Is vaccine response to SARS-CoV-2 preserved after switching to anti-CD20 therapies in patients with multiple sclerosis or related disorders?

BACKGROUND

Although vaccination against SARS-CoV-2 is recommended prior to introducing anti-CD20 therapies, limited data are available regarding the evolution of post-vaccinal immunity.

METHODS

This retrospective study compared anti-Spike antibody titres at 6 and 12 months from SARS-CoV-2 vaccination between patients vaccinated before switching to anti-CD20 ('Switch') and two control groups: (1) patients vaccinated under disease-modifying therapies (DMTs) other than fingolimod and anti-CD20 ('Other DMTs'); (2) patients vaccinated on anti-CD20 ('Anti-CD20'). Anti-Spike-specific T-cell responses were compared between 'Switch' and 'Anti-CD20' groups.

RESULTS

Fifty-three patients were included in the 'Switch' group, 54 in the 'Other DMTs' group and 141 in the 'Anti-CD20' group. At 6 months, in the subset of patients who received a booster dose, the 'Switch' group had lower anti-Spike titres compared with the 'Other DMTs' group (median 241.0 IQR (88.0; 504.0) BAU/mL vs 2034 (1155; 4634) BAU/mL, p<0.001), and less patients in the 'Switch' group reached the protective threshold of 264 BAU/mL. The 'Switch' group had higher anti-Spike titres than the 'Anti-CD20' group (7.5 (0.0; 62.1) BAU/mL, p=0.001). Anti-Spike titres were not different between the 'Switch' and 'Other DMTs' groups before booster administration. These results were similar at 12 months. Spike-specific T-cell positivity was similar between the 'Switch' and 'Anti-CD20' groups at 6 and 12 months (60.4% vs 61.0%, p=0.53, and 79.4% vs 87.5%, p=0.31, respectively).

CONCLUSIONS

Despite a primary vaccination performed before the first anti-CD20 cycle, our results suggest weaker immune responses at 6 and 12 months and decreased booster efficacy after introducing anti-CD20. Patients vaccinated prior to anti-CD20 introduction might falsely be considered as fully protected by vaccination.

Intermittent doravirine/lamivudine/tenofovir disoproxil fumarate (DOR/3TC/TDF) maintains a high level of viral suppression in virologically suppressed people living with HIV

INTRODUCTION

We aimed to determine whether doravirine/lamivudine/tenofovir disoproxil fumarate (DOR/3TC/TDF) given 5 or 4 days a week was able to maintain viral suppression in people living with HIV (PLHIV).

METHODS

In this observational, retrospective study, we included all PLHIVs who had received intermittent DOR/3TC/TDF between 10/01/2019 and 01/31/2021, in two French hospitals.

RESULTS

Forty-three PLHIVs were included, median (IQR) age: 52 years (48-58), ART duration: 15 years (8-23), duration of virological suppression: 6 years (2-10). Median follow-up was 78 weeks (IQR 62-97). One virological failure (VF) occurred at W38 (HIV-RNA = 61 and 76 copies/mL), in a patient with no viral resistance at baseline or at time of VF, and during the study period five individuals discontinued DOR/3TC/TDF due to adverse events. There were no significant changes during follow-up in the CD4 count, CD4/CD8 ratio, body weight or residual viremia rate.

CONCLUSION

These findings suggest the potential for intermittent DOR/3TC/TDF to maintain virological control.

Doravirine plus lamivudine two-drug regimen as maintenance antiretroviral therapy in people living with HIV: a French observational study

BACKGROUND

Two-drug regimens based on integrase strand transfer inhibitors (INSTIs) and boosted PIs have entered recommended ART. However, INSTIs and boosted PIs may not be suitable for all patients. We aimed to report our experience with doravirine/lamivudine as maintenance therapy in people living with HIV (PLWH) followed in French HIV settings.

METHODS

This observational study enrolled all adults who initiated doravirine/lamivudine between 1 September 2019 and 31 October 2021, in French HIV centres participating in the Dat'AIDS cohort. The primary outcome was the rate of virological success (plasma HIV-RNA < 50 copies/mL) at Week (W)48. Secondary outcomes included: rate of treatment discontinuation for non-virological reasons, evolution of CD4 count and CD4/CD8 ratio over follow-up.

RESULTS

Fifty patients were included, with 34 (68%) men; median age: 58 years (IQR 51-62), ART duration: 20 years (13-23), duration of virological suppression: 14 years (8-19), CD4 count: 784 cells/mm3 (636-889). Prior to switching, all had plasma HIV-RNA < 50 copies/mL. All but three were naive to doravirine, and 36 (72%) came from a three-drug regimen. Median follow-up was 79 weeks (IQR 60-96). Virological success rate at W48 was 98.0% (95% CI 89.4-99.9). One virological failure occurred at W18 (HIV-RNA = 101 copies/mL) in a patient who briefly discontinued doravirine/lamivudine due to intense nightmares; there was no resistance at baseline and no resistance emergence. There were three strategy discontinuations for adverse events (digestive disorders: n = 2; insomnia: n = 1). There was no significant change in CD4/CD8 ratio, while CD4 T cell count significantly increased.

CONCLUSIONS

These preliminary findings suggest that doravirine/lamivudine regimens can maintain high levels of viral suppression in highly ART-experienced PLWH with long-term viral suppression, and good CD4+ T cell count.

Four days/week antiretroviral maintenance strategy (ANRS 170 QUATUOR): substudies of reservoirs and ultrasensitive drug resistance

BACKGROUND

In a 4 days/week (4/7 days) maintenance strategy (ANRS-170 QUATUOR trial), the virological impact of an intermittent strategy was assessed by ultrasensitive virological analyses of reservoirs and resistance.

