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Article ; Online: Implementation of a SARS-CoV-2 Genotyping Panel for Prompt Omicron Variant Identification: A Pragmatic Tool for Clinical Laboratories.

Nussbaum, Eliezer Zachary / Thiriveedhi, Vamsi / Uddin, Rockib / Cho, Ha Eun / Carroll, Seamus / Rosenberg, Eric S / Lemieux, Jacob E / Turbett, Sarah E

Annals of internal medicine

2022 Volume 175, Issue 6, Page(s) 906–908

MeSH term(s)	COVID-19 ; Genotype ; Humans ; Laboratories, Clinical ; SARS-CoV-2/genetics
Language	English
Publishing date	2022-03-29
Publishing country	United States
Document type	Research Support, U.S. Gov't, P.H.S. ; Letter
ZDB-ID	336-0
ISSN	1539-3704 ; 0003-4819
ISSN (online)	1539-3704
ISSN	0003-4819
DOI	10.7326/M22-0023
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Article ; Online: Neuropathological features of SARS-CoV-2 delta and omicron variants.

Normandin, Erica / Valizadeh, Navid / Rudmann, Emily A / Uddin, Rockib / Dobbins, Sabrina T / MacInnis, Bronwyn L / Padera, Robert F / Siddle, Katherine J / Lemieux, Jacob E / Sabeti, Pardis C / Mukerji, Shibani S / Solomon, Isaac H

Journal of neuropathology and experimental neurology

2023 Volume 82, Issue 4, Page(s) 283–295

Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is continually evolving resulting in variants with increased transmissibility, more severe disease, reduced effectiveness of treatments or vaccines, or diagnostic detection failure. The SARS- ... ...

Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is continually evolving resulting in variants with increased transmissibility, more severe disease, reduced effectiveness of treatments or vaccines, or diagnostic detection failure. The SARS-CoV-2 Delta variant (B.1.617.2 and AY lineages) was the dominant circulating strain in the United States from July to mid-December 2021, followed by the Omicron variant (B.1.1.529 and BA lineages). Coronavirus disease 2019 (COVID-19) has been associated with neurological sequelae including loss of taste/smell, headache, encephalopathy, and stroke, yet little is known about the impact of viral strain on neuropathogenesis. Detailed postmortem brain evaluations were performed for 22 patients from Massachusetts, including 12 who died following infection with Delta variant and 5 with Omicron variant, compared to 5 patients who died earlier in the pandemic. Diffuse hypoxic injury, occasional microinfarcts and hemorrhage, perivascular fibrinogen, and rare lymphocytes were observed across the 3 groups. SARS-CoV-2 protein and RNA were not detected in any brain samples by immunohistochemistry, in situ hybridization, or real-time quantitative PCR. These results, although preliminary, demonstrate that, among a subset of severely ill patients, similar neuropathological features are present in Delta, Omicron, and non-Delta/non-Omicron variant patients, suggesting that SARS-CoV-2 variants are likely to affect the brain by common neuropathogenic mechanisms.
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19 ; Neuropathology ; Stroke
Language	English
Publishing date	2023-02-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	3088-0
ISSN	1554-6578 ; 0022-3069
ISSN (online)	1554-6578
ISSN	0022-3069
DOI	10.1093/jnen/nlad015
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Article: Detection of the Omicron Variant Virus With the Abbott BinaxNow SARS-CoV-2 Rapid Antigen Assay.

Regan, James / Flynn, James P / Choudhary, Manish C / Uddin, Rockib / Lemieux, Jacob / Boucau, Julie / Bhattacharyya, Roby P / Barczak, Amy K / Li, Jonathan Z / Siedner, Mark J

Open forum infectious diseases

2022 Volume 9, Issue 3, Page(s) ofac022

Abstract: We assessed the ability of the BinaxNow rapid test to detect severe acute respiratory syndrome coronavirus 2 antigen from 4 individuals with Omicron and Delta infections. We performed serial dilutions of nasal swab samples, and specimens with ... ...

Abstract	We assessed the ability of the BinaxNow rapid test to detect severe acute respiratory syndrome coronavirus 2 antigen from 4 individuals with Omicron and Delta infections. We performed serial dilutions of nasal swab samples, and specimens with concentrations of ≥100
Language	English
Publishing date	2022-01-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	2757767-3
ISSN	2328-8957
ISSN	2328-8957
DOI	10.1093/ofid/ofac022
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Article: SARS-CoV-2 virologic rebound with nirmatrelvir-ritonavir therapy.

medRxiv : the preprint server for health sciences

2023

Abstract: Objective: To compare the frequency of replication-competent virologic rebound with and without nirmatrelvir-ritonavir treatment for acute COVID-19. Secondary aims were to estimate the validity of symptoms to detect rebound and the incidence of emergent ...

