Evaluating the Association between Routine Pneumococcal Vaccination and COVID-19 Severity among Older Adults in the United States (preprint)

BackgroundThe relationship between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Streptococcus pneumoniae remains uncertain. This study investigates the association between routine pneumococcal vaccination and the progression to severe COVID-19 outcomes in a cohort of older adults in the United States. MethodsOur cohort study includes adults aged 65 and older from a subset of adults covered by Medicare in the United States with a documented COVID-19 diagnosis. Logistic regression models were employed to assess the association between pneumococcal vaccination (13-valent conjugate vaccine [PCV13] and 23-valent pneumococcal polysaccharide vaccine [PPSV23]) and COVID-19 severity. ResultsAmong 90,070 Medicare enrollees with a COVID-19 diagnosis, 28,124 individuals exhibited severe respiratory symptoms or were admitted to the intensive care unit (ICU). The odds ratio (OR) for progression from non-severe symptoms to respiratory symptoms with or without ICU admission with prior PCV13 receipt was 0.91 (95% confidence interval [CI], 0.88, 0.93), the OR for progression from severe respiratory symptoms to ICU critical care with prior PCV13 receipt was 0.92 (95% CI, 0.88, 0.97), and the OR for progression from non-severe symptoms to ICU critical care with prior PCV13 receipt was 0.85 (95% CI, 0.81, 0.90). There was no association between PPSV23 received more than five years before the COVID-19 diagnosis and the COVID-19 outcomes. ConclusionsOverall, our findings indicate moderate to no association between PCV vaccination and COVID-19 severity.

Expansion of profibrotic monocyte-derived alveolar macrophages in patients with persistent respiratory symptoms and radiographic abnormalities after COVID-19 (preprint)

As many as 10-30% of the over 760 million survivors of COVID-19 develop persistent symptoms, of which respiratory symptoms are among the most common. To understand the cellular and molecular basis for respiratory PASC, we combined a machine learning-based analysis of lung computed tomography (CT) with flow cytometry, single-cell RNA-sequencing analysis of bronchoalveolar lavage fluid and nasal curettage samples, and alveolar cytokine profiling in a cohort of thirty-five patients with respiratory symptoms and radiographic abnormalities more than 90 days after infection with COVID-19. CT images from patients with PASC revealed abnormalities involving 73% of the lung, which improved on subsequent imaging. Interstitial abnormalities suggestive of fibrosis on CT were associated with the increased numbers of neutrophils and presence of profibrotic monocyte-derived alveolar macrophages in BAL fluid, reflecting unresolved epithelial injury. Persistent infection with SARS-CoV-2 was identified in six patients and secondary bacterial or viral infections in two others. These findings suggest that despite its heterogenous clinical presentations, respiratory PASC with radiographic abnormalities results from a common pathobiology characterized by the ongoing recruitment of neutrophils and profibrotic monocyte-derived alveolar macrophages driving lung fibrosis with implications for diagnosis and therapy.

Impact of the Omicron strain on febrile convulsions in children: A single-center observational study (preprint)

<Purpose> The emergence of the Omicron strain of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the end of December 2021 has drastically increased the number of infected children in Japan, along with the number of children with febrile convulsions. However, impact of the Omicron strain on the febrile convulsions in children is not clear.<Methods> We compared the frequency of SARS-CoV-2 infection in children hospitalized with febrile convulsions with the frequency of SARS-CoV-2 infection in children with fever and respiratory symptoms without convulsions.<Results> In 2021 and 2022, 49 and 58 children, respectively, required emergency hospitalization for febrile convulsions (FC group), in which 24 and 38 children underwent a Filmarray respiratory panel ® test (FA test) and quantitative antigen test for SARS-CoV-2, respectively. In 2022, only six patients tested positive for SARS-CoV-2 (10.3%, 6/58). As a reference group, 655 children aged < 10 years who underwent the FA test for fever and respiratory symptoms during the same period were investigated, and 4 (1.8%, 4/223) and 42 (9.7%, 42/432) tested positive for SARS-CoV-2 in 2021 and 2022, respectively. Rhinovirus/enterovirus (RV/EV) was the most frequently detected virus, followed by respiratory syncytial virus (RSV) and parainfluenza virus 3 (PI3); no significant difference in the trend of detected viruses was observed between the two groups.<Conclusions> The frequency of febrile convulsions associated with SARS-CoV-2 infection of the Omicron strain in children may be similar to that of other common respiratory viruses.