METHODS

HIV-1 total DNA, ultra-sensitive plasma viral load (USpVL) and semen VL were measured in the first 121 participants. Sanger and ultra-deep sequencing (UDS) were performed on the HIV-1 genome (Illumina technology) according to the ANRS consensus. A generalized estimation equation with a Poisson distribution was used to compare changes in the proportion of residual viraemia, detectable semen HIV RNA and HIV DNA within and between the two groups over time.

RESULTS

The proportion of participants with residual viraemia at Day 0 (D0) and Week 48 (W48) was 16.7% and 25.0% in the 4/7 days group and 22.4% and 29.7% in the 7/7 days group, respectively (+8.3% versus +7.3%, P = 0.971). The proportion of detectable DNA (>40 copies/106 cells) at D0 and W48 was 53.7% and 57.4% in the 4/7 days group and 56.1% and 51.8% in the 7/7 days group, respectively (+3.7% versus -4.3%, P = 0.358). Semen HIV RNA was detectable (≥100  copies/mL) in 2.2% of participants at D0 and 4.5% at W48 in the 4/7 days group versus 6.1% and 9.1% in the 7/7 days group, respectively (+2.3% versus +3.0%, P = 0.743). Emerging resistance at failure was more frequent in the 4/7 days group detected by Sanger sequencing: 3/6 participants versus 1/4 in the 7/7 days group, and similar with the UDS assay: 5/6 versus 4/4, respectively.

CONCLUSIONS

These findings support the potency of a 4/7 days maintenance strategy on virological suppression at the reservoirs and emergent resistance level, including minority variants.

Intermittent Bictegravir/Emtricitabine/Tenofovir Alafenamide Treatment Maintains High Level of Viral Suppression in Virally Suppressed People Living with HIV

In this observational study, we aimed to evaluate whether bictegravir/emtricitabine/tenofovir alafenamide (B/F/TAF) administered 5 or 4 days a week is able to maintain viral suppression in people living with HIV (PLHIV). We enrolled 85 patients who initiated intermittent B/F/TAF between 28 November 2018 and 30 July 2020: median (IQR) age 52 years (46–59), duration of virological suppression 9 years (3–13), CD4 633/mm3 (461–781). Median follow-up was 101 weeks (82–111). The virological success rate (no virological failure [VF]: confirmed plasma viral load [pVL] ≥ 50 copies/mL, or single pVL ≥ 200 copies/mL, or ≥50 copies/mL with ART change) was 100% (95%CI 95.8–100) and the strategy success rate (pVL < 50 copies/mL with no ART regimen change) was 92.9% (95%CI 85.3–97.4) at W48. Two VF occurred at W49 and W70, in 2 patients self-reporting poor compliance. No resistance mutation emerged at time of VF. Eight patients presented strategy discontinuation for adverse events. There was no significant change in the CD4 count, residual viraemia rate, neither body weight during follow-up, but a slight increase in CD4/CD8 ratio (p = 0.02). In conclusion, our findings suggest that B/F/TAF administered 5 or 4 days a week could maintain the control of HIV replication in virologically suppressed PLHIV while reducing cumulative exposition of ART.

Prolonged replication of BA.1 and BA.2 Omicron lineages compared to Delta variant in nasopharyngeal samples from COVID-19 patients

OBJECTIVES

We aimed to characterize and compare the viral loads (VL) of the Omicron BA.1 and BA.2 lineages and the Delta variant in nasopharyngeal samples from newly diagnosed COVID-19 patients and their kinetics over time.

PATIENTS AND METHODS

The kinetics of the VL were measured on the CT data from 215 SARS-CoV-2 positive patients who presented at least two positive PCRs a day apart and were screened for SARS-CoV-2 viral lineages.

RESULTS

We observed no significant difference in median CT value during the first diagnostic test between the Delta variant and the two Omicron lineages. However, the kinetics of CT decreases for the BA.1 and BA.2 lineage were significantly lengthier in time than the kinetics for the Delta variant. The BA.2 lineage presented lower median CT value (-2 CT) (inversely proportional to the VL) than the BA.1 lineage.

CONCLUSIONS

BA.2 Omicron lineage presented higher VL than BA.1 Omicron lineage at diagnostic. Omicron BA.1 and BA.2 lineages have more prolonged replication than the Delta variant.

More HIV-1 RNA detected and quantified with the Cobas 6800 system in patients on antiretroviral therapy

BACKGROUND

Target-detected (TD) results or low-level viraemia (LLV) can be observed in HIV-1 patients on ART, which regularly raises questions.

OBJECTIVES

We describe here the impact on HIV-1 RNA quantification of switching from the COBAS AmpliPrep/COBAS TaqMan (CAP/CTM) to the Cobas 6800 system (C6800), based on analyses of viraemia close to the lower limit of quantification (LLoQ).

PATIENTS AND METHODS

We retrospectively selected two groups of patients: 200 individuals whose viral loads (VLs) were consistently <50 copies/mL with CAP/CTM for at least 3 years before switching to C6800 (group 1), and 35 other patients with confirmed LLV when C6800 was in use (group 2). In both groups, we compared several consecutive VL results performed before and after the change of quantification assay. Analyses were performed with McNemar's paired tests or Fisher's exact tests.

RESULTS

In group 1, the frequency of TD results (below or above the LLoQ) increased significantly after the switch to C6800 for patients with <25% of results being TD for VLs performed with CAP/CTM (P < 0.0001). Significantly more patients had at least one VL ≥20 or ≥50 copies/mL with C6800, in both group 1 (37.0% versus 18.5%; P < 0.0001 and 6.5% versus 0%; P = 0.0009, respectively) and group 2 (100% versus 66%; P = 0.0015 and 97% versus 40%; P < 0.0001, respectively).