Abstract	Objective: To compare the frequency of replication-competent virologic rebound with and without nirmatrelvir-ritonavir treatment for acute COVID-19. Secondary aims were to estimate the validity of symptoms to detect rebound and the incidence of emergent nirmatrelvir-resistance mutations after rebound. Design: Observational cohort study. Setting: Multicenter healthcare system in Boston, Massachusetts. Participants: We enrolled ambulatory adults with a positive COVID-19 test and/or a prescription for nirmatrelvir-ritonavir. Exposures: Receipt of 5 days of nirmatrelvir-ritonavir treatment versus no COVID-19 therapy. Main outcome and measures: The primary outcome was COVID-19 virologic rebound, defined as either (1) a positive SARS-CoV-2 viral culture following a prior negative culture or (2) two consecutive viral loads ≥4.0 log Results: Compared with untreated individuals (n=55), those taking nirmatrelvir-ritonavir (n=72) were older, received more COVID-19 vaccinations, and were more commonly immunosuppressed. Fifteen individuals (20.8%) taking nirmatrelvir-ritonavir experienced virologic rebound versus one (1.8%) of the untreated (absolute difference 19.0% [95%CI 9.0-29.0%], P=0.001). In multivariable models, only N-R was associated with VR (AOR 10.02, 95%CI 1.13-88.74). VR occurred more commonly among those with earlier nirmatrelvir-ritonavir initiation (29.0%, 16.7% and 0% when initiated days 0, 1, and ≥2 after diagnosis, respectively, P=0.089). Among participants on N-R, those experiencing rebound had prolonged shedding of replication-competent virus compared to those that did not rebound (median: 14 vs 3 days). Only 8/16 with virologic rebound reported worsening symptoms (50%, 95%CI 25%-75%); 2 were completely asymptomatic. We detected no post-rebound nirmatrelvir-resistance mutations in the NSP5 protease gene. Conclusions and relevance: Virologic rebound occurred in approximately one in five people taking nirmatrelvir-ritonavir and often occurred without worsening symptoms. Because it is associated with replication-competent viral shedding, close monitoring and potential isolation of those who rebound should be considered.
Language	English
Publishing date	2023-06-27
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.06.23.23288598
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Article: The 2022 RSV surge was driven by multiple viral lineages.

medRxiv : the preprint server for health sciences

2023

Abstract: The US experienced an early and severe respiratory syncytial virus (RSV) surge in autumn 2022. Despite the pressure this has put on hospitals and care centers, the factors promoting the surge in cases are unknown. To investigate whether viral ... ...

Abstract	The US experienced an early and severe respiratory syncytial virus (RSV) surge in autumn 2022. Despite the pressure this has put on hospitals and care centers, the factors promoting the surge in cases are unknown. To investigate whether viral characteristics contributed to the extent or severity of the surge, we sequenced 105 RSV-positive specimens from symptomatic patients diagnosed with RSV who presented to the Massachusetts General Hospital (MGH) and its outpatient practices in the Greater Boston Area. Genomic analysis of the resulting 77 genomes (54 with >80% coverage, and 23 with >5% coverage) demonstrated that the surge was driven by multiple lineages of RSV-A (91%; 70/77) and RSV-B (9%; 7/77). Phylogenetic analysis of all US RSV-A revealed 12 clades, 4 of which contained Massachusetts and Washington genomes. These clades individually had times to most recent common ancestor (tMRCA) between 2014 and 2017, and together had a tMRCA of 2009, suggesting that they emerged well before the COVID-19 pandemic. Similarly, the RSV-B genomes had a tMRCA between 2016 and 2019. We found that the RSV-A and RSV-B genomes in our sample did not differ statistically from the estimated clock rate of the larger phylogenetic tree (10.6 and 12.4 substitutions per year, respectively). In summary, the polyphyletic nature of viral genomes sequenced in the US during the autumn 2022 surge is inconsistent with the emergence of a single, highly transmissible causal RSV lineage.
Language	English
Publishing date	2023-01-05
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.01.04.23284195
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Article ; Online: SARS-CoV-2 viral clearance and evolution varies by type and severity of immunodeficiency.

