Association between Household Exposure and Cycle Threshold in COVID-19 Infected Health Care Workers (preprint)

Objective. Household COVID-19 contact constitutes a high-risk exposure for health care workers (HCWs). Cycle threshold (Ct) of reverse transcriptase–polymerase chain reaction testing provides an estimate of COVID-19 viral load, which can inform clinical and workplace management. We assessed whether Ct values differed between HCWs with and without household exposure. Methods. We analyzed HCW cases whose Ct data could be compared. We defined low Ct at a cut-point approximating a viral load of 4.6x106 copies per ml. Logistic regression tested the association of household exposure and symptoms at diagnosis with a low Ct value. Results. Of 77 HCWs, 20 were household exposures cases and 34 were symptomatic at testing (7 fell were both). Among household exposures, 9 (45%) manifested lower Ct values compared to 14 (25%) of all others. Both household exposure (Odds Ratio [OR] 1.3; 95 % Confidence Interval [CI] 1.03–1.6) and symptoms at diagnosis (OR 1.4; 95% CI 1.15–1.7) were associated a low Ct value. Discussion. Household exposure in HCWs was associated with lower Ct values, consistent with a higher viral load, supporting the hypothesis that contracting COVID-19 in that manner leads to a greater viral inoculum.

A Single Drop of Fingerstick Blood for Quantitative Antibody Response Evaluation After SARS-CoV-2 Vaccination (preprint)

Among several COVID vaccines that have been approved, the Moderna and Pfizer-BioNTech vaccines are mRNA vaccines that are safe and highly effective at preventing COVID-19 illness. Studies have demonstrated that neutralizing antibody responses elicited by these vaccines correlate strongly with antibodies measured by immunoassays such as ELISA. To monitor the antibody level duration of vaccine-induced immune responses in vaccinated population, cost-effective and easily implementable antibody testing methodologies are urgently needed. In this study, we evaluated the feasibility of using a single drop of fingerstick blood collected with flocked swabs for a high-throughput and quantitative anti-SARS-CoV-2 spike (S1) IgG antibody immunoassay. A total of 50 voluntary subjects participated and donated fingerstick blood samples before and after receiving the Moderna mRNA vaccine. Among all individuals tested, no anti-SARS-CoV-2 S1 IgG antibody was detected before vaccination and on day 7 after receiving the first vaccine dose. On day 14 after the first dose, a significant amount of anti-SARS-CoV-2 S1 IgG antibody was detected in all participants samples. By the end the third week from the first dose, the median anti-SARS-CoV-2 S1 IgG concentration increased to 44.9 ug/mL. No anti-SARS-CoV-2 nucleocapsid (N) protein IgG antibody was detected in any of the participants during the study period, indicating that the anti-SARS-CoV-2 S1 IgG assay is specific for the mRNA vaccine induced antibodies. Comaprison of venous blood plasma and fingerstick blood for anti-SARS-CoV-2 S1 IgG shown a higher correlation. Furthermore, the fingerstick blood dried swab samples are stable for at least 4 days. In summary, we demonstrated that a single drop of fingerstick blood collected with flocked swab can be used for quantitative detection and monitoring of anti-SARS-CoV-2 spike IgG responses after receiving COVID-19 vaccination. This testing platform does not require venous blood draw and can be easily implemented for large scale antibody testing in vaccinated populations.

A Rapid SARS-CoV-2 Variant Detection by Molecular-Clamping Based RT-qPCR (preprint)

We applied XNA-based Molecular Clamping Technology to develop a multiplex qPCR assay for rapid and accurate detection of SARS-CoV-2 mutations. A total of 278 previously tested SARS-COV-2 positive samples originating primarily from San Francisco Bay Area were tested, including 139 Samples collected in middle January and 139 samples collected at the end of February 2021, respectively. The SARS-CoV-2 Spike-gene D614G mutation was detected from 58 samples (41.7%) collected in January 2021 and, 78 samples (56.1%) collected in February. Notably, while there were no N501Y mutation detected in samples from January, seven of the February samples were tested positive for the N501Y and D614G mutations. The results suggest a relatively recent and speedy spreading of the UK variant (B.1.1.7) in Northern California. This new Molecular Clamping technology-based multiplex RT-qPCR assay is highly sensitive and specific and can help speed up large scale testing for SARS-CoV-2 variants.