CONCLUSIONS

C6800 revealed residual or low-level HIV-1 RNA that was not detected with CAP/CTM, resulting in twice as many patients being found to have a VL ≥20 copies/mL. Physicians and patients should be aware of possible differences in results between assays, and it is crucial to specify the quantitative assay used in studies.

Long-term evolution of humoral immune response after SARS-CoV-2 infection

Objective

We aimed to characterize the evolution of humoral immune response up to 1 year after SARS-CoV-2 infection in healthcare workers (HCWs) during the first wave of COVID-19 in Paris.

Methods

Serum samples from 92 HCWs were tested at month 0 (M0), M6, and M12 after SARS-CoV-2 infection for IgG targeting the nucleocapsid (N), IgG targeting the receptor-binding domain (RBD) of spike (S) protein, IgA targeting S, and anti-RBD neutralizing antibodies. After M6, 46 HCWs received a single dose of COVID-19 vaccine.

Results

We observed a significant decrease in all SARS-CoV-2 immunologic markers at M6 post-infection: median decreases were 0.26 log binding antibody units/mL (M0: 1.9 (interquartile range (IQR) 1.47–2.27); M6: 1.64 (IQR 1.22–1.92)) for anti-RBD IgG; 4.10 (index) (M0: 4.94 (IQR 2.72–6.82); M6: 0.84 (IQR 0.25–1.55)) for anti-N IgG; 0.64 (index) (M0: 2.50 (IQR 1.18–4.62); M6: 1.86 (IQR 0.85–3.54)) for anti-S IgA; and 24.4% (M0: 66.4 (IQR 39.7–82.5); M6: 42.0 (IQR 16.8–68.8)) inhibition activity for the RBD neutralizing antibodies. Between M6 and M12, anti-RBD IgG level, anti-S IgA index, and anti-RBD neutralizing activity significantly increased among COVID-19 vaccinated HCWs, whereas they remained stable among unvaccinated HCWs. Anti-N IgG index significantly decreased between M6 and M12 among both vaccinated (median: 0.73 (IQR 0.23–1.11) at M6 and 0.52 (IQR 0.20–0.73) at M12) and unvaccinated HCWs (median: 0.79 (IQR 0.21–4.67) at M6 and 0.34 (IQR 0.24–2.78) at M12).

Discussion

A steady decline in the anti-N IgG response was observed during the first year after SARS-CoV-2 infection among HCWs, whereas the anti-RBD IgG and the anti-S IgA responses remained stable and could be enhanced by COVID-19 vaccination.

Long COVID-19 symptoms: clinical characteristics and recovery rate among non-severe outpatients over a six-month follow-up

Background

To describe persistent symptoms in long COVID-19 non-severe outpatients and report the 6-month clinical recovery (CR) rate.

Methods

Observational study enrolling outpatients (≥ 18 years) with confirmed non-severe COVID-19 (positive nasopharyngeal RT-PCR or presence of SARS-CoV-2 antibodies) who consulted for persistent symptoms after the first pandemic wave (March-May 2020). CR was assessed at the 6-month visit and defined as complete (no symptom), partial (persistent symptoms of lower intensity) or lack of recovery (no improvement).

Results

Sixty-three patients (79% women, mean age: 48 years) enrolled; main symptoms (mean 81 days after acute infection): asthenia/myalgia (77%), dyspnea (51%), headaches (35%), cough (33%). At 6 months (n = 56), 30% had complete, 57% partial, and 13% lack of recovery. The proportion of patients with > 2 persistent symptoms was 26% at 6 months (main symptoms: dyspnea [54%] and asthenia/myalgia [46%]).

Conclusion

We observed a slow but high recovery rate at 6 months among these outpatients.

Anti-CD20 therapies decrease humoral immune response to SARS-CoV-2 in patients with multiple sclerosis or neuromyelitis optica spectrum disorders

BACKGROUND

SARS-CoV-2 seroconversion rate after COVID-19 may be influenced by disease-modifying therapies (DMTs) in patients with multiple sclerosis (MS) or neuromyelitis optica spectrum disorders (NMO-SD).

OBJECTIVE

To investigate the seroprevalence and the quantity of SARS-CoV-2 antibodies in a cohort of patients with MS or NMO-SD.

METHODS

Blood samples were collected in patients diagnosed with COVID-19 between 19 February 2020 and 26 February 2021. SARS-CoV-2 antibody positivity rates and Ig levels (anti-S IgG titre, anti-S IgA index, anti-N IgG index) were compared between DMTs groups. Multivariate logistic and linear regression models were used to estimate the influence of DMTs and other confounding variables on SARS-CoV-2 serological outcomes.

RESULTS

119 patients (115 MS, 4 NMO, mean age: 43.0 years) were analysed. Overall, seroconversion rate was 80.6% within 5.0 (SD 3.4) months after infection. 20/21 (95.2%) patients without DMT and 66/77 (85.7%) patients on DMTs other than anti-CD20 had at least one SARS-CoV-2 Ig positivity, while this rate decreased to only 10/21 (47.6%) for patients on anti-CD20 (p<0.001). Being on anti-CD20 was associated with a decreased odd of positive serology (OR, 0.07 (95% CI 0.01 to 0.69), p=0.02) independently from time to COVID-19, total IgG level, age, sex and COVID-19 severity. Time between last anti-CD20 infusion and COVID-19 was longer (mean (SD), 3.7 (2.0) months) in seropositive patients compared with seronegative patients (mean (SD), 1.9 (1.5) months, p=0.04).

