Determinants of protection against SARS-CoV-2 Omicron BA.1 and Delta infections in fully vaccinated outpatients (preprint)

We aimed to evaluate the association between the humoral and cellular immune responses and symptomatic SARS-CoV-2 infection with Delta or Omicron BA.1 variants in fully vaccinated outpatients. Anti-RBD IgG levels and IFN-{gamma} release were evaluated at PCR-diagnosis of SARS-CoV-2 in 636 samples from negative and positive patients during Delta and Omicron BA.1 periods. Median levels of anti-RBD IgG in positive patients were significantly lower than in negative patients for both variants (p < 0.05). The risk of Delta infection was inversely correlated with anti-RBD IgG titres (aOR = 0.63, 95% CI [0.41; 0.95], p = 0.03) and it was lower in the hybrid immunity group compared to the homologous vaccination group (aOR = 0.22, 95% CI [0.05; 0.62], p = 0.01). In contrast, neither the vaccination scheme nor anti-RBD IgG titers were associated with the risk of BA.1 infection in multivariable analysis. IFN-{gamma} release post-SARS-CoV-2 peptide stimulation was not different between samples from patients infected (either with Delta or Omicron BA.1 variant) or not (p = 0.77). Our results show that high circulating levels of anti-RBD IgG and hybrid immunity were independently associated with a lower risk of symptomatic SARS-CoV-2 infection in outpatients with differences according to the infecting variant.

Long-term humoral response following simultaneous Delta and Omicron BA.1 co-infection (preprint)

To provide insight into the long-term immune response following bivalent vaccines, we sampled vaccinated patients simultaneously co-infected with Delta and BA.1. We reported that simultaneous exposure to the Delta and BA.1 S protein does not confer an additional immune advantage compared to exposure to the Omicron BA.1 S protein alone.

SARS-CoV-2 spike 340 and 337 mutations in Omicron variants are selected after Sotrovimab infusion in immunocompromised patients (preprint)

After monoclonal antibody sotrovimab implementation, Rockett et al have warned on March 9th about two resistant mutations in the spike at position 337 and 340 occurring within the first week in four immunocompromised patients infected by a Delta variant and resulting in viable infection up to 25 days. As sotrovimab is currently the only effective treatment against BA.1 lineage of Omicron variant, we investigated the presence of these mutations in our 22,908 Omicron sequences performed from December 2021 to March 2022. Among 25 Omicron sequences with S:337 and S:340 substitutions, 9 were reported in six patients who had available clinical data and a follow up. All were immunicompromised, and presented a rapid selection of these mutations after sotrovimab monotherapy infusion. With these findings, we underscore that although these mutations are rare, they have been exclusively reported in immunocompromised patients treated with sotrovimab. We urge to consider monoclonal antibody as monotherapy in immunocompromised patients as a risk for escape mutants selection.

Detection and prevalence of SARS-CoV-2 co-infections during the Omicron variant circulation, France, December 2021 - February 2022 (preprint)

In Dec 2021-Feb 2022, an intense and unprecedented co-circulation of SARS-CoV-2 variants with high genetic diversity raised the question of possible co-infections between variants and how to detect them. Using 11 mixes of Delta:Omicron isolates at different ratios, we evaluated the performance of 4 different sets of primers used for whole-genome sequencing and we developed an unbiased bioinformatics method which can detect all co-infections irrespective of the SARS-CoV-2 lineages involved. Applied on 21,387 samples collected between weeks 49-2021 and 08-2022 from random genomic surveillance in France, we detected 53 co-infections between different lineages. The prevalence of Delta and Omicron (BA.1) co-infections and Omicron lineages BA.1 and BA.2 co-infections were estimated at 0.18% and 0.26%, respectively. Among 6,242 hospitalized patients, the intensive care unit (ICU) admission rates were 1.64%, 4.81% and 15.38% in Omicron, Delta and Delta/Omicron patients, respectively. No BA.1/BA.2 co-infections were reported among ICU admitted patients. Although SARS-CoV-2 co-infections were rare in this study, their proper detection is crucial to evaluate their clinical impact and the risk of the emergence of potential recombinants.

Evidence of co-infection during Delta and Omicron variants of concern co-circulation, weeks 49-2021 to 02-2022, France (preprint)

We report evidence of Delta/Omicron SARS-CoV-2 co-infections during the fifth wave of COVID-19 pandemics in France for 7 immunocompetent and epidemiologically unrelated patients. These co-infections were detected by PCR assays targeting SARS-CoV-2 S-gene mutations K417N and L452R and confirmed by whole genome sequencing which allowed the proportion estimation of each subpopulation. For 2 patients, the analyses of longitudinal samples collected 7 to 11 days apart showed that Delta or Omicron can outcompete the other variant during dual infection.