Li, Yijia / Choudhary, Manish C / Regan, James / Boucau, Julie / Nathan, Anusha / Speidel, Tessa / Liew, May Yee / Edelstein, Gregory E / Kawano, Yumeko / Uddin, Rockib / Deo, Rinki / Marino, Caitlin / Getz, Matthew A / Reynolds, Zahra / Barry, Mamadou / Gilbert, Rebecca F / Tien, Dessie / Sagar, Shruti / Vyas, Tammy D /

Flynn, James P / Hammond, Sarah P / Novack, Lewis A / Choi, Bina / Cernadas, Manuela / Wallace, Zachary S / Sparks, Jeffrey A / Vyas, Jatin M / Seaman, Michael S / Gaiha, Gaurav D / Siedner, Mark J / Barczak, Amy K / Lemieux, Jacob E / Li, Jonathan Z

Science translational medicine

2024 Volume 16, Issue 731, Page(s) eadk1599

Abstract: Despite vaccination and antiviral therapies, immunocompromised individuals are at risk for prolonged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but the immune defects that predispose an individual to persistent coronavirus ... ...

Abstract	Despite vaccination and antiviral therapies, immunocompromised individuals are at risk for prolonged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but the immune defects that predispose an individual to persistent coronavirus disease 2019 (COVID-19) remain incompletely understood. In this study, we performed detailed viro-immunologic analyses of a prospective cohort of participants with COVID-19. The median times to nasal viral RNA and culture clearance in individuals with severe immunosuppression due to hematologic malignancy or transplant (S-HT) were 72 and 40 days, respectively, both of which were significantly longer than clearance rates in individuals with severe immunosuppression due to autoimmunity or B cell deficiency (S-A), individuals with nonsevere immunodeficiency, and nonimmunocompromised groups (
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19 ; Prospective Studies ; Kinetics ; Immunosuppression Therapy
Language	English
Publishing date	2024-01-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	2518854-9
ISSN	1946-6242 ; 1946-6234
ISSN (online)	1946-6242
ISSN	1946-6234
DOI	10.1126/scitranslmed.adk1599
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Article ; Online: Viral Lineages in the 2022 RSV Surge in the United States.

The New England journal of medicine

2023 Volume 388, Issue 14, Page(s) 1335–1337

MeSH term(s)	Humans ; Infant ; Respiratory Syncytial Virus Infections/epidemiology ; Respiratory Syncytial Virus Infections/genetics ; Respiratory Syncytial Virus Infections/virology ; Seasons ; United States/epidemiology ; Disease Outbreaks ; Respiratory Syncytial Viruses/genetics
Language	English
Publishing date	2023-02-22
Publishing country	United States
Document type	Letter
ZDB-ID	207154-x
ISSN	1533-4406 ; 0028-4793
ISSN (online)	1533-4406
ISSN	0028-4793
DOI	10.1056/NEJMc2216153
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Article ; Online: SARS-CoV-2 Virologic Rebound With Nirmatrelvir-Ritonavir Therapy : An Observational Study.

Annals of internal medicine

2023 Volume 176, Issue 12, Page(s) 1577–1585

Abstract: Background: Data are conflicting regarding an association between treatment of acute COVID-19 with nirmatrelvir-ritonavir (N-R) and virologic rebound (VR).: Objective: To compare the frequency of VR in patients with and without N-R treatment for ... ...

Abstract	Background: Data are conflicting regarding an association between treatment of acute COVID-19 with nirmatrelvir-ritonavir (N-R) and virologic rebound (VR). Objective: To compare the frequency of VR in patients with and without N-R treatment for acute COVID-19. Design: Observational cohort study. Setting: Multicenter health care system in Boston, Massachusetts. Participants: Ambulatory adults with acute COVID-19 with and without use of N-R. Intervention: Receipt of 5 days of N-R treatment versus no COVID-19 therapy. Measurements: The primary outcome was VR, defined as either a positive SARS-CoV-2 viral culture result after a prior negative result or 2 consecutive viral loads above 4.0 log Results: Compared with untreated persons ( Limitations: Observational study design with differences between the treated and untreated groups; positive viral culture result was used as a surrogate marker for risk for ongoing viral transmission. Conclusion: Virologic rebound occurred in approximately 1 in 5 people taking N-R, often without symptom rebound, and was associated with shedding of replication-competent virus. Primary funding source: National Institutes of Health.
MeSH term(s)	Adult ; Humans ; SARS-CoV-2 ; COVID-19 ; Ritonavir/therapeutic use ; COVID-19 Drug Treatment
Chemical Substances	nirmatrelvir (7R9A5P7H32) ; Ritonavir (O3J8G9O825)
Language	English
Publishing date	2023-11-14
Publishing country	United States
Document type	Observational Study ; Multicenter Study ; Journal Article
ZDB-ID	336-0
ISSN	1539-3704 ; 0003-4819
ISSN (online)	1539-3704
ISSN	0003-4819
DOI	10.7326/M23-1756
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Article ; Online: Performance of three rapid antigen tests against the SARS-CoV-2 Omicron variant