CONCLUSIONS

SARS-CoV-2 antibody response was decreased in patients with MS or NMO-SD treated with anti-CD20 therapies. Monitoring long-term risk of reinfection and specific vaccination strategies in this population may be warranted.

TRIAL REGISTRATION NUMBER

NCT04568707.

SARS-CoV-2 infection in patients with primary central nervous system lymphoma

BACKGROUND

Cancer patients may be at higher risk for severe coronavirus infectious disease-19 (COVID-19); however, the outcome of Primary Central Nervous System Lymphoma (PCNSL) patients with SARS-CoV-2 infection has not been described yet.

METHODS

We conducted a retrospective study within the Lymphomes Oculo-Cérébraux national network (LOC) to assess the clinical characteristics and outcome of SARS-CoV-2 infection in PCNSL patients (positive real-time polymerase chain reaction of nasopharyngeal swab or evocative lung computed tomography scan). We compared clinical characteristics between patients with severe (death and/or intensive care unit admission) and mild disease.

RESULTS

Between March and May 2020, 13 PCNSL patients were diagnosed with SARS-CoV-2 infection, 11 (85%) of whom were undergoing chemotherapy at the time of infection. The mortality rate was 23% (3/13), and two additional patients (15%) required mechanical ventilation. Two patients (15%) had no COVID-19 symptoms. History of diabetes mellitus was more common in severe patients (3/5 vs 0/8, p = 0.03). Two patients recovered from COVID-19 after mechanical ventilation during more than two weeks and resumed chemotherapy. In all, chemotherapy was resumed after COVID-19 recovery in nine patients (69%) after a median delay of 16 days (range 3-32), none of whom developed unusual chemotherapy complication nor SARS-Cov2 reactivation.

CONCLUSION

This preliminary analysis suggests that, while being at higher risk be for severe illness, PCNSL patients with COVID-19 might be treated maximally especially if they achieved oncological response at the time of SARS-CoV-2 infection. Chemotherapy might be resumed without prolonged delay in PCNSL patients with COVID-19.

Kinetics of archived M184V mutation in treatment-experienced virally suppressed HIV-infected patients

BACKGROUND

We aimed to assess the kinetics of drug-resistant viral variants (DRVs) harboring the M184V mutation in the proviral DNA of long-term virally suppressed patients, and factors associated with DRV persistence.

METHODS

HIV-DNA from blood cells stored in 2019 and 2016 was sequenced using both Sanger and ultradeep sequencing (SS and UDS, with a detection threshold of 1%) in ART-treated patients with HIV-RNA <50 copies/mL for at least 5 years, with past M184V mutation documented in HIV-RNA.

RESULTS

Among the 79 tested patients, by combining SS and UDS, the M184V was found to be absent in 26/79 (33%) patients (M184V- patients), and persisted in 53/79 (67%) (M184V+ patients). The M184V+ patients had a longer history of ART, a lower CD4 nadir and higher pretherapeutic HIV-RNA. Among the 37 patients with viral sequences assessed by UDS, the proportion of M184V+ DRVs significantly decreased between 2016 and 2019 (40% versus 14%, p=0.005). The persistence of M184V was associated with the duration and level of HIV-RNA replication under 3TC/FTC (p=0.0009 and p=0.009, respectively).

CONCLUSION

While it decreased over time in HIV-DNA, the M184V mutation was more frequently persistent in the HIV-DNA of more experienced patients with longer past replication under 3TC/FTC.

Presence of HIV-1 G-to-A mutations linked to APOBEC editing is more prevalent in non-B HIV-1 subtypes and is associated with lower HIV-1 reservoir

OBJECTIVES

APOBEC3 editing activity contributes to sequences variation and viral diversification. We aimed to characterize virological and clinical factors associated with G-to-A mutations and stop codons in the HIV-1 reservoir, markers of APOBEC3 footprints, in order to better understand HIV-1 diversity among virologically suppressed HIV-1-infected patients.

METHODS

Immuno-virological and clinical factors were compared between 92 patients harbouring G-to-A mutations and stop codons (APOBEC+) in the reverse transcriptase gene and 92 patients without G-to-A mutations (APOBEC-) and stop codons in their DNA genotypes.

RESULTS

Patients were predominantly men (74.5%) and were mostly infected by B-subtype (69.0%), with 44.1% and 55.9% in APOBEC+ and APOBEC- groups, respectively. At time of HIV DNA genotypes, the total cell-associated HIV-1 DNA load was 2.34 log10 copies/106 cells (IQR 1.85-2.67) and 33.2% of them had a detectable ultrasensitive plasma viral load. Hypermutated sequences were identified in 28.2% of the APOBEC+ group. The median total cell-associated HIV-1 DNA level was significantly lower in APOBEC+ than APOBEC- group: 2.13 log10 copies/106 cells (IQR 1.60-2.60) versus 2.52 log10 copies/106 cells (IQR 2.19-2.71) (P < 0.001), respectively. Presence of G-to-A mutations and stop codon was independently associated with HIV-1 subtype non-B (P = 0.017).

CONCLUSIONS

These results show an independent association between the presence of G-to-A mutations and stop codons with HIV-1 subtype non-B and low proviral DNA that could be explained by the APOBEC3 footprints and restriction of DNA synthesis and integration. However, further investigations are needed to study the contribution of Vif amino acid variability among HIV-1 subtypes.

No difference in HIV-1 integrase inhibitor resistance between CSF and blood compartments

BACKGROUND

Little is known about HIV-1 integrase inhibitor resistance in the CNS.