SARS-CoV-2 Omicron variant, lineage BA.1, is associated with lower viral load in nasopharyngeal samples compared to Delta variant. (preprint)

High viral load in upper respiratory tract specimens observed for Delta cases may contributed to its increased infectivity compared to the Alpha variant. Herein, we showed that the RT-PCR Ct values in Health Care Workers sampled within five days after symptom onset were significantly higher for Omicron cases than Delta cases (+2.84 Ct, p=0.008). This result comfort the studies showing that the increased transmissibility of Omicron is related to other mechanisms than higher virus excretion.

Evaluation of Commercial Anti-SARS-CoV-2 Neutralizing Antibody Assays in seropositive subjects (preprint)

The virus neutralization test (VNT) is the reference for the assessment of the functional ability of neutralizing antibodies (NAb) to block SARS-CoV-2 entry into cells. New competitive immunoassays measuring antibodies preventing interaction between the spike protein and its cellular receptor are proposed as surrogate VNT (sVNT). We tested three commercial sVNT (a qualitative immunochromatographic test and two quantitative immunoassays named YHLO and TECO) together with a conventional anti-spike IgG assay (bioMerieux) in comparison with an in-house plaque reduction neutralization test (PRNT50) using the original 19A strain and different variants of concern (VOC), on a panel of 306 sera from naturally-infected or vaccinated patients. The qualitative test was rapidly discarded because of poor sensitivity and specificity. Areas under the curve of YHLO and TECO assays were, respectively, 85.83 and 84.07 (p-value >0.05) using a positivity threshold of 20 for PRNT50, and 95.63 and 90.35 (p-value =0.02) using a threshold of 80. However, the performances of YHLO and bioMerieux were very close for both thresholds, demonstrating the absence of added value of sVNT compared to a conventional assay for the evaluation of the presence of NAb in seropositive subjects. In addition, the PRNT50 assay showed a reduction of NAb titers towards different VOC in comparison to the 19A strain that could not be appreciated by the commercial tests. Despite the good correlation between the anti-spike antibody titer and the titer of NAb by PRNT50, our results highlight the difficulty to distinguish true NAb among the anti-RBD antibodies with commercial user-friendly immunoassays.

Investigation of Vaccine Breakthrough Infections by Vaccine strategy during the Delta Variant Wave in France (preprint)

Herein, we describe the characteristics of vaccine breakthrough infections (VBI) in fully vaccinated individuals according to five vaccine strategies during the Delta wave in France. Inclusion criterion was a positive test at least 2 weeks after a full vaccine schedule: homologous vaccination with Pfizer-BioNTech (BNT162b2) or Moderna (mRNA-1273); heterologous vaccination with Astrazeneca and Pfizer-BioNTech (ChadOx1/BNT162b2); single-dose vaccines Johnson & Johnson (Ad26.COV2.S) or Astrazeneca (ChadOx1). A total of 1630 VBI from patients fully vaccinated between February and July were included in this study. SARS-CoV-2 sequencing performed for 1366 samples showed that the delta variant represented 94.1% (1286/1366). Delta-VBI were mainly symptomatic (mild symptoms) with no difference according to the vaccine strategy (p=0.362). The median RT-PCR Ct values at diagnosis were significantly different between symptomatic and asymptomatic cases only for BNT162b2 group (17.7 (15.07, 20.51) vs 19.00 (16.00, 23.00), p=0.004). Up to 50% of VBI was classified as early-VBI (infected less than one month after full immunization) for BNT162b2, mRNA-1273, ChadOx1, and J Ad26.COV2.S. People aged 14-49 yo were overrepresented in early VBI compared to non-early VBI for BNT162b2 and mRNA-1273 (73.92% vs 37.87% for BNT162b2 and 77.78% vs 46.67 % for mRNA-1273, p<0.05). Our data emphasize a high prevalence of Delta-VBI occurring only one month after full immunization in young patients that might be related to relaxation of barrier gestures.