Kanjilal, Sanjat / Chalise, Sujata / Shah, Adnan Shami / Cheng, Chi-An / Senussi, Yasmeen / Uddin, Rockib / Thiriveedhi, Vamsi / Cho, Ha Eun / Carroll, Seamus / Lemieux, Jacob / Turbett, Sarah / Walt, David R

medRxiv

Abstract: Rapid antigen detection tests (RADTs) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are now in widespread use in the United States. RADTs play an important role in maintaining an open society but require periodic reassessment to ensure ...

Abstract	Rapid antigen detection tests (RADTs) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are now in widespread use in the United States. RADTs play an important role in maintaining an open society but require periodic reassessment to ensure test performance remains intact as the virus evolves. The nucleocapsid (N) protein is the target for the majority of RADTs and the SARS-CoV-2 Omicron variant has several N protein mutations that are previously uncharacterized. We sought to assess the impact of these mutations by testing 30 Omicron variant samples across a wide range of viral loads on three widely used RADTs: the iHealth COVID-19 Antigen Rapid Test, the ACON Laboratories FlowFlex COVID-19 Antigen Home Test, and the Abbott BinaxNOW COVID-19 Antigen Card, using 30 Delta variant samples as a comparator. We found no change in the analytic sensitivity of all three RADTs for detection of Omicron versus Delta, but noted differences in performance between assays. No RADT was able to detect samples with a cycle threshold (Ct) value of ≥27.5 for the envelope gene target on the Roche cobas RT-PCR assay. Epidemiologic studies are necessary to correlate these findings with their real-world performance.
Keywords	covid19
Language	English
Publishing date	2022-02-19
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2022.02.17.22271142
Database	COVID19

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Article ; Online: Duration of viral shedding and culture positivity with postvaccination SARS-CoV-2 delta variant infections.

JCI insight

2022 Volume 7, Issue 2

Abstract: Isolation guidelines for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are largely derived from data collected prior to the emergence of the delta variant. We followed a cohort of ambulatory patients with postvaccination breakthrough SARS- ... ...

Abstract	Isolation guidelines for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are largely derived from data collected prior to the emergence of the delta variant. We followed a cohort of ambulatory patients with postvaccination breakthrough SARS-CoV-2 infections with longitudinal collection of nasal swabs for SARS-CoV-2 viral load quantification, whole-genome sequencing, and viral culture. All delta variant infections in our cohort were symptomatic, compared with 64% of non-delta variant infections. Symptomatic delta variant breakthrough infections were characterized by higher initial viral load, longer duration of virologic shedding by PCR, greater likelihood of replication-competent virus at early stages of infection, and longer duration of culturable virus compared with non-delta variants. The duration of time since vaccination was also correlated with both duration of PCR positivity and duration of detection of replication-competent virus. Nonetheless, no individuals with symptomatic delta variant infections had replication-competent virus by day 10 after symptom onset or 24 hours after resolution of symptoms. These data support US CDC isolation guidelines as of November 2021, which recommend isolation for 10 days or until symptom resolution and reinforce the importance of prompt testing and isolation among symptomatic individuals with delta breakthrough infections. Additional data are needed to evaluate these relationships among asymptomatic and more severe delta variant breakthrough infections.
MeSH term(s)	Adult ; COVID-19/genetics ; COVID-19/metabolism ; COVID-19/prevention & control ; COVID-19 Vaccines/administration & dosage ; Female ; Humans ; Male ; Middle Aged ; SARS-CoV-2/physiology ; Time Factors ; Virus Replication ; Virus Shedding/physiology
Chemical Substances	COVID-19 Vaccines
Language	English
Publishing date	2022-01-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	2379-3708
ISSN (online)	2379-3708
DOI	10.1172/jci.insight.155483
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