Kidney involvement in children during SARS-CoV-2 Omicron variant pandemic (preprint)

Background As the COVID-19 pandemic persists with the Omicron variants, infection rates in children have rapidly increased compared to previous years. We aimed to investigate the presentation of kidney involvement in children after COVID-19 Omicron variant infection.Methods We retrospectively reviewed the medical records of pediatric patients who presented with kidney involvement between January and August 2022 with a temporal relationship with COVID-19 infection from a Korean single tertiary center.Results Fifteen children presented with kidney involvement after Omicron infection, with a median age of 10.6 (6.8–18.3) years. Aside from fever, cough, sore throat, and diarrhea, none of the patients had severe respiratory symptoms. The median time from infection to renal symptom onset was 3 (0–49) days. Among 10 patients with underlying kidney disease, 6 had previously been diagnosed with nephrotic syndrome (NS) that relapsed after COVID-19 infection, 2 with immunoglobulin A nephropathy (IgAN) showed transient gross hematuria (GHU) with or without acute kidney injury (AKI), and 2 with kidney transplantation presented with AKI. Of the 5 patients without underlying kidney disease, one patient had NS, and the other 4 patients had GHU and proteinuria (PU), of whom one was eventually diagnosed with Henoch-Shönlein purpura nephritis (HSPN). Seven NS patients (1 new-onset, 6 relapsed) showed uneventful remission with corticosteroids. Other than one patient with new-onset HSPN, patients with GHU and PU resolved spontaneously, and patients with AKI also resolved with supportive care.Conclusions Kidney involvement can occur in various, but mostly non-fatal manifestations in children after COVID-19 Omicron variant infection.

Systematic Mendelian randomization study of the effect of gut microbiome and plasma metabolome on severe COVID-19 (preprint)

Background COVID-19 could develop severe respiratory symptoms in certain infected patients, especially in the patients with immune disorders. Gut microbiome and plasma metabolome act important immunological modulators in the human body and could contribute to the immune responses impacting the progression of COVID-19.Methods Based on two-sample Mendelian randomization framework, the causal effects of 131 microbiota in genus or species level and 452 plasma metabolites on severe COVID-19 are estimated. Single nucleotide polymorphisms (SNPs) strongly associated with the abundance of intestinal bacteria in gut and the concentration of metabolites in plasma have been utilized as the instrument variables to infer whether they are causal factors of severe COVID-19. In addition, mediation analysis is conducted to find the potential link between the microbiota and metabolite which identified by polygenic Mendelian randomization analysis, while colocalization analysis has been performed to validate the causal relationships which identified by cis-Mendelian randomization analysis.Results Mendelian randomization support 13 microbiota and 53 metabolites, which are significantly causal association with severe COVID-19. Mediation analysis find 11 mediated relations, such as myo-inositol, 2-stearoylglycerophosphocholine and alpha-glutamyltyrosine, which appeared to mediate the association of Howardella and Ruminiclostridium 6 with severe COVID-19 respectively, while Butyrivibrio and Ruminococcus gnavus appeared to mediate the association of myo-inositol and N-acetylalanine respectively. Ruminococcus torques abundance was colocalized with severe COVID-19 (PP.H4 = 0.77) and the colon expression of permeability related protein RASIP1 (PP.H4 = 0.95).Conclusions Our study results highlight the causal relationships of gut microbiome and plasma metabolome for severe COVID-19, which have the promise to be served as clinical biomarkers for risk stratification and prognostication, and novel basis to unravel the pathophysiological mechanisms of severe COVID-19.