Evaluation of commercial anti-SARS-CoV-2 antibody assays and comparison of standardized titers in vaccinated healthcare workers. (preprint)

With the availability of vaccines, commercial assays detecting anti-SARS-CoV-2 antibodies (Ab) evolved towards quantitative assays directed to the spike glycoprotein or its receptor binding domain (RBD). The main objective of the present study was to compare the Ab titers obtained with quantitative commercial binding Ab assays, after 1 dose (convalescent individuals) or 2 doses (naive individuals) of vaccine, in healthcare workers (HCW). Antibody titers were measured in 263 sera (from 150 HCW) with 5 quantitative immunoassays (Abbott RBD IgG II quant, bioMerieux RBD IgG, DiaSorin Trimeric spike IgG, Siemens Healthineers RBD IgG, Wantai RBD IgG). One qualitative total antibody anti RBD detection assay (Wantai) was used to detect previous infection before vaccination. The results are presented in binding Ab units (BAU)/mL after application, when possible, of a conversion factor provided by the manufacturers and established from a World Health Organization (WHO) internal standard. There was a 100% seroconversion with all assays evaluated after two doses of vaccine. With assays allowing BAU/ml correction, Ab titers were correlated ({rho}= 0.84-0.99). However, a significant difference between values persisted. The titer differences varied by a mean 3.04% between Siemens and bioMerieux assays to 50.54% between Siemens and DiaSorin assays. Titer harmonization is still to be improved despite better results were obtained between assays detecting the same Ab against the same antigen. The next step towards a true standardization of the assays would be to include the International Standard in the calibration of each assays to express the results in IU/mL.

Immunity to SARS-CoV-2 in a Dialyzed Patient Who Developed COVID-19 Twenty Days After the Second Dose of BNT162b2 Vaccine: a Case Report (preprint)

Introduction: End stage kidney disease (ESKD) and cancer have been identified as risk factors for severe and fatal cases of COVID-19, making vaccination in these patients a priority. Patients suffering from ESKD have a significantly weaker response to common vaccines than general population. However, humoral and cellular immune responses after two doses of RNA-based vaccine BNT162b2 (Pfizer–BioNTech) have been poorly explored in this vulnerable population.Case presentationA 69-year-old male patient was followed for ESKD and myeloma. He developed a severe SARS-CoV-2 pneumonia twenty days after two doses of BNT162b2 vaccine. Whole genome sequencing found that the virus belonged to the 20I/501Y.V1 clade. A serology draws eight days after the 2 nd vaccine dose showed positive RBD IgG without neutralizing activity. A serum specimen sampled thirty days after the onset of SARS-CoV-2 infection showed seroconversion against both RBD and N antigens. This specimen was shown to exhibit a frank neutralizing activity. The QuantiFERON® SARS-CoV-2 (Qiagen) showed a positive specific cellular response although the QuantiFERON monitor displayed a weak cellular response. ConclusionsImpaired immunity due to renal failure probably explain the severe pneumonia despite vaccination. The fact that the patient developpe a neutralizing activity and a cellular response after a third stimulation by infection may suggest to systemically administrate a third dose of vaccine in ESKD patients.

Live virus neutralization testing in convalescent and vaccinated subjects against 19A, 20B, 20I/501Y.V1 and 20H/501.V2 isolates of SARS-CoV-2 (preprint)

Background: SARS-CoV-2 mutations appeared recently and can lead to conformational changes in the spike protein and probably induce modifications in antigenicity. In this study, we wanted to assess the neutralizing capacity of antibodies to prevent cell infection, using a live virus neutralisation test. Methods: Sera samples were collected from different populations: two-dose vaccinated COVID-19-naive healthcare workers (HCWs; Pfizer-BioNTech BNT161b2), 6-months post mild COVID-19 HCWs, and critical COVID-19 patients. We tested various clades such as 19A (initial one), 20B (B.1.1.241 lineage), 20I/501Y.V1 (B.1.1.7 lineage), and 20H/501Y.V2 (B.1.351 lineage). Results: No significant difference was observed between the 20B and 19A isolates for HCWs with mild COVID-19 and critical patients. However, a significant decrease in neutralisation ability was found for 20I/501Y.V1 in comparison with 19A isolate for critical patients and HCWs 6-months post infection. Concerning 20H/501Y.V2, all populations had a significant reduction in neutralising antibody titres in comparison with the 19A isolate. Interestingly, a significant difference in neutralisation capacity was observed for vaccinated HCWs between the two variants whereas it was not significant for the convalescent groups. Conclusion: Neutralisation capacity was slightly reduced for critical patients and HCWs 6-months post infection. No neutralisation escape could be feared concerning the two variants of concern in both populations. The reduced neutralising response observed towards the 20H/501Y.V2 in comparison with the 19A and 20I/501Y.V1 isolates in fully immunized subjects with the BNT162b2 vaccine is a striking finding of the study.

