Doctor taking a nasal swab test

July 8, 2022

Clinical Reports

  • Mild respiratory COVID can cause multi-lineage neural cell and myelin dysregulation
    COVID survivors frequently experience lingering neurological symptoms that resemble cancer-therapy-related cognitive impairment, a syndrome for which white matter microglial reactivity and consequent neural dysregulation is central. Here, researchers explored the neurobiological effects of respiratory SARS-CoV-2 infection and found white-matter-selective microglial reactivity in mice and humans. Following mild respiratory COVID in mice, persistently impaired hippocampal neurogenesis, decreased oligodendrocytes, and myelin loss were evident together with elevated CSF cytokines/chemokines including CCL11. Systemic CCL11 administration specifically caused hippocampal microglial reactivity and impaired neurogenesis. Concordantly, humans with lasting cognitive symptoms post-COVID exhibit elevated CCL11 levels. Compared with SARS-CoV-2, mild respiratory influenza in mice caused similar patterns of white-matter-selective microglial reactivity, oligodendrocyte loss, impaired neurogenesis, and elevated CCL11 at early time points, but after influenza, only elevated CCL11 and hippocampal pathology persisted. These findings illustrate similar neuropathophysiology after cancer therapy and respiratory SARS-CoV-2 infection which may contribute to cognitive impairment following even mild COVID.
  • Health Impairments in Children and Adolescents After Hospitalization for Acute COVID-19 or MIS-C
    The purpose of this study was to evaluate risk factors for post-discharge sequelae in children and adolescents after hospitalization for acute COVID-19 or multisystem inflammatory syndrome in children (MIS-C). This was a multicenter prospective observational cohort study conducted in 25 US pediatric hospitals. Patients <21-years-old, hospitalized May 2020 to May 2021 for acute COVID-19 or MIS-C with follow-up 2-4 months after admission. Researchers assessed readmissions, caregiver-reported persistent symptoms or activity impairment, and new morbidities identified by the Functional Status Scale. Multivariable regression was used to calculate adjusted risk ratios (aRR). Of 358 eligible patients, 2-4 month survey data were available for 119/155 (76.8%) with acute COVID-19 and 160/203 (78.8%) with MIS-C. Thirteen (11%) patients with acute COVID-19 and 12 (8%) with MIS-C had a readmission. Thirty-two (26.9%) patients with acute COVID-19 had persistent symptoms (22.7%) or activity impairment (14.3%) and 48 (30.0%) patients with MIS-C had persistent symptoms (20.0%) or activity impairment (21.3%). For patients with acute COVID-19, persistent symptoms (aRR, 1.29[95% CI, 1.04-1.59]) and activity impairment (aRR, 1.37[95% CI, 1.06-1.78]) were associated with more organs systems involved. Patients with MIS-C and pre-existing respiratory conditions more frequently had persistent symptoms (aRR, 3.09[95% CI, 1.55-6.14]) and those with obesity more frequently had activity impairment (aRR, 2.52[95% CI, 1.35-4.69]). New morbidities were infrequent (9% COVID-19 and 1% MIS-C). Over one in four children hospitalized with acute COVID-19 or MIS-C experienced persistent symptoms or activity impairment for at least 2 months. Patients with MIS-C and respiratory conditions or obesity are at higher risk of prolonged recovery.
  • Duration of Shedding of Culturable Virus in SARS-CoV-2 Omicron (BA.1) Infection
    Authors used longitudinal sampling of nasal swabs for determination of viral load, sequencing, and viral culture in outpatients with newly diagnosed coronavirus disease 2019 (Covid-19). From July 2021 through January 2022. They enrolled 66 participants, including 32 with samples that were sequenced and identified as the B.1.617.2 (delta) variant and 34 with samples that were sequenced and identified as the omicron subvariant BA.1, inclusive of sublineages. Participants who received Covid-19–specific therapies were excluded; all but 1 participant had symptomatic infection. In this longitudinal cohort of participants, most of whom had symptomatic, nonsevere Covid-19 infection, the viral decay kinetics were similar with omicron infection and delta infection. Although vaccination has been shown to reduce the incidence of infection and the severity of disease, researchers did not find large differences in the median duration of viral shedding among participants who were unvaccinated, those who were vaccinated but not boosted, and those who were vaccinated and boosted.
  • Children and COVID-19: State level Data Report
    A joint report from the American Academy of Pediatrics and the Children’s Hospital Association. Summary of publicly reported data from 49 states, NYC, DC, PR, and GU Version: 6/30/22. The numbers in this report represent cumulative counts since states began reporting. The data are based on how public agencies collect, categorize and post information. All data reported by state/local health departments are preliminary and subject to change and reporting may change over time. Notably, in the summer of 2021 and winter of 2022, some states have revised cases counts previously reported, begun reporting less frequently, or dropped metrics previously reported. For example, due to several changes on their dashboards and the data currently available, AL, TX, HI, DC and MS data in this report are not current (cumulative data through 7/29/21, 8/26/21, 1/13/22, 3/3/22, and 3/10/22 respectively). Readers should consider these factors. States may have additional information on their web sites.