TMPRSS2 and ADAM17 interactions with ACE2 complexed with SARS-CoV-2 and B0AT1 putatively in intestine, cardiomyocytes, and kidney (preprint)

COVID-19 outcomes reflect organ-specific interplay of SARS-CoV-2 and its receptor, ACE2, with TMPRSS2 and ADAM17. Confirmed active tropism of SARS-CoV-2 in epithelial cells of intestine and kidney proximal tubule, and in aging cardiomyocytes, capriciously manifests extra pulmonary organ-related clinical symptoms in about half of COVID-19 patients, occurring by poorly understood mechanisms. We approached this knowledge gap by recognizing a clue that these three particular cell types share a common denominator kindred of uniquely expressing the SLC6A19 neutral amino acid transporter B0AT1 protein (alternatively called NBB, B, B0) serving glutamine and tryptophan uptake. B0AT1 is a cellular trafficking chaperone partner of ACE2, shown by cryo-EM to form a thermodynamically-favored stabilized 2ACE2:2B0AT1 dimer-of-heterodimers. The gut is the body's site of greatest magnitude expression depot of both ACE2 and B0AT1. This starkly contrasts with pulmonary pneumocyte expression of monomeric ACE2 with conspicuously undetectable B0AT1. We hypothesized that B0AT1 steers the organ-related interplay amongst ACE2, TMPRSS2, ADAM17, and SARS-CoV-2 RBD. The present study employed molecular docking modeling that indicated active site catalytic pocket residues of TMPRSS2 and ADAM17 each formed bonds [≤] 2 [A] with monomer ACE2 specific residues within a span R652-D713 involved in cleaving sACE2 soluble ectodomain release. These bonds are consistent with competitive binding interactions of experimental anti-SARS-CoV-2 drug small molecules including Camostat and Nafamostat. Without B0AT1, ACE2 residues K657 and N699 dominated docking bonding with TMPRSS2 or ADAM17 active sites, with ACE2 R710 and R709 contributing electrostatic attractions, but notably ACE2 S708 never closer than 16-44 [A]. However, in the dimer-of-heterodimers arrangement all ACE2 neck region residues were limited to TMPRSS2 or ADAM17 approaches [≥]{approx} 35 [A], with the interference directly attributed to the presence of a neighboring B0AT1 subunit complexed to the partnering ACE2 subunit of 2ACE2:2B0AT1; ADAM17 failed to dock by bumping its active site pocket oriented dysfunctionally outwardly facing 180{degrees} away. Results were the same whether the dimer-of-heterodimers was in either the "closed" or "open" conformation, or whether or not SARS-CoV-2 RBD was complexed to ACE2. The results implicate B0AT1-and in particular the 2ACE2:2B0AT1 complex-as a major player in the landscape of COVID-19 pathophysiology engaging TMPRSS2 and ADAM17, consistent with experimental evidence in the literature and in clinical reports. These findings provide a gateway to understanding the roles of B0AT1 relating to COVID-19 manifestations putatively assigned to intestinal and renal epithelial cells and cardiomyocytes, with underpinnings useful for considerations in public hygiene policy and drug development.

