we show that patients infected with SARS-CoV-2 Delta 121 variant of concern harbour elevated levels of infectious viral titres, while vaccination leads to a 122 reduction of infectious virus. 123 124

Participants 126

Nasopharyngeal swabs for diagnostics of SARS-CoV-2 by RT-PCR collected from symptomatic 128 individuals in the outpatient testing center of the Geneva University Hospital were included in this 129 study. Infection with SARS-CoV-2 was diagnosed by RT-PCR assay (Cobas 6800, Roche). All samples 130 originate from the diagnostic unit of the virology laboratory of the hospital and were received for 131 primary diagnosis of SARS-CoV-2. Remaining samples were stored at -80°C, usually on the same day 132 or within 24h. All samples had only one freeze-thaw cycle for the purpose of this study. All specimens 133 from vaccinated individuals were characterized by full genome sequencing for their infecting SARS-134

CoV-2 variant. Initial identification of the Omicron VOC was done by S gene target failure of the 135

TaqPath COVID19 assay (Thermofisher) and confirmed by partial Sanger sequencing of the Spike (32). 136

Final confirmation was done by next-generation sequencing. No sequence information was obtained 137

for patients infected with pre-VOC SARS-CoV-2, as all samples were collected in 2020, in a time period 138 before first detection of the VOCs in Switzerland. Clinical information of the patients was collected by 139 a standardized questionnaire in our testing Centre and/or through the Cantonal Health Service. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted January 11, 2022. ; https://doi.org/10. 1101 /2022 Viral loads in each sample were determined by quantitative real time PCR (RT-qPCR) using 143

SuperScript™ III Platinum™ One-Step qRT-PCR Kit (Invitrogen). RT-PCR for SARS-CoV-2 E gene and 144 quantification of genome copy number was performed as described previously (33). 145

Vero E6 and Vero E6-TMPRSS were cultured in complete DMEM GlutaMax I medium supplemented 147 with 10% fetal bovine serum, 1x Non-essential Amino Acids, and 1% antibiotics 148 (Penicillin/Streptomycin) (all reagents from Gibco, USA). Vero-TMPRSS were kindly received from 149

National Institute for Biological Standards and Controls (NIBSC, Cat. Nr. 100978). 150

Nasopharyngeal swab samples were serially diluted and applied on a monolayer of VeroE6 cells in 151 duplicates. Following 1 hour of incubation at 37°C, the virus-containing inoculum was removed and 152 the cells were overlaid with prewarmed medium mixed with 2·4% Avicel (DuPont) at a 1:1 ratio. Plates 153 were incubated at 37°C for 24 hours and then fixed using 6% paraformaldehyde for 1 hour at room 154 temperature. Cells were permeabilized with 0·1% Triton X-100 and blocked with 1% BSA (Sigma). 155

Plates were incubated with an anti-SARS-CoV monoclonal nucleocapsid protein primary antibody 156

targeting SARS-CoV-2 nucleocapsid protein (Geneva Antibody facility; JS02) for 1 hour at room 157 temperature and then with peroxidase-conjugated secondary antibody (Jackson ImmunoResearch, 158

#109-036-09) for 30 minutes at room temperature. Foci were visualized using True Blue HRP substrate 159

(Avantor) and imaged on an ELISPOT reader (CTL). Focus-forming assay for comparison of infectious 160 viral loads in Delta vs Omicron was performed in Vero E6-TMPRSS cells. 161

Nasopharyngeal samples were applied on the monolayer of Vero E6 cells in 24 well plates. 100 µl of 163 each sample was added and inoculated for 1 hour at 37°C. Following the incubation, the infectious 164 supernatant was discarded and virus culture medium was added. 50 µL of the medium was collected 165

to define the viral load at day 0. 3 to 4 days post inoculation the medium was replaced with fresh one, 166

and 6 days post infection the infectious medium was collected to define the viral load at day 6. The 167

change of viral load for at least 1 log of SARS-CoV-2 genome copies from day 0 till day 6 was considered 168 as successful isolation. 169