Antiviral Therapeutics and Vaccines

  • COVID-19 rebound after Paxlovid and Molnupiravir during January-June 2022
    Recent case reports document that some patients who were treated with Paxlovid experienced rebound COVID-19 infections and symptoms 2 to 8 days after completing a 5-day course of Paxlovid. The Centers for Disease Control and Prevention (CDC) has recently issued a Health Alert Network Health Advisory to update the public on the potential for COVID-19 rebound after Paxlovid treatments. However, the rates of COVID-19 rebound in a real-world population or whether rebound is unique to Paxlovid remains unknown. The objective of this study was to examine the rates and relative risks of COVID-19 rebound in patients treated with Paxlovid or with Molnupiravir and to compare characteristics of patients who experienced COVID-19 rebound to those who did not. The study population comprised 13,644 patients age 18 years or older who contracted COVID-19 between 1/1/2022-6/8/2022 and were treated with Paxlovid (n =11,270) or with Molnupiravir (n =2,374) within 5 days of their COVID-19 infection. Three types of COVID-19 rebound outcomes (COVID-19 infections, COVID-19 related symptoms, and hospitalizations) were examined. Hazard ratios and 95% confidence interval (CI) of 7-day and 30-day risk for COVID-19 rebound between patients treated with Paxlovid and patients treated with Molnupiravir were calculated before and after propensity-score matching. The 7-day and 30-day COVID-19 rebound rates after Paxlovid treatment were 3.53% and 5.40% for COVID-19 infection, 2.31% and 5.87% for COVID-19 symptoms, and 0.44% and 0.77% for hospitalizations. The 7-day and 30-day COVID-19 rebound rates after Molnupiravir treatment were 5.86% and 8.59% for COVID-19 infection, 3.75% and 8.21% for COVID-19 symptoms, and 0.84% and 1.39% for hospitalizations. After propensity-score matching, there were no significant differences in COVID-19 rebound risks between Paxlovid and Molnupiravir: infection (HR 0.90, 95% CI: 0.73-1.11), COVID-19 symptoms (HR: 1.03, 95% CI: 0.83-1.27), or hospitalizations (HR: 0.92, 95% CI: 0.56-1.55). Patients with COVID-19 rebound had significantly higher prevalence of underlying medical conditions than those without. COVID-19 rebound occurred both after Paxlovid and Molnupiravir, especially in patients with underlying medical conditions. This indicates that COVID-19 rebound is not unique to Paxlovid and the risks were similar for Paxlovid and Molnupiravir. For both drugs the rates of COVID-19 rebound increased with time after treatments. Our results call for continuous surveillance of COVID-19 rebound after Paxlovid and Molnupiravir treatments. Studies are necessary to determine the mechanisms underlying COVID-19 rebounds and to test dosing and duration regimes that might prevent such rebounds in vulnerable patients.
  • Comparative Effectiveness of the SARS-CoV-2 Vaccines During Delta
    Several vaccines with demonstrated efficacy for coronavirus disease 2019 (Covid-19) are available. The vaccines’ differential effectiveness may have significant impacts, but information on comparative efficacy in large populations is limited. Researchers used de-identified claims in a research database that included vaccination status and Covid-positivity status. Individuals > 18 years, fully vaccinated with Ad26.COV2.S /J&J/Janssen, mRNA-1273/Moderna, or BNT162b2/Pfizer-BioNTech by September 30, 2021, were included. Outcomes were SARS-CoV-2-infection, emergency department visits, outpatient visits, inpatient hospitalizations, intensive care unit (ICU) transfers, death, and hospice transfers through September 30, 2021.  