Six-month antibody response to SARS-CoV-2 in healthcare workers assessed by virus neutralisation and commercial assays (preprint)

We conducted a prospective study in healthcare workers (n=296) of the University Hospital of Lyon, France. Serum samples (n=296) collected six months after disease onset were tested using three commercial assays: the Wantai Ab assay detecting total antibodies against the receptor binding domain (RBD) of the S protein, the bioMerieux Vidas assay detecting IgG to the RBD and the Abbott Architect assay detecting IgG to the N protein. The neutralising antibody (NAb) titre was also determined for all samples with a virus neutralisation assay (VNA) using live virus. The positivity rate was 100% with the Wantai assay, 84.8% with the bioMerieux assay and 55.4% with the Abbott assay. Only 51% of HCWs were positive for the presence of NAb. Less than 10 % of HCWs had a NAb titre greater than 80. At a neutralising titre of 80, the area under the curves [IC 95%] was 0.71 [0.62-0.81], 0.75 [0.65-0.85] and 0.95 [0.92-0.97] for Wantai, Abbott and Vidas respectively. The data presented herein suggest that commercial assays detecting antibodies against the N protein must not be used in long-term seroprevalence surveys while the Wantai assay could be useful for this purpose. VNA should remain the gold standard to assess the protective antibody response, but some commercial assays could be used as first-line screening of long-term presence of NAb.

Clinical and Microbiological Assessments of COVID-19 in Healthcare Workers: A Prospective Longitudinal Study (preprint)

Background: A comprehensive assessment of COVID-19 in healthcare workers (HCWs) including the investigation of viral shedding duration is critical.Methods: A longitudinal study including 319 HCWs was conducted. After SARS-CoV-2 screening with RT-PCR assay, other respiratory pathogens were tested with a multiplex molecular panel. For SARS-CoV-2 positive HCWs, the normalized viral load was determined weekly; viral culture and virus neutralization assay were also performed. For 190 HCWs tested negative for SARS-CoV-2, serological testing was performed one month after the inclusion.Findings: Of the 319 HCWs included, 67 (21.0%) were tested positive for SARS-CoV-2; two of them developed severe COVID-19. The proportion of smell and taste dysfunction was significantly higher in SARS-CoV-2 positive HCWs than in negative ones (38.8% vs 9.5% and 37.3% vs 10.7%, respectively, p<0.001). Of 67 positive patients, 9.1% were tested positive for at least another respiratory pathogen ( vs 19.5%, p=0.07). The proportion of HCWs with a viral load > 5.0 log 10 cp/ml (Ct value <25) was less than 15% at 8 days after symptom onset; 12% of them were still positive after 40 days (Ct >37). More than 90% of samples with cultivable virus had a viral load > 4.5 log 10 cp/ml (Ct < 26) and were collected within 10 days after symptom onset. From HCWs tested negative, 6/190 (3.2%) exhibited seroconversion for SARS-CoV-2 IgG antibodies.Interpretation: Our data suggest that the monitoring of normalized viral load (or its estimation through Ct values) can be useful for discontinuing isolation of HCWs and facilitating their safe return to work. HCWs presenting mild COVID-19 are unlikely infectious 10 days after symptom onset.Trial Registration: The clinical study registered on ClinicalTrial.gov (NCT04341142) has been fully detailed.Funding: Fondation des Hospices Civils de Lyon. bioMérieux provided diagnostic kits.Declaration of Interests: Several authors (KBP, FAF, GO, VC) are bioMérieux employees. AB has received a grant from bioMérieux and has served as consultant for bioMérieux. KBP, FAF, GO VC and AB were involved in data analysis, interpretation and wrote the article.Ethics Approval Statement: Written informed consent was obtained from all participants and approval was obtained from the national review board for biomedical research in April 2020 (Comité de Protection des Personnes Sud Méditerranée I, Marseille, France; ID RCB 2020-A00932-37).