All statistical analyses were performed using R Statistical Software version 4.1.1 (Foundation for  171 Statistical 185 Computing, Austria) and Prism version 8.0.1 (GraphPad, San Diego, CA, USA). 172

The study was approved by the Cantonal ethics committee (CCER Nr. 2021-01488). All study 174 participants and/or their legal guardians provided informed consent. 175

In this study, we analysed the viral load characteristics in the URT of unvaccinated pre-VOC-as well as 177 vaccinated and unvaccinated Delta VOC-infected COVID-19 subjects up to 5 days post onset of 178 symptoms (DPOS). We included a total of 384 samples in our cohort of which 118 originated from 179 patients infected with pre-VOC SARS-CoV-2 and 248 from patients infected with the Delta VOC. Of the 180

Delta VOC infected patients, 121 were vaccinated twice prior infection and 127 were unvaccinated. In 181 . CC-BY-NC-ND 4.0 International license It is made available under a perpetuity.

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The copyright holder for this this version posted January 11, 2022. isolation success has been used as a correlate of infectious viral shedding for SARS-CoV-2(6, 36-38), 201 but lacks the ability to differentiate between high and low viral load samples. We were able to quantify 202 viral titres using the focus forming assay in 91·9%, 91·7% and 83·8% of culture positive samples in the 203

Pre-VOC, Delta and Delta vaccinated group, respectively, indicating a high sensitivity for our assay 204 ( Figure 1A) . Overall, the Cohens kappa agreement was 0·69, 0·71 and 0·53 for the 3 groups, showing 205 a moderate to substantial agreement (Figure 1 B) . 206

First, we investigated whether RNA genome copies are a good proxy for infectious virus shedding. We 208 observed only a very low correlation (R 2 = 0·119, p=0·0001) between viral genome copies and 209 infectious virus particles for pre-VOC samples (Figure 2 A) , while the samples from unvaccinated and 210

vaccinated Delta patients showed slightly higher, yet still low correlation (R 2 = 0·312, p <0·0001 and R 2 211 = 0·3962, p <0·0001, respectively) ( Figure 2B, C) . 212

Next, we tested if infectious viral loads from patient samples are associated with patient age and sex. 214 We did not observe any correlation between the age and infectious viral load for all three groups 215 (Supplementary figure S1) . Similarly, no significant differences of infectious viral loads between male 216 and female patients were detected for pre-VOC or Delta variant samples from vaccinated or 217 unvaccinated patients (Supplementary figure S2) . 218

Next, we compared genome copies and infectious viral loads in pre-VOC and Delta VOC samples from 220 unvaccinated patients during the first 5 symptomatic days. Overall, pre-VOC samples had significantly 221

higher genome copies (0·653 log, p<0·0001) compared to Delta VOC, but infectious viral titres were 222 . CC-BY-NC-ND 4.0 International license It is made available under a perpetuity.

is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted January 11, 2022. ; https://doi.org/10.1101/2022.01.10.22269010 doi: medRxiv preprint significantly higher in Delta VOC infected individuals (0·343 log, p=0·0373) ( Figure 3A ). When we 223

analysed the kinetics of viral shedding, we found that genome copies for pre-VOC samples were higher 224 at one and two dpos but similar to Delta VOC at 0, 3, 4, 5 dpos ( Figure 3B) . Conversely, infectious virus 225

shedding was higher for Delta VOC at 3-5 dpos, but similar at 0-2 dpos ( Figure 3C ). In addition, we 226 observed that genome copies remained largely stable until 5 dpos, with only a minimal decline at 5 227 dpos, while infectious viral load substantially declined ( Figure 3B and C) . 228

The association of the levels SARS-CoV-2 infectious shedding with patient age and sex is highly debated 229 (17). In this study we also did not detect a correlation between patients age or sex with their 230

infectiousness. However, there is increasing evidences of more severe outcomes of COVID-19 disease 231

in older male patients (36, 38, 39) . Thus, to eliminate possible confounders, 84 Delta infected patients 232

were matched with pre-VOC infected patients in regard to sex, age and dpos. Similarly, significantly 233

higher infectious viral loads (0·51 log, p=0·001170) were detected in Delta variant samples in 234 comparison to matched pre-VOC samples (Supplementary figure 3A) . 235