Resolving the developmental mechanisms of coagulation abnormalities characteristic of SARS-CoV2 based on single-cell transcriptome analysis (preprint)

The COVID-19 outbreak caused by the SARS-CoV-2 virus has developed into a global health emergency. In addition to causing respiratory symptoms following SARS-CoV-2 infection, COVID-19-associated coagulopathy (CAC) is the main cause of death in patients with severe COVID-19. In this study, we performed single-cell sequencing analysis of the right ventricular free wall tissue from healthy donors, patients who died in the hypercoagulable phase of CAC, and patients in the fibrinolytic phase of CAC. Among these, we collected 61,187 cells, which were enriched in 24 immune cell subsets and 13 cardiac-resident cell subsets. We found that in response to SARS-CoV-2 infection, CD9highCCR2high monocyte-derived mo promoted hyperactivation of the immune system and initiated the extrinsic coagulation pathway by activating CXCR-GNB/G-PI3K-AKT. This sequence of events is the main process contributing the development of coagulation disorders subsequent to SARS-CoV-2 infection. In the characteristic coagulation disorder caused by SARS-CoV-2, excessive immune activation is accompanied by an increase in cellular iron content, which in turn promotes oxidative stress and intensifies intercellular competition. This induces cells to alter their metabolic environment, resulting in an increase in sugar uptake, such as that via the glycosaminoglycan synthesis pathway, in CAC coagulation disorders. In addition, high levels of reactive oxygen species generated in response elevated iron levels promote the activation of unsaturated fatty acid metabolic pathways in endothelial cell subgroups, including vascular endothelial cells. This in turn promotes the excessive production of the toxic peroxidation by-product malondialdehyde, which exacerbates both the damage caused to endothelial cells and coagulation disorders.

Performance evaluation of the LumiraDx SARS-CoV-2 & Flu A/B Test in diagnosing COVID-19 and influenza in patients with respiratory symptoms (preprint)

IntroductionCoronavirus disease 2019 (COVID-19) and influenza share similar symptoms, which hampers diagnosis. Given that they require different containment and treatment strategies, fast and accurate distinction between the two infections is needed. This study evaluates the sensitivity and specificity of the LumiraDx SARS-CoV-2 & Flu A/B Test for simultaneous detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A/B from a single nasal swab. MethodsNasal samples were collected from patients as part of the ASPIRE (NCT04557046) and INSPIRE (NCT04288921) studies at point-of-care testing sites in the USA. ASPIRE study participants were included after developing COVID-19 symptoms in the last 14 days or following a positive SARS-CoV-2 test in the last 48 hours. INSPIRE study participants were included after developing influenza symptoms in the last 4 days. Samples were extracted into proprietary buffer and analysed using the LumiraDx SARS-CoV-2 & Flu A/B Test. A reference sample was taken from each subject, placed into universal transport medium and tested using reference SARS-CoV-2 and influenza reverse transcription polymerase chain reaction (RT-PCR) tests. The test and reference samples were compared using the positive percent agreement (PPA) and negative percent agreement (NPA), together with their 95% confidence intervals (CI). ResultsAnalysis of the data from the ASPIRE (N=124) and INSPIRE (N=159) studies revealed high levels of agreement between the LumiraDx SARS-CoV-2 & Flu A/B Test and the reference tests in detecting SARS-CoV-2 (PPA=95.5% [95% CI: 84.9%, 98.7%]; NPA=96.0% [95% CI: 90.9%, 98.3%]), influenza A (PPA=83.3% [95% CI: 66.4%, 92.7%]; NPA=97.7% [95% CI: 93.4%, 99.2%]) and influenza B (PPA=80.0% [95% CI: 62.7%, 90.5%]; NPA=95.3% [95% CI: 90.2%, 97.9%]). ConclusionsThe LumiraDx SARS-CoV-2 & Flu A/B Test shows a high agreement with the reference RT-PCR tests while simultaneously detecting and differentiating between SARS-CoV-2 and influenza A/B. Trial registration, ClinicalTrials.gov identifier: NCT04557046 and NCT04288921

Diagnostic accuracy of the Panbio COVID-19 Antigen rapid test device for SARS-CoV-2 detection in Kenya, 2021: A field evaluation (preprint)