Among ~6.5 million fully vaccinated individuals, mRNA-1273 performed better than BNT162b2 for infection, composite-hospitalization (hospitalization/ICU transfer/hospice transfer/death), and composite-ICU transfer (ICU transfer/hospice transfer/death) caused by B.1.612.7 (delta) variant infection. AD26.COV2.S performed worse than BNT162b2 for infection, composite-hospitalization, and composite-ICU transfers. The number needed to vaccinate (NNV) with mRNA1273 to prevent one hospitalization at 90 days was 3130 compared to AD26.COV2.S and 15,472 compared to BNT162b2. The NNV with mRNA1273 to prevent one ICU transfer at 90 days was 6358 compared to AD26.COV2.S and 34,279 compared to BNT162b2. For every one million individuals vaccinated with BNT162b compared to mRNA-1273, the approximate incremental inpatient cost would be $405,000 and the approximate incremental ICU cost would be $662,000. The two-dose mRNA vaccines’ effectiveness significantly exceeded the single-dose Ad26.COV2.S vaccine’s effectiveness from population health and cost-effectiveness perspectives. The mRNA1273 vaccine showed slightly more effectiveness than the BNT162b vaccine.
  • In adults hospitalized with COVID-19, high- vs low-dose venous thromboprophylaxis reduces venous thromboembolism but increases major bleeding
    A total of 5470 patients from 9 RCTs were included. Four trials included critically ill patients, four non-critically ill patients, and one included both. VTE occurred in 2.9% of patients on high-dose and in 5.7% of patients on low-dose thromboprophylaxis (relative risk [RR] 0.53; 95% confidence intervals [CIs], 0.41-0.69; I2 = 0%; number needed to treat for an additional beneficial outcome, 22). Major bleeding occurred in 2.5% and 1.4% of patients, respectively (RR 1.78; 95% CI, 1.20-2.66; I2 = 0%; number needed to treat for an additional harmful outcome, 100). All-cause mortality did not differ between groups (RR 0.97; 95% CI, 0.75-1.26; I2 = 47%). The risk of VTE was significantly reduced by high-dose thromboprophylaxis in non-critically ill (RR 0.54; 95% CI, 0.35-0.86; I2 = 0%), but not in critically ill patients (RR 0.69; 95% CI, 0.39-1.21; I2 = 36%). In hospitalized patients with COVID-19, high-dose thromboprophylaxis is more effective than low-dose for the prevention of VTE but increases the risk of major bleeding.
  • Immunocompromise and durability of BNT162b2 vaccine against severe outcomes due to omicron and delta variants
    Updated findings suggest that waning effectiveness against hospital and emergency department admission after receiving a third dose of BNT162b2 vaccine is likely nuanced; that it is likely occurring for some high-risk individuals and in some settings (as was initially identified), but not in others. Despite emerging evidence from Israel showing that a fourth dose improves protection against severe outcomes, including hospitalization and death, in the general older adult population,5–7 more data are needed to fully understand long-term protection against omicron after a third dose and to inform recommendations for fourth doses (ie, second boosters) in those who are not high risk.
  • Association Between BNT162b2 Vaccination and Long COVID After Infections Not Requiring Hospitalization in Health Care WorkersIn this longitudinal observational study conducted among health care workers with SARS-CoV-2 infections not requiring hospitalization, 2 or 3 doses of vaccine, compared with no vaccination, were associated with lower long COVID prevalence. Study limitations include that symptoms and duration were self-reported, and causality cannot be inferred.