OBJECTIVES

This study aimed to evaluate integrase inhibitor resistance in CSF, as a marker of the CNS, and compare it with the resistance in plasma.

METHODS

HIV integrase was sequenced both in plasma and CSF for 59 HIV-1 patients. The clinical and biological data were collected from clinical routine care.

RESULTS

Among the 59 HIV-1 patients, 32 (54.2%) were under antiretroviral (ARV) treatment. The median (IQR) HIV-1 RNA in the plasma of viraemic patients was 5.32 (3.85-5.80) and 3.59 (2.16-4.50) log10 copies/mL versus 4.79 (3.56-5.25) and 3.80 (2.68-4.33) log10 copies/mL in the CSF of ARV-naive and ARV-treated patients, respectively. The patients were mainly infected with non-B subtypes (72.2%) with the most prevalent recombinant form being CRF02_AG (42.4%). The HIV-1 integrase sequences from CSF presented resistance mutations for 9/27 (33.3%) and 8/32 (25.0%) for ARV-naive (L74I, n = 3; L74I/M, n = 1; T97A, n = 1; E157Q, n = 4) and ARV-treated (L74I, n = 6; L74M, n = 1; T97A, n = 1; N155H, n = 1) patients, respectively. Integrase inhibitor resistance mutations in CSF were similar to those in plasma, except for 1/59 patients.

CONCLUSIONS

This work shows similar integrase inhibitor resistance profiles in the CNS and plasma in a population of HIV-1 viraemic patients.

Intermittent two-drug antiretroviral therapies maintain long-term viral suppression in real life in highly experienced HIV-infected patients

OBJECTIVES

To assess in real life whether two-drug regimens (2-DRs) given 4-5 days a week in virally suppressed patients can maintain viral suppression over 48 and 96 weeks.

METHODS

This observational single-centre study enrolled all patients who initiated an intermittent 2-DR between 01/01/2016 and 30/06/2019. The primary outcome was the rate of virological failure (VF), defined as confirmed plasma viral load (pVL) ≥50 copies/mL or single pVL ≥50 copies/mL followed by ART change at week 48 (W48) and W96. Secondary outcomes were the 2-DR intermittent strategy success rate (pVL <50 copies/mL with no ART change), change in CD4 count, CD4/CD8 ratio and rate of residual viraemia.

RESULTS

Eighty-five patients were included; 67/85 (79%) were men, median age = 57 years (IQR = 50-63), CD4 nadir = 233 cells/mm3 (110-327), ART duration = 21 years (13-24), duration of virological suppression = 6.5 years (3.7-10.8) and CD4 count = 658 cells/mm3 (519-867). Intermittent 2-DRs consisted of integrase strand transfer inhibitor (INSTI)/NNRTI (58%), INSTI/NRTI (13%), two NRTIs (11%), PI/NRTI (7%) and other combinations (11%). The median follow-up was 90 weeks (IQR = 64-111). Overall, four VFs occurred, leading to a virological success rate of 98.8% (95% CI = 93.6-100) at W48 and 95.3% (95% CI = 88.4-98.7) at W96. Resuming the same 2-DR 7 days a week led to viral resuppression in three patients, whereas the M184V mutation emerged in one patient, leading to ART modification. There was no significant change in the CD4 count or residual viraemia rate, but a small increase in the CD4/CD8 ratio (P = 0.009) occurred over the study period.

CONCLUSIONS

This observational study shows the potential for intermittent 2-DRs to maintain a high virological success rate, which should be assessed in larger prospective randomized studies.

Persistent low-level viraemia in antiretroviral treatment-experienced patients is not linked to viral resistance or inadequate drug concentrations

OBJECTIVES

To assess genotypic sensitivity scores (GSSs), plasma antiretroviral concentrations (PACs) and immunovirological outcomes at Week 96 (W96) in patients with persistent low-level viraemia (LLV).

METHODS

On 1 January 2017, we analysed data from patients on three-drug regimens with persistent LLV defined as at least two consecutive plasma viral loads (pVLs) between 21 and 200 copies/mL (including one pVL of ≥50 copies/mL), at the Pitié-Salpêtrière Hospital. Outcomes were: GSS, PACs and HIV-DNA load at study entry; and virological status and proportion of patients with resistance-associated mutations (RAMs) at W96.

RESULTS

Fifty-seven patients were included, with median age of 52.6 years (IQR 45.2-57.9), last CD4 count of 658 cells/mm3 (IQR 462-909) and total ART duration of 10.2 years (IQR 5.7-15.2). LLV duration was 14.0 months (IQR 5.5-22.3). GSS was 3 in 46/57 (81%) patients and PACs were adequate in 53/57 (93%) patients. Median total HIV-DNA was 2.65 log10 copies/106 cells (IQR 2.44-2.86). During follow-up, 26/57 (46%) had experienced ART modifications. At W96, 38/57 (67%) patients remained with LLV, 15/60 (26%) had achieved confirmed pVL of <20 copies/mL and 4/57 (7%) had virological failure. The four virological failures were due to three ART interruptions and one incomplete adherence (selection of Y181C RAM). No factors (patient characteristics at study entry, GSS, PACs, total HIV-DNA load and ART modification) were associated with W96 viral outcome, except for time from HIV diagnosis and the LLV duration at study entry.

CONCLUSIONS

A substantial number of patients harbouring LLV had no resistance to ART and adequate PACs. Two-thirds of these patients remained with this LLV status.