Background: Accurate and timely diagnosis is essential in limiting the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Real-time reverse transcription-polymerase chain reaction (rRT-PCR), the reference standard, requires specialized laboratories, costly reagents, and a long turnaround time. Antigen rapid diagnostic tests (Ag RDTs) provide a feasible alternative to rRT-PCR since they are quick, relatively inexpensive, and do not require a laboratory. The WHO requires that Ag RDTs have a sensitivity [≥]80% and specificity [≥]97%. Methods: This evaluation was conducted at 11 health facilities in Kenya between March and July 2021. We enrolled persons of any age with respiratory symptoms and asymptomatic contacts of confirmed COVID-19 cases. We collected demographic and clinical information and two nasopharyngeal specimens from each participant for Ag RDT testing and rRT-PCR. We calculated the diagnostic performance of the Panbio Ag RDT against the US Centers for Disease Control and Prevention's (CDC) rRT-PCR test. Results: We evaluated the Ag RDT in 2,245 individuals where 551 (24.5%, 95% CI: 22.8-26.3%) tested positive by rRT-PCR. Overall sensitivity of the Ag RDT was 46.6% (95% CI: 42.4-50.9%), specificity 98.5% (95% CI: 97.8-99.0%), PPV 90.8% (95% CI: 86.8-93.9%) and NPV 85.0% (95% CI: 83.4-86.6%). Among symptomatic individuals, sensitivity was 60.6% (95% CI: 54.3-66.7%) and specificity was 98.1% (95% CI: 96.7-99.0%). Among asymptomatic individuals, sensitivity was 34.7% (95% CI 29.3-40.4%) and specificity was 98.7% (95% CI: 97.8-99.3%). In persons with onset of symptoms <5 days (594/876, 67.8%), sensitivity was 67.1% (95% CI: 59.2-74.3%), and 53.3% (95% CI: 40.0-66.3%) among those with onset of symptoms >7 days (157/876, 17.9%). The highest sensitivity was 87.0% (95% CI: 80.9-91.8%) in symptomatic individuals with cycle threshold (Ct) values [≤]30. Conclusion: The overall sensitivity and NPV of the Panbio Ag RDT were much lower than expected. The specificity of the Ag RDT was high and satisfactory; therefore, a positive result may not require confirmation by rRT-PCR. The kit may be useful as a rapid screening tool for only symptomatic patients in high-risk settings with limited access to RT-PCR. A negative result should be interpreted based on clinical and epidemiological information and may require retesting by rRT-PCR.

SARS-CoV-2 reinfections with BA.1 (Omicron) variant among fully vaccinated individuals in the northeast of Brazil (preprint)

Background: The first case of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Rio Grande do Norte, northeast Brazil, was diagnosed on March 12, 2020; thereafter, the pattern of COVID-19 followed the multiple waves as seen elsewhere. The waves were mostly due to the SARS-CoV-2 virus mutations leading to emergence of variants of concern (VoC). The introduction of new VoCs in a population context of prior SARS-CoV-2 infections or after vaccination has been a challenge in understanding the kinetics of the protective immune response against SARS-CoV-2 . The aim of this study was to investigate the outbreak of SARS-CoV-2 reinfections observed in mid-January 2022 in Rio Grande do Norte state, Brazil when the omicron variant was introduced. Methodology/Principal findings: From a total of 172,965 individuals with mild to severe respiratory symptoms, 58,097 tested positive for SARS-CoV-2 between March 2020 through mid-February 2022. Of those previously infected, 444 had documented a second SARS-CoV-2 infection and 9 of these reinfection cases were selected for sequencing. Genomic analysis revealed that virus lineages diverged between primary and the reinfection, with the latter caused by the Omicron (BA.1) variant among individuals fully vaccinated against SARS-CoV-2. Conclusions/Significance: Once all subjects whose samples were sequenced had prior SARS-CoV-2 infection and were also fully vaccinated, our data suggest that the Omicron variant evades natural and vaccine-induced immunities, confirming the continuous need to decrease transmission and to develop effective blocking vaccines.