To determine the influence of vaccination on virus shedding, we compared genome copies and 237

infectious viral loads in unvaccinated and vaccinated patients infected with the Delta VOC during the 238 first 5 dpos. Overall, genome copies did not significantly differ between vaccinated and unvaccinated 239 patients, while infectious viral load was significantly decreased in vaccinated patients (0·68 log, 240 ****p<0.0001) ( Figure 4A ). The kinetics of RNA genome copies were largely similar between vaccinated 241 and unvaccinated patients with a slight trend of faster decline for vaccinated patients starting at 4 242 dpos ( Figure 4B ). In contrast, infectious viral titres were substantially lower in vaccinated patients at 243 all dpos with the biggest effect observed at 3-5 dpos ( Figure 4C) . Still, at 5 dpos we were able to detect 244 infectious virus in 7/13 (53·8%) vaccinated and 11/13 (84·6%) unvaccinated patients. Additionally, 67 245

Delta VOC infected patients were matched with Delta VOC vaccination breakthrough patients in 246 regard to age, sex and dpos. Infectious viral titres were elevated in unvaccinated patients in 247 comparison to vaccine breakthroughs (0·97 log, p<0·0001) (Supplementary figure 3B) confirming a 248 significant reduction of infectious viral titres among vaccinated patients. We further analysed if there 249 is a correlation between infectious viral titres and the time interval since the administration of the last 250 vaccine dose. We observed a high heterogeneity between patient samples, that resulted in no 251 significant correlation between the time post vaccination and infectious viral shedding 252 (Supplementary figure S4) . 253 infected patients, however this difference was not statistically significant (0·69 log, p= 0.1033) ( Figure  261 5). Same moderate but non-significant reduction of infectious viral titres was observed for Omicron 262 samples when matching patients for age, sex and dpos (Supplementary figure 3C) . is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

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In this study we analysed virus shedding in COVID-19 patients infected with pre-VOC, Delta VOC and 266

Omicron VOC SARS-CoV-2 and evaluated the impact of vaccination on viral load in the URT during the 267 first 5 dpos. To our knowledge, this is the first study which quantified infectious viral loads in patients 268

infected with different SARS-CoV-2 variants and vaccination breakthrough cases. We could 269 demonstrate a higher infectious viral load in unvaccinated Delta-infected compared to pre-VOC-270

infected patients and showed a significant reduction of infectious viral loads in vaccinated patients. 271

Furthermore, we found no difference in infectious viral load between Delta and Omicron 272 breakthrough cases. 273

Determining the magnitude and timing of infectiousness of COVID-19 patients is a key requirement to 274 make informed public health decisions on the duration of isolation of patients and on the need to 275 quarantine contacts. Infectiousness is strongly influenced by viral load in the URT of infected patients 276

(4). However, in most studies viral load is measured as RNA genome copies and not actual infectious 277

virus. In this study we could show that detection of RNA genome copies in URT swab samples is only 278

poorly correlated with infectious virus shedding. This is in line with several other studies that found 279 that RNA is a poor indicator of infectiousness especially in the presence of neutralising antibodies (12, 280 37).In addition, in a golden hamster animal model it was demonstrated that only infectious virus but 281 not RNA is a good proxy for onward transmission (10). 282

Virus isolation success in cell culture has been widely used as a proxy for infectiousness (6, 12, 33, 40). 283 Several studies have shown that virus isolation success significantly drops when RNA viral loads are 284 below 6 log10 copies per mL in viral transport medium, or collected later than 8 days post symptom 285 onset. Of note, with only a qualitative result on either successful isolation or not, overall virus isolation 286 success cannot distinguish between high and low infectious viral loads in a patient sample, a key 287 determinant of the size of the transmitted inoculum. Differences in infectious virus load however can 288

have an impact on transmission probability. Therefore, we decided to use a focus forming assay 289 instead that can reliably quantify infectious viral particles from original patient specimens. Focus 290 forming assays have long been used as a standard to quantify excretion of virus in animal infection 291 models for respiratory viruses such as SARS-CoV-2 and influenza virus and are therefore considered 292 one of the best available proxies for infectiousness (41, 42) . 293