Characterization of viral rebounds on dual etravirine/raltegravir maintenance therapy (ANRS-163 ETRAL trial)

BACKGROUND

The ANRS-163 ETRAL trial, a switch study to an etravirine 200 mg/raltegravir 400 mg twice-daily regimen in 165 patients with HIV-1 infection, showed durable efficacy until Week 96. The aim of this work was to investigate in detail the virological rebounds (VRs), defined as at least one plasma HIV viral load (VL) >50 copies/mL.

METHODS

Quantification of HIV-DNA level was assessed at baseline, Week 48 and Week 96 (n = 157). VLs were measured in seminal plasma at Week 48 (n = 26). Genotypic resistance testing by ultra-deep sequencing (UDS) for reverse transcriptase (RT) and integrase regions was performed at baseline and at the time of VR.

RESULTS

In this study, 19 patients experienced VR, with 2 patients having virological failure (VF; two consecutive VLs >50 copies/mL). For the first patient with VF, UDS detected minority resistant variants only in RT (K103N, 9.6%; Y181C, 4.9%) at baseline. Some RT variants became dominant at VF (K101E, 86.3%; Y181C, 100.0%; G190A, 100.0%) and others emerged in integrase (Y143C, 2.4%; Q148R, 6.2%; N155H, 18.8%). For the second patient with VF, neither RT nor integrase mutations were detected at baseline and VF. Median HIV-DNA level was similar at baseline, Week 48 and Week 96 (2.17, 2.06 and 2.11 log10 copies/106 cells, respectively). Only one patient had a detectable seminal HIV VL (505 copies/mL).

CONCLUSIONS

The dual etravirine/raltegravir regimen as maintenance therapy was effective and the emergence of mutations in cases of VF was similar to that seen in other dual-regimen studies. No HIV-DNA level modification was evidenced by Week 96.

Factors associated with the emergence of integrase resistance mutations in patients failing dual or triple integrase inhibitor-based regimens in a French national survey

BACKGROUND

Successful 2-drug regimens (2DRs) for HIV were made possible by the availability of drugs combining potency and tolerability with a high genetic barrier to resistance. How these deal with resistance development/re-emergence, compared with 3DRs, is thus of paramount importance.

MATERIALS AND METHODS

A national survey including patients who were either naive or experienced with any 2DR or 3DR but failing integrase strand transfer inhibitor (INSTI)-containing regimens [two consecutive plasma viral load (VL) values >50 copies/mL] was conducted between 2014 and 2019. Genotypic resistance tests were interpreted with the v28 ANRS algorithm.

RESULTS

Overall, 1104 patients failing any INSTI-containing regimen (2DRs, n = 207; 3DRs, n = 897) were analysed. Five hundred and seventy-seven (52.3%) patients were infected with a B subtype and 527 (47.3%) with non-B subtypes. Overall, 644 (58%) patients showed no known integrase resistance mutations at failure. In multivariate analysis, factors associated with the emergence of at least one integrase mutation were: high VL at failure (OR = 1.24 per 1 log10 copies/mL increase); non-B versus B subtype (OR = 1.75); low genotypic sensitivity score (GSS) (OR = 0.10 for GSS = 2 versus GSS = 0-0.5); and dolutegravir versus raltegravir (OR = 0.46). Although 3DRs versus 2DRs reached statistical significance in univariate analysis (OR = 0.59, P = 0.007), the variable is not retained in the final model.

CONCLUSIONS

This study is one of the largest studies characterizing integrase resistance in patients failing any INSTI-containing 2DR or 3DR in routine clinical care and reveals factors associated with emergence of integrase resistance that should be taken into consideration in clinical management. No difference was evidenced between patients receiving a 2DR or a 3DR.

Neutralization heterogeneity of United Kingdom and South-African SARS-CoV-2 variants in BNT162b2-vaccinated or convalescent COVID-19 healthcare workers

There are concerns about neutralizing antibodies (NAbs) potency against SARS-CoV-2 variants. Despite decreased NAb titers elicited by BNT162b2-vaccine against VOC202012/01 and 501Y.V2 strains, 28/29 healthcare workers (HCW) had a NAb titer ≥1:10. In contrast, six months after COVID-19 mild-forms, only 9/15 (60%) of HCW displayed detectable NAbs against 501Y.V2 strain.

Infection par le SARS-CoV 2 chez les patients avec lymphome cérébral primitif du système nerveux central : étude préliminaire de la sévérité et des facteurs pronostics

Introduction

Les patients avec cancer semblent à risque d’atteinte sévère de la maladie liée au coronavirus 19 (COVID-19). Néanmoins, ces données ne permettent pas d’établir de recommandations dans les cancers rares.

Objectifs

L’objectif de cette étude était de décrire le pronostic des patients avec lymphome cérébral primitif du système nerveux central (PCNSL) présentant une infection par le SARS-CoV-2.

Patients et méthodes

Nous avons réalisé une étude rétrospective dans le réseau national Lymphomes Oculo-Cérébraux (LOC) afin d’évaluer les caractéristiques cliniques et le devenir après infection par le SARS-CoV-2 chez les patients suivis pour PCNSL (diagnostic par PCR sur prélèvement nasopharyngé ou scanner thoracique évocateur). Nous avons comparé les caractéristiques cliniques des patients avec atteinte sévère (décès ou admission en réanimation) ou modérée et étudié les facteurs pronostics.

Résultats

Entre mars et mai 2020, 13 patients PCNSL ont présenté une infection au SARS-CoV-2, dont 85 % étaient en cours de chimiothérapie. Trente-huit pour cent ont présenté une forme sévère : 23 % de décès, 15 % de ventilation mécanique (VM). Quinze pour cent sont restés asymptomatiques. Un antécédent de diabète était plus fréquent en cas d’atteinte sévère (3/5 vs 0/8, p = 0,03). La chimiothérapie a été reprise chez 9 patients après un délai médian de 16 jours après guérison clinique, sans complication inhabituelle ni réactivation virale, y compris chez 2 patients ayant nécessité une VM.