  • Analytic survey: In persons with mild to moderate respiratory symptoms, saliva and nasopharyngeal samples were compared for detecting COVID-19 using RT-PCR
    Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, molecular diagnostics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have taken center stage in the detection of infected individuals for isolation purposes but also in the mass surveillance as a preventive strategy to contain the virus spread. While nasopharyngeal swabs (NPS) have remained the golden standard substrate, salivary diagnostic for SARS-CoV-2 has been proposed as an alternative and noninvasive measure in vulnerable individuals. Nevertheless, there is a widespread assumption that salivary reverse-transcription polymerase chain reaction (RT-PCR) does not match the quality of testing using NPS and particular care should be taken in respect to food or beverage intake, when sampling saliva. Our study indicates that without any precaution in the selection of 190 patients, nor restriction over the time window of sampling, there is 99% match in the COVID-19 positivity between NPS and saliva when using RT-PCR, with a reported Delta in thermal cycles (Cts) values for the viral genes Envelope (E) and Open reading frame 1ab (Orf1ab) between 0 and 2, a 98.7% sensitivity and 100% specificity. This high accuracy is maintained in pooling configurations that can be used for mass-testing purposes in professional and educational settings. The further advantage to using crude saliva as compared to NPS or mouthwash is that direct methods yield robust results. Overall, this study validates and promotes the use of salivary diagnostic for COVID-19 eliminating the need of a medical practitioner for the sampling, resolving the unpleasantness of the NPS intervention and empowering the patient to do self-testing in times of need.


  • COVID-19 Vaccine Provider Availability and Vaccination Coverage Among Children Aged 5-11 Years- United States, November 1, 2021-April 25, 2022
    Among 2,586 U.S. counties included in the analysis, 87.5% had at least one active COVID-19 vaccine provider serving children aged 5-11 years. Among the five assessed active provider types, most counties had at least one pharmacy (69.1%) or public health clinic (61.3%), whereas fewer counties had at least one pediatric clinic (29.7%), family medicine clinic (29.0%), or federally qualified health center (FQHC)* (22.8%). Median county-level vaccination coverage was 14.5% (IQR = 8.9%–23.6%). After adjusting for social vulnerability index (SVI)and urbanicity, the analysis found that vaccination coverage among children aged 5–11 years was higher in counties with at least one active COVID-19 vaccine provider than in counties with no active providers (adjusted rate ratio [aRR] = 1.66) (adjusted rate ratio). For each provider type, presence of at least one provider in the county was associated with higher coverage; the largest difference in vaccination coverage was observed between counties with and without pediatric clinics (aRR = 1.37).
  • The latent period of coronavirus disease 2019 with SARS-CoV-2 B.1.617.2 Delta variant of concern in the postvaccination era
    Emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have resulted in new challenges for epidemic prevention and control worldwide. However, little is known about the latent period of coronavirus disease by the SARS-CoV-2 Delta variant of concern (VOC) in the postvaccination era. The epidemiology and clinical data of cases with confirmed SARS-CoV-2 Delta VOC infection were retrospective collected. Dates of the first positive PCR test were collected to estimate the distribution of latent period. Of the 40 patients, 16 were male (40%). The median age of patients was 47.5 years. The median latent period of patients was 6.0 days (interquartile range [IQR], 4.0-9.0 days) and the longest latent period was 13.0 days after exposure. The latent periods were longer in male patients compared to female patients (median, 8.5 days vs. 5.0 days, p = .041). The median latent period was comparable among fully vaccinated cases (6.5 days), no vaccinated cases (7.5 days), and partially vaccinated cases (5.5 days). The median latent period of SARS-CoV-2 Delta VOC infection was 6.0 days. The latent period between vaccinated and non-vaccinated patients was not significantly different. The 14-day quarantine program is sufficient to prevent the transmission of COVID-19 by Delta VOC in the postvaccination era.

Situation Dashboards


World Health Organization (WHO)

Novel Coronavirus (COVID-19) Situation from World Health Organization (WHO)

Johns Hopkins University (JHU)

Coronavirus COVID-19 Global Cases by the Center for Systems Science and Engineering (CSSE) at JHU

COVID-19 in US and Canada

1Point3Acres Real-Time Coronavirus (COVID-19) Updates in US and Canada with Credible Sources

Genomic Epidemiology COVID-19

Genomic Epidemiology of (COVID-19) Maintained by the Nextstrain team, enabled by data from GISAID.

Sources for COVID-19 Information


World Health Organization (WHO)


Centers for Disease Control, US


International Society for Infectious Diseases


This Week in Virology (TWIV)

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