An insight into SARS-CoV-2 Membrane protein interaction with Spike, Envelope, and Nucleocapsid proteins (preprint)

Intraviral protein-protein interactions are crucial for replication, pathogenicity, and viral assembly. Among these, virus assembly is a critical step as it regulates the arrangements of viral structural proteins and helps in the encapsulation of genomic material. SARS-CoV-2 structural proteins play an essential role in the self-rearrangement, RNA encapsulation, and mature virus particle formation. In SARS-CoV, the membrane protein interacts with the envelope and spike protein in Endoplasmic Reticulum Golgi Intermediate Complex (ERGIC) to form an assembly in the lipid bilayer, followed by membrane-ribonucleoprotein (nucleocapsid) interaction. In this study, using protein-protein docking, we tried to understand the interaction of membrane protein's interaction with envelope, spike and nucleocapsid proteins. Further, simulation studies performed up to 100ns agreed that protein complexes M-E, M-S, and M-N were stable. Moreover, the calculated free binding energy and dissociation constant values support the protein complex formation. The interaction identified in the study will be of great importance, as it provides valuable insight into the protein complex, which could be the potential drug targets for future studies.

Saliva as a testing specimen with or without pooling for SARS-CoV-2 detection by multiplex RT-PCR test (preprint)

BackgroundSensitive and high throughput molecular detection assays are essential during the coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The vast majority of the SARS-CoV-2 molecular assays use nasopharyngeal swab (NPS) or oropharyngeal swab (OPS) specimens collected from suspected individuals. However, using NPS or OPS as specimens has apparent drawbacks, e.g. the collection procedures for NPS or OPS specimens can be uncomfortable to some people and may cause sneezing and coughing which in turn generate droplets and/or aerosol particles that are of risk to healthcare workers, requiring heavy use of personal protective equipment. There have been recent studies indicating that self-collected saliva specimens can be used for molecular detection of SARS-CoV-2 and provides more comfort and ease of use for the patient. Here we report the performance of QuantiVirus SARS-CoV-2 multiplex test using saliva as the testing specimens with or without pooling. MethodsDevelopment and validation studies were conducted following FDA-EUA and molecular assay validation guidelines. Using SeraCare Accuplex SARS-CoV-2 reference panel, the limit of detection (LOD) and clinical evaluation studies were performed with the QuantiVirus SARS-CoV-2 multiplex test. For clinical evaluation, 85 known positive and 90 known negative clinical NPS samples were tested. Additionally, twenty paired NPS and saliva samples collected from recovering COVID-19 patients were tested and the results were further compared to that of the Abbott m2000 SARS-CoV-2 PCR assay. Results of community collected 389 saliva samples for COVID-19 screening by QuantiVirus SARS-CoV-2 multiplex test were also obtained and analyzed. Moreover, saliva pooling with 6 and 12 samples together were also evaluated. ResultsThe LOD for the QuantiVirus SARS-CoV-2 multiplex test was confirmed to be 100-200 copies/mL. The clinical evaluation using contrived saliva samples indicated that the positive percentage agreement (PPA) of the QuantiVirus SARS-CoV-2 multiplex test is 100% at 1xLOD, 1.5xLOD and 2.5xLOD. No cross-reactivity was observed for the QuantiVirus SARS-CoV-2 multiplex test with common respiratory pathogens. Testing of clinical samples showed a positive percentage agreement (PPA) of 100% (95% CI: 94.6% to 100%) and a negative percentage agreement (NPA) of 98.9% (95% CI: 93.1% to 99.9%). QuantiVirus SARS CoV-2 multiplex test had 80% concordance rate and no significant difference (p=0.13) in paired saliva and NPS specimens by Wilcoxon matched pairs signed rank test. Positive test rate was 1.79% for 389 saliva specimens collected from the communities for COVID-19 screening. Preliminary data showed that saliva sample pooling up to 6 samples for SARS-CoV-2 detection is feasible (sensitivity 94.8% and specificity 100%). ConclusionThe studies demonstrated that the QuantiVirus SARS-CoV-2 multiplex test has a LOD of 200 copies/mL in contrived saliva samples. The clinical performance of saliva-based testing is comparable to that of NPS-based testing. Pooling of saliva specimens for SARS-CoV-2 detection is feasible. Saliva based and high-throughput QuantiVirusSARS-CoV-2 multiplex test offers a highly desirable test during the ongoing COVID-19 pandemic.