Discussion

Cette analyse préliminaire suggère que, bien qu’à plus haut risque d’infection sévère, les patients PCNSL infectés par le SARS-CoV-2 devraient être pris en charge de façon maximale, en particulier s’ils sont en réponse oncologique lors de l’infection au SARS-CoV-2. Ces données représentent la première série de PCNSL rapportée et aideront à l’établissement de recommandations internationales pour cette population.

Conclusion

La chimiothérapie pourrait être reprise sans délai prolongé chez les patients suivis pour PCNSL avec COVID-19.

Olfactory and gustatory dysfunctions in COVID-19 outpatients: A prospective cohort study

OBJECTIVES

To describe the characteristics, evolution and risk factors for long-term persistence of olfactory and gustatory dysfunctions (OGD) in COVID-19 outpatients.

PATIENTS AND METHODS

We conducted a prospective study in SARS-CoV-2 infected outpatients with OGD. Weekly phone interviews were set up starting from COVID-19 onset symptoms and over the course of 60 days, using standardized questionnaires that included a detailed description of general symptoms and OGD. The primary outcome was the proportion of patients with complete recovery of OGD at D30. Rate and time to recovery of OGD, as well as risk factors for late recovery (>30 days), were evaluated using Cox regression models.

RESULTS

Ninety-eight outpatients were included. The median time to onset of OGD after first COVID-19 symptoms was 2 days (IQR 0-4). The 30-day recovery rate from OGD was 67.5% (95% CI 57.1-75.4) and the estimated median time of OGD recovery was 20 days (95% CI 13-26). Risk factors for late recovery of OGD were a complete loss of smell or taste at diagnosis (HR=0.26, 95% CI 0.12-0.56, P=0.0005) and age over 40 years (HR=0.56, 95% CI 0.36-0.89, P=0.01).

CONCLUSIONS

COVID-19 patients with complete loss of smell or taste and over age 40 are more likely to develop persistent OGD and should rapidly receive sensorial rehabilitation.

Evolution of viral quasispecies during SARS-CoV-2 infection

Objectives

Studies are needed to better understand the genomic evolution of the recently emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study aimed to describe genomic diversity of SARS-CoV-2 by next-generation sequencing (NGS) in a patient with longitudinal follow-up for SARS-CoV-2 infection.

Methods

Sequential samples collected between January 29th and February 4th, 2020, from a patient infected by SARS-CoV-2 were used to perform amplification of two genome fragments—including genes encoding spike, envelope, membrane and nucleocapsid proteins—and NGS was carried out with Illumina® technology. Phylogenetic analysis was performed with PhyML and viral variant identification with VarScan.

Results

Majority consensus sequences were identical in most of the samples (5/7) and differed in one synonymous mutation from the Wuhan reference sequence. We identified 233 variants; each sample harboured in median 38 different minority variants, and only four were shared by different samples. The frequency of mutation was similar between genes and correlated with the length of the gene (r = 0.93, p = 0.0002). Most of mutations were substitution variations (n = 217, 93.1%) and about 50% had moderate or high impact on gene expression. Viral variants also differed between lower and upper respiratory tract samples collected on the same day, suggesting independent sites of replication of SARS-CoV-2.

Conclusions

We report for the first time minority viral populations representing up to 1% during the course of SARS-CoV-2 infection. Quasispecies were different from one day to the next, as well as between anatomical sites, suggesting that in vivo this new coronavirus appears as a complex and dynamic distributions of variants.

OP0254 CHROMATIN CONFORMATION SIGNATURE ANALYSIS IN EARLY VS LATE SCLERODERMA PHENOTYPES

Background:

Systemic sclerosis (scleroderma, SSc) is a heterogeneous disease in which clinical outcomes vary widely. Predicting outcomes on an individual basis remains challenging despite progress made through autoantibody analysis and gene expression profiling. Effective targeted therapies are evolving and accurately predicting outcomes is important to enable patient stratification for therapy.

Chromatin Conformation Signature (CCS) profiling of peripheral blood for systemic epigenetic deregulations could be used for such a purpose. The EpiSwitch platform offering high throughput and resolution chromosome conformation (3C) capture detects significant regulatory changes in 3D genome architecture and maps long range interaction between distant genomic locations. This then reveals the spatial disposition and physical properties of the chromosome, such as chromatin loops and inter-chromosomal connections, which have a role in network organization and genetic epistasis controlling gene expression. EpiSwitch automated platform has been successfully utilised in patient stratification in RA, MS and other indications.

This methodology could be applied to patients with SSc to identify CCS associated with different phenotypes and may ultimately be used to stratify and identify patients into pathogenic subtypes.

Objectives:

We aimed to determine significant CCSs associated with early and late phenotypes of SSc.

Methods:

The EpiSwitch-based chromosome conformation capture (3C) method was applied to blood samples from early phenotype, and late phenotype SSc patients. Intact nuclei were isolated from peripheral blood mononuclear cells and subjected to formaldehyde fixation resulting in crosslinking between physically touching segments of the genome via contacts between their DNA bound proteins. For quantification of cross-linking frequencies, the cross linked DNA was digested and then subjected to ligation. Cross-linking was then reversed and individual ligation products detected and quantified by EpiSwitch custom oligo array annotated across the whole genome to the anchoring sites of 3D genome architecture.