Screening of the H69 and V70 deletions in the SARS-CoV-2 spike protein with a RT-PCR diagnosis assay reveals low prevalence in Lyon, France (preprint)

We report the implementation of a two-step strategy for the identification of SARS-CoV-2 variants carrying the spike deletion H69-V70 ({Delta}H69/{Delta}V70). This spike deletion resulted in a S-gene target failure (SGTF) of a three-target RT-PCR assay (TaqPath kit). Whole genome sequencing performed on 37 samples with SGTF revealed several receptor-binding domain mutations co-occurring with {Delta}H69/{Delta}V70. More importantly, this strategy enabled the first detection of the variant of concern 202012/01 in France on December 21th 2020. Since September a SARS-CoV-2 spike (S) deletion H69-V70 ({Delta}H69/{Delta}V70) has attracted increasing attention. This deletion was detected in the cluster-5 variant identified both in minks and humans in Denmark. This cluster-5 variant carries a receptor binding domain (RBD) mutation Y453F and was associated with reduced susceptibility to neutralizing antibodies to sera from recovered COVID-19 patients [1-3]. The {Delta}H69/{Delta}V70 has also co-occurred with two other RBD mutations of increasing interest [4]: N439K that is currently spreading in Europe and might also have reduced susceptibility to SARS-CoV-2 antibodies [5]; and N501Y that is part of the SARS-CoV-2 variant of concern (VOC) 202012/01 recently detected in England [6]. Although the impact of {Delta}H69/{Delta}V70 on SARS-CoV-2 pathogenesis is not clear, enhanced surveillance is urgently needed. Herein we report the implementation of a two-step strategy enabling a rapid detection of VOC 202012/01 or other variants carrying {Delta}H69/{Delta}V70.

Clinical and microbiological assessments of COVID-19 in healthcare workers: a prospective longitudinal study (preprint)

Background A comprehensive assessment of COVID-19 in healthcare workers (HCWs) including the investigation of viral shedding duration is critical. Methods A longitudinal study including 319 HCWs was conducted. After SARS-CoV-2 screening with RT-PCR assay, other respiratory pathogens were tested with a multiplex molecular panel. For SARS-CoV-2 positive HCWs, the normalized viral load was determined weekly; viral culture and virus neutralization assays were also performed. For 190 HCWs tested negative, SARS-CoV-2 serological testing was performed one month after the inclusion. Findings Of the 319 HCWs included, 67 (21.0%) were tested positive for SARS-CoV-2; two of them developed severe COVID-19. The proportion of smell and taste dysfunction was significantly higher in SARS-CoV-2 positive HCWs than in negative ones (38.8% vs 9.5% and 37.3% vs 10.7%, respectively, p<0.001). Of the 67 positive patients, 9.1% were tested positive for at least another respiratory pathogen (vs 19.5%, p=0.07). The proportion of HCWs with a viral load > 5.0 log10 cp/ml (Ct value <25) was less than 15% at 8 days after symptom onset; 12% of them were still positive after 40 days (Ct >37). More than 90% of culturable virus had a viral load > 4.5 log10 cp/ml (Ct < 26) and were collected within 10 days after symptom onset. From HCWs tested negative, 6/190 (3.2%) exhibited seroconversion for IgG antibodies. Interpretation Our data suggest that the determination of normalized viral load (or its estimation through Ct values) can be useful for discontinuing isolation of HCWs and facilitating their safe return to work. HCWs presenting mild COVID-19 are unlikely infectious 10 days after symptom onset.

A viral perspective on worldwide non-pharmaceutical interventions against COVID-19 (preprint)

Quantifying the effectiveness of large-scale non-pharmaceutical interventions (NPIs) against COVID-19 is critical to adapting responses against future waves of the pandemic. Most studies of NPIs thus far have relied on epidemiological data. Here, we report the impact of NPIs on the evolution of SARS-CoV-2, taking the perspective of the virus. We examined how variations through time and space of SARS-CoV-2 genomic divergence rates, which reflect variations of the epidemic reproduction number Rt, can be explained by NPIs and combinations thereof. Based on the analysis of 5,198 SARS-CoV-2 genomes from 57 countries along with a detailed chronology of 9 non-pharmaceutical interventions during the early epidemic phase up to May 2020, we find that home containment (35% Rt reduction) and education lockdown (26%) had the strongest predicted effectiveness. To estimate the cumulative effect of NPIs, we modelled the probability of reducing Rt below 1, which is required to stop the epidemic, for various intervention combinations and initial Rt values. In these models, no intervention implemented alone was sufficient to stop the epidemic for Rt’s above 2 and all interventions combined were required for Rt’s above 3. Our approach can help inform decisions on the minimal set of NPIs required to control the epidemic depending on the current Rt value.