Boceprevir, calpain inhibitors II and XII, and GC-376 have broad-spectrum antiviral activity against coronaviruses in cell culture (preprint)

As the COVID-19 pandemic continues to fold out, the morbidity and mortality are increasing daily. Effective treatment for SARS-CoV-2 is urgently needed. We recently discovered four SARS-CoV-2 main protease (Mpro) inhibitors including boceprevir, calpain inhibitors II and XII and GC-376 with potent antiviral activity against infectious SARS-CoV-2 in cell culture. Despite the weaker enzymatic inhibition of calpain inhibitors II and XII against Mpro compared to GC-376, calpain inhibitors II and XII had more potent cellular antiviral activity. This observation promoted us to hypothesize that the cellular antiviral activity of calpain inhibitors II and XII might also involve the inhibition of cathepsin L in addition to Mpro. To test this hypothesis, we tested calpain inhibitors II and XII in the SARS-CoV-2 pseudovirus neutralization assay in Vero E6 cells and found that both compounds significantly decreased pseudoviral particle entry into cells, indicating their role in inhibiting cathepsin L. The involvement of cathepsin L was further confirmed in the drug time-of-addition experiment. In addition, we found that these four compounds not only inhibit SARS-CoV-2, but also SARS-CoV, MERS-CoV, as well as human coronaviruses (CoVs) 229E, OC43, and NL63. The mechanism of action is through targeting the viral Mpro, which was supported by the thermal shift binding assay and enzymatic FRET assay. We further showed that these four compounds have additive antiviral effect when combined with remdesivir. Altogether, these results suggest that boceprevir, calpain inhibitors II and XII, and GC-376 are not only promising antiviral drug candidates against existing human coronaviruses, but also might work against future emerging CoVs.

A High-throughput Anti-SARS-CoV-2 IgG Testing Platform for COVID-19 (preprint)

BackgroundSerology tests for detecting the antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can identify previous infection and help to confirm the presence of current infection. ObjectiveThe aim of this study was to evaluate the performances of a newly developed high throughput immunoassay for anti-SARS-CoV-2 IgG antibody detection. ResultsClinical agreement studies were performed in 77 COVID-19 patient serum samples and 226 negative donor serum/plasma samples. Positive percent agreement (PPA) was 42.86% (95% CI: 9.90% to 81.59%), 55.56% (95% CI: 21.20% to 86.30%), and 96.72% (95% CI: 88.65% to 99.60%) for samples collected on 0-7 days, 8-14 days, and [≥]15 days from symptom onset, respectively. Negative Percent Agreement (NPA) was 98.23% (95% CI: 95.53% to 99.52%). No cross-reactivity was observed to patient samples positive for IgG antibodies against the following pathogens: HIV, HAV, HBV, RSV, CMV, EBV, Rubella, Influenza A, and Influenza B. Hemoglobin (200 mg/dL), bilirubin (2 mg/dL) and EDTA (10 mM) showed no significant interfering effect on this assay. ConclusionAn anti-SARS-CoV-2 IgG antibody assay with high sensitivity and specificity has been developed. With the high throughput, this assay will speed up the anti-SARS-CoV-2 IgG testing.

SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood from the San Francisco Bay Area (preprint)

We report very low SARS-CoV-2 seroprevalence in two San Francisco Bay Area populations. Seropositivity was 0.26% in 387 hospitalized patients admitted for non-respiratory indications and 0.1% in 1,000 blood donors. We additionally describe the longitudinal dynamics of immunoglobulin-G, immunoglobulin-M, and in vitro neutralizing antibody titers in COVID-19 patients. Neutralizing antibodies rise in tandem with immunoglobulin levels following symptom onset, exhibiting median time to seroconversion within one day of each other, and there is >93% positive percent agreement between detection of immunoglobulin-G and neutralizing titers.