Results:

7 significant CCSs were found over the HLA-C, HLA-B and TNF regions on Chromosome 6 in the early phenotype. The top 8 pathways for genetic locations associated to the CCSs are shown in Table 1.

Table 1.

Top 8 pathways for genetic locations associated to significant CCS for the early phenotype.

GeneSet1Natural Killer cell mediated cytotoxicity2Immunoregulatory interations between a lymphoid cell and a non-lymphoid cell3Antigen Processing & presentation4Phagosome5Graft versus host disease6Type 1 diabetes mellitus7Osteoclast differentiation8Class 1 MHC mediated antigen processing & presentation

2 significant CCSs were found centred around the IFNG region of chromosome 12 in the late phenotype. The top 8 pathways for genetic locations associated to significant CCSs are shown in Table 2.

Table 2.

Top 8 pathways for genetic locations associated to significant CCS for the late phenotype.

GeneSet1Surfactant metabolism2IL12 signalling mediated by STAT43Protein digestion & absorption4Calcineruin regulated NFAT dependent transcription in lymphocytes5Transcriptional misregulation in cancer6Kaposi’s sarcoma associated herpes virus infection7IL2 mediated signalling events8Inflammatory bowel disease

Conclusion:

Significant CCSs, as part of 3D genomic regulatory control, and their associated pathways for the genetic locations, were identified in both late and early phenotypes. There were distinct CCSs in the early phenotype compared to the late suggesting the CCSs change as the disease progresses and varies between phenotypes. If CCSs could be linked to each clinically defined subgroup across a SSc cohort they could be used as a biomarker tool to predict outcome and progression in patients.

Disclosure of Interests:

Megan Galloway: None declared, Ewan Hunter: None declared, Alexandre Akoulitchev: None declared, Shivanee Vigneswaran: None declared, Bahja Abdi: None declared, Christopher Denton Grant/research support from: GlaxoSmithKline, Inventiva, CSF Behring, Consultant of: Roche-Genentech, Actelion, GlaxoSmithKline, Sanofi Aventis, Inventiva, CSL Behring, Boehringer Ingelheim, Bayer, David Abraham: None declared, Richard Stratton: None declared

Prevalence of doravirine-associated resistance mutations in HIV-1-infected antiretroviral-experienced patients from two large databases in France and Italy

Objectives

Doravirine, a novel NNRTI, selects for specific mutations in vitro, including mutations at reverse transcriptase (RT) positions 106, 108, 188, 227, 230 and 234. The aim of this study was to examine the prevalence of doravirine-associated resistance mutations in HIV-1-infected antiretroviral-experienced patients.

Methods

Doravirine-associated resistance mutations identified in vitro or in vivo were studied in a set of 9199 HIV-1 RT sequences from HIV-1 antiretroviral-experienced patients, including 381 NNRTI-failing patients in France and Italy between 2012 and 2017. The following mutations were considered as resistance mutations: V106A/M, V108I, Y188L, G190S, F227C/L/V, M230I/L, L234I, P236L, K103N + Y181C, K103N + P225H and K103N + L100I.

Results

The frequencies of doravirine-associated resistance mutations (total dataset versus NNRTI-failing patients) were: V106A/M, 0.8% versus 2.6%; V108I, 3.3% versus 9.2%; Y188L, 1.2% versus 2.6%; G190S, 0.3% versus 2.1%; F227C/L/V, 0.5% versus 1.8%; M230I/L, 2.8% versus 0%; L234I, 0.1% versus 0.5%; K103N + Y181C, 3.9% versus 3.9%; K103N + P225H, 2.9% versus 4.7%; and K103N + L100I, 1.7% versus 3.9%, with a significantly higher proportion of these mutations in the NNRTI-failing group (P &lt; 0.05), except for M230I/L and K103N + Y181C. The overall prevalence of sequences with at least one doravirine-associated resistance mutation was 12.2% and 34.9% in the total dataset and NNRTI-failing patients (P &lt; 0.001), respectively. In comparison, the prevalence of the common NNRTI mutations V90I, K101E/P, K103N/S, E138A/G/K/Q/R/S, Y181C/I/V and G190A/E/S/Q were higher (8.9%, 7.9%, 28.6%, 12.6%, 14.2% and 8.9%, respectively).

Conclusions

These results suggest that doravirine resistance in antiretroviral-experienced patients generally and specifically among NNRTI-failing patients is lower than resistance to other NNRTIs currently used, confirming its distinguishing resistance pattern.

[Diagnostic performance of graphical anomalies in the detection of large platelets and platelet clumps]

Thrombocytopenia is a current situation for making a blood smear in routine practice in a medical analysis laboratory. Recent automated hematology analyzers enumerate platelets and generate histograms and specific flags. Operators must be aware of the characteristics of their analyzer in order to avoid spurious results in the case where microscopy review is not possible.

OBJECTIVE

We evaluated the diagnostic performance of various graphical anomalies in the detection of large platelets and platelet clumps.

PATIENTS AND METHODS

Three hundred cases of thrombocytopenia were included in the study on the basis of a platelet count less than 150 × 10(9)/L. This evaluation is expressed by the results of the sensitivity, specificity, positive predictive value and negative predictive value compared to the microscopic review of blood smear.

RESULTS

Graphical performances are variable according to microscopic review of blood smears. Indeed, a not fitted curve is the most sensitive change on platelet histogram to the presence of large platelet. A high specificity to the presence of platelet clumps is announced when the platelet curve fails to return to the baseline. Moreover, characteristic findings on the DIFF scattergram are very specific to the presence of platelet clumps.

CONCLUSION

A normal platelet histogram can validate with great confidence thrombocytopenia in cases where a blood smear cannot be read immediately.