Within the first 5 dpos, we found higher RNA genome copies in swabs of unvaccinated patients 294 infected with pre-VOC compared to Delta VOC, but infectious viral titres were higher for Delta VOC. 295

These results are in disagreement with other studies that analysed only nucleic acid detection and 296

found 3-10-fold higher RNA genome copies in Delta VOC infected patients compared to pre-VOC (18, 297 43). However, these studies did not control for days post symptom onset, age or sex. Other studies 298 found either no difference in RNA genome copies between Delta and pre-VOC swabs (44) occur for pre-VOC SARS-CoV-2 strains (5), indicating that a reduction of viral load could considerably 309 . CC-BY-NC-ND 4.0 International license It is made available under a perpetuity.

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The copyright holder for this this version posted January 11, 2022. ; https://doi.org/10.1101/2022.01.10.22269010 doi: medRxiv preprint contribute to a decreased secondary attack rate. Similar observations were made in other studies that 310 found no difference in RNA genome copies between vaccinated and unvaccinated early after symptom 311 onset (29, 30), but detected a lower probability of virus isolation success (30). Conversely, another 312 study detected up to 10-fold reduced RNA genome copies in vaccinated patients but only during the 313 first 60 days after complete vaccination (27). Similarly, two more studies reported decreased RNA 314 genome copies for vaccine breakthrough infection with pre-VOC and Alpha VOC SARS-CoV-2 (26), but 315 the effect vanished around 6 months post vaccination when Delta VOC was present (28). Of note, we 316

were still able to detect infectious viral particles in 53·8%% of vaccinated subjects at 5 dpos, indicating 317 that it might be beneficial is not shortened to 5 days as recently recommended by the CDC(49).. 318

Whether lower infectious viral load translates into lower secondary attack rate remains controversial 319 and depends on other influencing factors, i.e. environmental stability of virus particles. Several studies 320 did find a correlation between higher viral load and increased secondary attack rate, with viral load of 321 the index case being the leading driver of transmission (3, 4). In agreement with these finding, 322

epidemiological studies also showed reduced transmission rates when index cases were vaccinated, 323

but the effect size depends on the prevalent variant, the vaccine used and the time elapsed since 324 complete vaccination (22). In contrast, another study found that the vaccination status of the index 325 case did not influence the secondary attack rate (25). While VL is a key element of transmission, the 326 process of human-to-human transmission is complex and other factors, such as recommended 327

protection measures in a certain country at a certain time, overall incidence, perceived risks and the 328 context of contacts (household vs community transmission) can influence outcomes in the studies 329

reported. 330

To date, few data exist on viral load in vaccine breakthrough infections caused by the Omicron VOC 331 due to the recent emergence in late November 2021. Reduced neutralization of Omicron by infection-332

and vaccine-derived antibodies was reported in vitro and epidemiological studies show an increased 333 risk of (re-)infection with Omicron in vaccinated and previously infected individuals (50, 51). 334

Furthermore, very high transmissibility of Omicron breakthrough infections was observed, with high 335 secondary attack rates even among vaccinated individuals (52). Higher RNA viral loads as described in 336 some studies were discussed as one potential contributing factor for the emergence of Alpha and 337

Delta VOC, although for Delta we could only confirm this for infectious viral load in our data. The 338

contribution of VL to the high transmissibility of Omicron is not known so far, neither is the mechanism 339 behind higher transmissibility of Omicron. First in vitro data hint towards alternative entry 340 mechanisms as well as early replication peak in cell culture (53), but no clinical data for this 341 phenomenon exist so far. Our findings indicate that with comparable RNA viral load as well as 342 comparable infectious virus shedding, the higher transmissibility in Omicron doesn't seem to be 343 related to the shedding of an increased number of infectious viral particles in vaccinated individuals. 344