Non-invasive Vagus Nerve Stimulation for Respiratory Symptoms of COVID-19: Results From a Randomized Controlled Trial (SAVIOR I) (preprint)

BackgroundSevere coronavirus disease 2019 (COVID-19) is characterized, in part, by an excessive inflammatory response. Evidence from animal and human studies suggests that vagus nerve stimulation can lead to reduced levels of various pro-inflammatory cytokines. We conducted a prospective randomized controlled study (SAVIOR-I) to assess the feasibility, efficacy, and safety of non-invasive vagus nerve stimulation (nVNS) for the treatment of respiratory symptoms and inflammatory markers among patients who were hospitalized for COVID-19 (ClinicalTrials.gov identifier: NCT04368156). MethodsParticipants were randomly assigned in a 1:1 allocation to receive either the standard of care (SoC) alone or nVNS therapy plus the SoC. The nVNS group received 2 consecutive 2-minute doses of nVNS 3 times daily as prophylaxis. Efficacy and safety were evaluated via the incidence of specific clinical events, inflammatory biomarker levels, and the occurrence of adverse events. ResultsOf the 110 participants who were enrolled and randomly assigned, 97 (nVNS, n=47; SoC, n=50) had sufficient available data and comprised the evaluable population. C-reactive protein (CRP) levels decreased from baseline to a significantly greater degree in the nVNS group than in the SoC group at day 5 and overall (ie, all postbaseline data points collected through day 5, combined). Procalcitonin level also showed significantly greater decreases from baseline to day 5 in the nVNS group than in the SoC group. D-dimer levels were decreased from baseline for the nVNS group and increased from baseline for the SoC group at day 5 and overall, although the difference between the treatment groups did not reach statistical significance. No significant treatment differences were seen for clinical respiratory outcomes or any of the other biochemical markers evaluated. No serious nVNS-related adverse events occurred during the study. ConclusionsnVNS therapy led to significant reductions in levels of inflammatory markers, specifically CRP and procalcitonin. Because nVNS has multiple mechanisms of action that may be relevant to COVID-19, additional research into its potential to be used earlier in the course of COVID-19 and possibly mitigate some of the symptoms associated with post-acute COVID-19 syndrome is warranted.

COVID-19 in hospitalized patients in 4 hospitals in San Isidro, Buenos Aires, Argentina (preprint)

In December 2019, a novel illness called coronavirus disease 2019 (COVID 19) was described in China and became pandemic in a few months. The first case was detected in Argentina on March 3, 2020. A multicentre prospective observational cohort study on hospitalized patients with COVID 19 was conducted in 4 hospitals in San Isidro district from March 1, 2020 to October 31. Data was obtained by the attendant physician. 668 patients were included, the median age was 54 years, and 42.7% were female. Male sex and older age were associated with COVID 19 disease and more strongly with severity. Most frequent symptoms were fever and cough followed by dyspnoea, myalgia, odynophagia, headache, anosmia, and diarrhoea. Nonsevere patients had more upper respiratory symptoms while severe patients had mainly lower respiratory symptoms on admission. Most common comorbidities were arterial hypertension, diabetes, and cardiovascular disease. A great proportion of patients had normal thorax X ray and ground-glass opacity in tomography. In severe patients, radiography and tomography had a predominant ground glass pattern, but normal radiography and tomography on presentation were present in 22% and 5.9%, respectively. The absence of fever and normal radiology on admission neither excluded the disease nor further severity. PCR elevation was related with COVID 19 disease and with severity, while lymphopenia was more related with the disease and leukocytosis and thrombocytopenia with severity. 8, 4% of patients were health care workers. The mortality rate was 12.4%, 32.7% in severe patients and 61.2% in ventilated patients. Mortality was higher in the public hospital, probably associated with patients with older age and more comorbidities. All these observations can contribute to the knowledge of this disease in terms of diagnosis and prognosis.

Severe Acute Respiratory Syndrome Coronavirus-2 genome sequence variations relate to morbidity and mortality in Coronavirus Disease-19 (preprint)