Evaluation of high-throughput SARS-CoV-2 serological assays in a longitudinal cohort of mild COVID-19 patients: sensitivity, specificity and association with virus neutralization test (preprint)

ObjectivesWe evaluated widely-used SARS-CoV-2 serological tests and their potential association with virus neutralization test (VNT) in a cohort of mild COVID-19 patients. MethodsA total of 439 specimens were longitudinally collected from 76 healthcare workers with RT-PCR-confirmed mild COVID-19. Nine serological assays developed by leading global companies (Abbott, DiaSorin, Siemens, Bio-Rad, Wantai, bioMerieux, Euroimmun) were assessed. For each test the sensitivity to detect SARS-CoV-2 antibodies was determined weekly after symptom onset. Correlation and concordance were assessed using the Spearman and Cohens Kappa coefficients, respectively. Positive percent agreement and negative percent agreement (NPA) with the VNT were also determined. ResultsThe Wantai Total Ab assay targeting the receptor binding domain (RBD) within the S protein presented the best sensitivity at different times during the course of disease. The best correlation between antibody level and neutralizing antibody titer was found with the Euroimmun S1-based IgA assay (Spearman coefficient [95%CI]: 0.71 [0.61-0.79]). A moderate concordance (Kappa [95%CI]: 0.43[0.23-0.63]) as well as the lowest NPA (33%) was found between the Wantai Total Ab assay and the VNT. Compared to the Wantai Total Ab assay, other total Ab or IgG assays targeting the S or the RBD (bioMerieux, DiaSorin, Siemens,) were more concordant with the VNT (Kappa>0.7 for the three tests) and had a higher NPA (range: 90% to 97%). ConclusionsAlthough some assays presented a better concordance with VNT than others, the present findings emphasize that commercialized serological tests including those targeting the RBD cannot substitute VNT for the assessment of functional antibody response.

SARS-CoV-2 phylodynamics differentiates the effectiveness of non-pharmaceutical interventions (preprint)

Quantifying the effectiveness of large-scale non-pharmaceutical interventions against COVID-19 is critical to adapting responses against future waves of the pandemic. By combining phylogenetic data of 5,198 SARS-CoV-2 genomes with the chronology of non-pharmaceutical interventions in 57 countries, we examine how interventions and combinations thereof alter the divergence rate of viral lineages, which is directly related to the epidemic reproduction number. Home containment and education lockdown had the largest independent impacts and were predicted to reduce the reproduction number by 35% and 26%, respectively. However, we find that in contexts with a reproduction number >2, no individual intervention is sufficient to stop the epidemic and increasingly stringent intervention combinations may be required. Our phylodynamic approach can complement epidemiological models to inform public health strategies against COVID-19.

Characterization of SARS-CoV-2 ORF6 deletion variants detected in a nosocomial cluster during routine genomic surveillance, Lyon, France (preprint)

Through routine genomic surveillance of the novel SARS-CoV-2 virus (n=229 whole genome sequences), 2 different frameshifting deletions were newly detected in the open reading frame (ORF) 6, starting at the same position (27267). While the 26-nucleotide deletion variant was only found in one sample in March 2020, the 34-nucleotide deletion variant was found within a single geriatric hospital unit in 5/9 patients sequenced and one health care worker with samples collected between April 2nd and 9th, 2020. Both the presence of the 34-nucleotide deletion variant limited to this unit and the clustering of the corresponding whole genome sequences by phylogeny analysis strongly suggested a nosocomial transmission between patients. Interestingly, prolonged viral excretion of the 34-nucleotide deletion variant was identified in a stool sample 14 days after initial diagnosis for one patient. Clinical data revealed no significant difference in disease severity between patients harboring the wild-type or the 34-nucleotide deletion variants. The in vitro infection of the two deletion variants on primate endothelial kidney cells (BGM) and human lung adenocarcinoma cells (Calu-3) yielded comparable replication kinetics with the wild-type strain. Furthermore, high viral loads were found in vivo regardless of the presence or absence of the ORF6 deletion. Our study highlights the transmission and replication capacity of two newly described deletion variants in the same ORF6 region. ImportanceWhile the SARS-CoV-2 genome has remained relatively stable since its emergence in the human population, genomic deletions are an evolutionary pattern previously described for the related SARS-CoV. Real-time genomic monitoring of the circulating variants is paramount to detect strain prevalence and transmission dynamics. Given the role of ORF6 in interferon modulation, further characterization, such as mechanistic interactions and interferon monitoring in patients, is crucial in understanding the viral-host factors driving disease evolution.