Our study has several limitations. We included only samples with Ct values below 27, collected during 345 the first 5 dpos but not afterwards. Therefore, absolute numbers on RNA copies are biased towards 346 higher viral loads as patients with low viral load were not included here. However, patients with low 347 viral load have likely little relevance in terms of transmission and other factors, such as poor swab 348 quality can be a confounding factor leading to low viral loads. Furthermore, our focus was on 349

infectious virus shedding and it has been shown that SARS-CoV-2 culture is unlikely to be successfully 350 from samples with higher Ct values (35) and that the vast majority of secondary transmission occurs 351 before 5 dpos although this needs to be formally assessed in Omicron cases (5). Due to its recent 352 emergence, we did not yet have access to samples from Omicron infected unvaccinated individuals. 353

Last, we also would like to emphasize that almost all patients in this study were vaccinated with mRNA 354 vaccines that induce high titres of neutralizing antibodies in the blood but relatively low mucosal 355 . CC-BY-NC-ND 4.0 International license It is made available under a perpetuity.

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The copyright holder for this this version posted January 11, 2022. ; https://doi.org/10.1101 https://doi.org/10. /2022 antibodies. Therefore, our results cannot be generalized to other vaccines, i.e. those that are used 356 mainly in low-and middle-income countries. 357

In conclusion, this study provides strong evidence for higher infectiousness of the Delta VOC as well 358 as a significantly lower infectiousness and a faster clearance of infectious virus in vaccinated 359

individuals. In addition, we could show that Omicron has similar infectious viral loads than Delta VOC. 360

Furthermore, we show a more detailed picture of viral load assessment in addition to overall virus 361 isolation success, and that quantifying viral loads can give better insights into viral shedding kinetics 362

in We thank all patients for their willingness to participate in our research. We thank the staff of the 371 laboratory of virology from the University Hospitals of Geneva for their support. 372 . CC-BY-NC-ND 4.0 International license It is made available under a perpetuity.

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The copyright holder for this this version posted January 11, 2022. ; https://doi.org/10.1101/2022.01.10.22269010 doi: medRxiv preprint VOC and Delta unvaccinated patients. Error bars indicate mean±SD. The t-test was used to 396 determined differences of means. *p=0·0373; **** p<0·0001. Genome copies (B) and infectious viral 397 loads (C) measured for pre-VOC and Delta VOC infected patients at different dpos. The solid lines 398 represent the fitted curve calculated using (locally estimated scatterplot smoothing) LOESS method. 399 . CC-BY-NC-ND 4.0 International license It is made available under a perpetuity.

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Laboratory Mice to SARS-CoV-2 with a Replication-Deficient Adenovirus Expressing Human 527 ACE2

Pathogenicity of 529 different PR8 influenza A virus variants in mice is determined by both viral and host factors

Infections caused by the Delta variant (B.1.617.2) of SARS-CoV-2 are 533 associated with increased viral loads compared to infections with the Alpha variant (B.1.1.7) 534 or non-Variants of Concern2021

Viral loads and 536 profile of the patients infected with SARS-CoV-2 Delta, Alpha, or R.1 variants in Tokyo

Duration of viral shedding 539 and culture positivity with post-vaccination SARS-CoV-2 delta variant infections

Transmission, viral kinetics and clinical 542 characteristics of the emergent SARS-CoV-2 Delta VOC

Isolation of 4000 SARS-CoV-2 545 shows that contagiousness is associated with viral load, not vaccine or symptomatic status

Infection with the 548 SARS-CoV-2 Delta Variant is Associated with Higher Recovery of Infectious Virus Compared 549 to the Alpha Variant in both Unvaccinated and Vaccinated Individuals. Clin Infect Dis. 2021. 550 49. Prevention CfDCa. CDC Updates and Shortens Recommended Isolation and Quarantine 551 Period for General Population

553 Increased risk of infection with SARS-CoV-2 Omicron compared to Delta in vaccinated and 554 previously infected individuals, the Netherlands

Increased risk of SARS-CoV-2 reinfection associated with emergence of the Omicron variant 558 in South Africa

Outbreak caused by the 560 SARS-CoV-2 Omicron variant in Norway

The SARS-CoV-2 563 variant, Omicron, shows rapid replication in human primary nasal epithelial cultures and 564 efficiently uses the endosomal route of entry