Outcome of infection with Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) may depend on the host, virus or the host-virus interaction related factors. Complete SARS-CoV-2 genome was sequenced using Illumina and Nanopore platforms from naso-/oro-pharyngeal ri-bonucleic acid (RNA) specimens from COVID-19 patients of varying severity and outcomes, including patients with mild upper respiratory symptoms (n=35), severe disease admitted to intensive care with respiratory and gastrointestinal symptoms (n=21), fatal COVID-19 outcome (n=17) and asymptomatic (n=42). Of a number of genome variants observed, p.16L>L (Nsp1), p.39C>C (Nsp3), p.57Q>H (ORF3a), p.71Y>Y (Membrane glycoprotein), p.194S>L (Nucleocapsid protein) were observed in similar frequencies in different patient subgroups. However, seventeen other variants were observed only in symptomatic patients with severe and fatal COVID-19. Out of the latter, one was in the 5UTR (g.241C>T), eight were synonymous (p.14V>V and p.92L>L in Nsp1 protein, p.226D>D, p.253V>V, and p.305N>N in Nsp3, p.34G>G and p.79C>C in Nsp10 protein, p.789Y>Y in Spike protein), and eight were non-synonymous (p.106P>S, p.157V>F and p.159A>V in Nsp2, p.1197S>R and p.1198T>K in Nsp3, p.97A>V in RdRp, p.614D>G in Spike protein, p.13P>L in nucleocapsid). These were completely absent in the asymptomatic group. SARS-CoV-2 genome variations have a significant impact on COVID-19 presentation, severity and outcome.

COVID-19 Related Chemosensory Changes in Individuals with Self-Reported Obesity (preprint)

Background/objectives: Individuals with obesity show alterations in smell and taste abilities. Smell and taste loss are also the most prominent neurological symptoms of COVID-19, yet how chemosensory ability present in individuals with obesity with a positive COVID-19 diagnosis is unknown. Subjects/Methods: In this secondary analysis of a cross-sectional global dataset, we compared self-reported chemosensory ability in participants with a respiratory illness reporting a positive (C19+; n = 5156) or a negative (C19-; n = 659) COVID-19 laboratory test outcome, who also self-reported to be obese (C19+; n = 433, C19-; n = 86) or non-obese. Results: Compared to the C19- group, C19+ exhibited a greater decline in smell, taste, and chemesthesis during illness, though these symptoms did not differ between participants with obesity and without obesity. In 68% of participants who reported recovery from respiratory illness symptoms (n=3431 C19+ and n= 539 C19-), post-recovery chemosensory perception did not differ in C19+ and C19- diagnosis, and by self-reported obesity. Finally, we found that all chemosensory and other symptoms combined predicted the C19+ diagnosis in participants with obesity with a moderately good estimate (63% accuracy). However, in C19+ participants with obesity, we observed a greater relative prevalence of non-chemosensory symptoms, including respiratory as respiratory and GI symptoms. Conclusions: We conclude that despite a presumed lower sensitivity to chemosensory stimuli, COVID-19 respondents with obesity experience a similar self-reported chemosensory loss as those without obesity, and in both groups self-reported chemosensory symptoms are similarly predictive of COVID-19.

Before the Surge: Molecular Evidence of SARS-CoV-2 in New York City Prior to the First Report (preprint)

New York City (NYC) emerged as a coronavirus disease 2019 (COVID-19) epicenter in March 2020, but there is limited information regarding potentially unrecognized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections before the first reported case. We utilized a sample pooling strategy to screen for SARS-CoV-2 RNA in de-identified, respiratory pathogen-negative nasopharyngeal specimens from 3,040 patients across our NYC health system who were evaluated for respiratory symptoms or influenza-like illness during the first 10 weeks of 2020. We obtained complete SARS-CoV-2 genome sequences from samples collected between late February and early March. Additionally, we detected SARS-CoV-2 RNA in pooled specimens collected in the week ending 25 January 2020, indicating that SARS-CoV-2 caused sporadic infections in NYC a full month before the first officially documented case.

