Development of a hybrid alphavirus-SARS-CoV-2 pseudovirion for rapid quantification of neutralization antibodies and antiviral drugs.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein (S)-pseudotyped viruses are commonly used for quantifying antiviral drugs and neutralizing antibodies. Here, we describe the development of a hybrid alphavirus-SARS-CoV-2 (Ha-CoV-2) pseudovirion, which is a non-replicating SARS-CoV-2 virus-like particle composed of viral structural proteins (S, M, N, and E) and an RNA genome derived from a fast-expressing alphaviral vector. We validated Ha-CoV-2 for rapid quantification of neutralization antibodies, antiviral drugs, and viral variants. In addition, as a proof of concept, we used Ha-CoV-2 to quantify the neutralizing antibodies from an infected and vaccinated individual and found that the one-dose vaccination with Moderna mRNA-1273 greatly increased the anti-serum titer by approximately 6-fold. The post-vaccination serum can neutralize all nine variants tested. These results demonstrate that Ha-CoV-2 can be used as a robust platform for the rapid quantification of neutralizing antibodies against SARS-CoV-2 and its emerging variants.

Analysis of Symptomology, Infectiveness, and Reinfections between Male and Female COVID-19 Patients: Evidence from Japanese Registry Data

Background: Hokkaido was the first Japanese prefecture to be affected by COVID-19. Since the beginning of the pandemic, the Japanese government has been publishing the information of each individual who was tested positive for the virus. Method: The current study analyzed the 1269 SARS-CoV-2 cases confirmed in Hokkaido in order to examine sex-based differences in symptomology and infectiveness, as well as the status of reinfections and the viral transmission networks. Results: The majority of asymptomatic patients were females and older. Females were 1.3-fold more likely to be asymptomatic (p <0.001) while a decade of difference in age increased the likelihood of being asymptomatic by 1% (p <0.001). The data contained information up to quaternary viral transmission. The transmission network revealed that, although asymptomatic patients are more likely to transmit the virus, the individuals infected by asymptomatic cases are likely to be asymptomatic (p <0.001). Four distinct co-occurrences of symptoms were observed, including (i) fever/fatigue, (ii) pharyngitis/rhinitis, (iii) ageusia/anosmia, and (iv) nausea/vomiting/diarrhea. The presences of diarrhea (p = 0.05) as well as nausea/vomiting (p <0.001) were predictive of developing dyspnea, i.e., severe disease. About 1% of the patients experienced reinfection. Conclusions: Sex and symptomatology appear to play important roles in determining the levels of viral transmission as well as disease severity.

Symptom and Age Homophilies in SARS-CoV-2 Transmission Networks during the Early Phase of the Pandemic in Japan.

Kanagawa and Hokkaido were affected by COVID-19 in the early stage of the pandemic. Japan's initial response included contact tracing and PCR analysis on anyone who was suspected of having been exposed to SARS-CoV-2. In this retrospective study, we analyzed publicly available COVID-19 registry data from Kanagawa and Hokkaido (n = 4392). Exponential random graph model (ERGM) network analysis was performed to examine demographic and symptomological homophilies. Age, symptomatic, and asymptomatic status homophilies were seen in both prefectures. Symptom homophilies suggest that nuanced genetic differences in the virus may affect its epithelial cell type range and can result in the diversity of symptoms seen in individuals infected by SARS-CoV-2. Environmental variables such as temperature and humidity may also play a role in the overall pathogenesis of the virus. A higher level of asymptomatic transmission was observed in Kanagawa. Moreover, patients who contracted the virus through secondary or tertiary contacts were shown to be asymptomatic more frequently than those who contracted it from primary cases. Additionally, most of the transmissions stopped at the primary and secondary levels. As expected, significant viral transmission was seen in healthcare settings.

Identification of the SHREK Family of Proteins as Broad-Spectrum Host Antiviral Factors.

Mucins and mucin-like molecules are highly glycosylated, high-molecular-weight cell surface proteins that possess a semi-rigid and highly extended extracellular domain. P-selectin glycoprotein ligand-1 (PSGL-1), a mucin-like glycoprotein, has recently been found to restrict HIV-1 infectivity through virion incorporation that sterically hinders virus particle attachment to target cells. Here, we report the identification of a family of antiviral cellular proteins, named the Surface-Hinged, Rigidly-Extended Killer (SHREK) family of virion inactivators (PSGL-1, CD43, TIM-1, CD34, PODXL1, PODXL2, CD164, MUC1, MUC4, and TMEM123) that share similar structural characteristics with PSGL-1. We demonstrate that SHREK proteins block HIV-1 infectivity by inhibiting virus particle attachment to target cells. In addition, we demonstrate that SHREK proteins are broad-spectrum host antiviral factors that block the infection of diverse viruses such as influenza A. Furthermore, we demonstrate that a subset of SHREKs also blocks the infectivity of a hybrid alphavirus-SARS-CoV-2 (Ha-CoV-2) pseudovirus. These results suggest that SHREK proteins may be a part of host innate immunity against enveloped viruses.