Follow-up of a hospital cohort during the first 3,530 suspected cases of COVID-19 in Sao Jose do Rio Preto, Sao Paulo, Brazil (preprint)

Introduction: In a global context, COVID-19 is the most significant health threat in the present days, evidenced by the fact that, in just over four months, SARS-CoV-2 has spread to 171 countries, reaching a Pandemic status. Most patients with COVID-19 have a mild course of the disease. However, approximately 20% develop severe illness with a high mortality rate which is associated with age, comorbidities, and immunosuppression. Epidemiological studies are used to reveal the extent of viral spread in homes, communities, and hospitals. Thus, preventive and control measures can be established by the authorities. Objective: In this study, patients with suspect COVID-19 symptoms who search for hospital care at the city of Sao Jose do Rio Preto (Sao Paulo, Brazil) were monitored, in order to identify the first case of this new disease in the region. In the first two months (March and April), more than 3000 individuals looked for the public and private health system with suspected respiratory symptoms, but only 164 (8.4%) were COVID-19 confirmed. Results: From those, males (56.1%) and patients of the age distribution of 16-59 (91.2%), with diarrhea (22.2%), runny nose (25%), altered taste (15.9%), and anosmia (11.6%) presented statistical significance, although none comorbidities were related with COVID-19 occurrence. The odds ratio analysis supports this finding. Days of onset of symptoms are positively associated with whit viral load, and the same happens with the occurrence of symptoms (dyspnea and low saturation).

HLA-A*11:01:01:01, HLA*C*12:02:02:01-HLA-B*52:01:02:02, age and sex are associated with severity of Japanese COVID-19 with respiratory failure (preprint)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing coronavirus disease 2019 (COVID-19) was announced as an outbreak by the World Health Organization (WHO) in January 2020 and as a pandemic in March 2020. The majority of infected individuals have experienced no or only mild symptoms, ranging from fully asymptomatic cases to mild pneumonic disease. However, a minority of infected individuals develop severe respiratory symptoms. The objective of this study was to identify susceptible HLA alleles and clinical markers for the early identification of severe COVID-19 among hospitalized COVID-19 patients. A total of 137 patients with mild COVID-19 (mCOVID-19) and 53 patients with severe COVID-19 (sCOVID-19) were recruited from the Center Hospital of the National Center for Global Health and Medicine (NCGM), Tokyo, Japan for the period of February-August 2020. High-resolution sequencing-based typing for eight HLA genes was performed using next-generation sequencing. In the HLA association studies, HLA-A*11:01:01:01 [Pc = 0.013, OR = 2.26 (1.27-3.91)] and HLA-C*12:02:02:01-HLA-B*52:01:01:02 [Pc = 0.020, OR = 2.25 (1.24-3.92)] were found to be significantly associated with the severity of COVID-19. After multivariate analysis controlling for other confounding factors and comorbidities, HLA-A*11:01:01:01 [P = 3.34E-03, OR = 3.41 (1.50-7.73)], age at diagnosis [P = 1.29E-02, OR = 1.04 (1.01-1.07)] and sex at birth [P = 8.88E-03, OR = 2.92 (1.31-6.54)] remained significant. Early identification of potential sCOVID-19 could help clinicians prioritize medical utility and significantly decrease mortality from COVID-19.

SARS-CoV-2 viral load distribution in different patient populations and age groups reveals that viral loads increase with age. (preprint)

Objectives: To describe the SARS-CoV-2 viral load distribution in different patient groups and age categories. Methods: All SARS-CoV-2 RT-PCR results from nasopharyngeal (NP) and oropharyngeal (OP) swabs (first PCR from unique patients only) that were collected between January 1 and December 1, 2020, in the Public Health Services regions Kennemerland and Hollands Noorden, province of Northern Holland, the Netherlands were included in this study. Swabs were derived from patients with respiratory symptoms who were presented at the general practitioner (GP) or hospital, hospital health care workers (HCWs) of four regional hospitals, nursing home residents and HCWs of multiple nursing homes, and in majority (>75%) from Public Health testing facilities of the two Public Health Services. SARS-CoV-2 PCR crossing point (Cp) values were used to estimate viral loads (higher Cp-values indicate lower viral loads). Results: In total, 278.470 unique patients were tested of whom 9.1% (n=25.365) were SARS-CoV-2 positive. As there were differences in viral load distribution between tested populations, further analyses focused on PCRs performed by public health services (n=211.933) where sampling and inclusion were uniform. These data present reveal a clear relation between age and SARS-CoV-2 viral load, with especially children aged<12 years showing lower viral loads than shown in adults ({beta}: -0.03, 95CI% -0.03 to -0.02, p<0.001), independent of sex and/or symptom duration. Interestingly, the median Cp values between the oldest (>79 years) and youngest (<12 years) population differed by over 4 PCR cycles, suggesting approximately a 16 fold difference in viral load. In addition, the proportion of children aged < 12 years with a Cp-value >30 was significantly higher compared to the other patients (31.1% vs. 16.9%, p-value<0.001). Conclusion: We observed that in patients tested by public health services, SARS-CoV2 viral load increases significantly with age. Previous studies suggest that young children (<12 years) play a limited role in SARS-CoV-2 transmission. Currently, the relation between viral load and infectivity is not yet well understood, and further studies should elucidate whether the lower viral load in children is indeed related to their suggested limited role in SARS-CoV-2 transmission. Moreover, as antigen tests are less sensitive than PCR, these results suggest that SARS-CoV-2 antigen tests could have lower sensitivity in children than in adults.

SNPnexus COVID: Facilitating the analysis of COVID-19 host genetics (preprint)

The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has presented a crisis for global healthcare systems. Human SARS-CoV-2 infection can result in coronavirus disease 2019 (COVID-19), which has been characterised as an acute respiratory illness, with most patients displaying flu-like symptoms, such as a fever, cough and dyspnoea. However, the range and severity of individual symptoms experienced by patients can vary significantly, indicating a role for host genetics in impacting the susceptibility and severity of COVID-19 disease. Whilst most symptomatic infections are known to manifest in mild to moderate respiratory symptoms, severe pneumonia and complications including cytokine release syndrome, which can lead to multi-organ dysfunction, have also been observed in cases worldwide. Global initiatives to sequence the genomes of patients with COVID-19 have driven an expanding new field of host genomics research, to characterise the genetic determinants of COVID-19 disease. The functional annotation and analysis of incoming genomic data, within a clinically relevant turnaround time, is therefore imperative given the importance and urgency of research efforts to understand the biology of SARS-CoV-2 infection and disease. To address these requirements, we developed SNPnexus COVID. This is a web-based variant annotation tool, powered by the SNPnexus software.

Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2 (preprint)

The ongoing SARS-CoV-2 pandemic has brought an urgent need for animal models to study the pathogenicity of the virus. Herein, we generated and characterized a novel mouse-adapted SARS-CoV-2 strain named MASCp36 that causes acute respiratory symptoms and mortality in standard laboratory mice. Particularly, this model exhibits age and gender related skewed distribution of mortality akin to severe COVID-19, and the 50% lethal dose (LD50) of MASCp36 was ~100 PFU in aged, male BALB/c mice. Deep sequencing identified three amino acid mutations, N501Y, Q493H, and K417N, subsequently emerged at the receptor binding domain (RBD) of MASCp36, which significantly enhanced the binding affinity to its endogenous receptor, mouse ACE2 (mACE2). Cryo-electron microscopy (cryo-EM) analysis of mACE2 in complex with the RBD of MASCp36 at 3.7-angstrom resolution elucidates molecular basis for the receptor-binding switch driven by amino acid substitutions. Our study not only provides a robust platform for studying the pathogenesis of severe COVID-19 and rapid evaluation of coutermeasures against SARS-CoV-2, but also unveils the molecular mechanism for the rapid adaption and evolution of SARS-CoV-2 in mice.

SARS-CoV-2 infects brain astrocytes of COVID-19 patients and impairs neuronal viability (preprint)

COVID-19 patients may exhibit neuropsychiatric and neurological symptoms. We found that anxiety and cognitive impairment are manifested by 28-56% of SARS-CoV-2-infected individuals with mild respiratory symptoms and are associated with altered cerebral cortical thickness. Using an independent cohort, we found histopathological signs of brain damage in 25% of individuals who died of COVID-19. All of the affected brain tissues exhibited foci of SARS-CoV-2 infection and replication, particularly in astrocytes. Infection of neural stem cell-derived astrocytes changed energy metabolism, altered key proteins and metabolites used to fuel neurons and for biogenesis of neurotransmitters, and elicited a secretory phenotype that reduces neuronal viability. Our data support the model where SARS-CoV-2 reaches the brain, infects astrocytes and triggers neuropathological changes that contribute to the structural and functional alterations in the brain of COVID-19 patients.