Culturing of SARS-CoV-2 from patient samples: Protocol for optimal virus recovery and assessment of infectious viral load

Optimal sampling, preservation, and culturing of SARS-CoV-2 from COVID-19 patients are critical for successful recovery of virus isolates and to accurately estimate contagiousness of the patient. In this study, we investigated the influence of the type of sampling media, storage time, freezing conditions, sterile filtration, and combinations of these to determine the optimal pre-analytic conditions for virus recovery and estimation of infectious viral load in COVID-19 patients. Further, we investigated the viral shedding kinetics and mucosal antibody response in 38 COVID-19 hospitalized patients. We found Universal Transport Medium (Copan) to be the most optimal medium for preservation of SARS-CoV-2 infectivity. Our data showed that the probability of a positive viral culture was strongly correlated to Ct values, however some samples did not follow the general trend. We found a significant correlation between plaque forming units and levels of mucosal antibodies and found that high levels of mucosal antibodies correlated with reduced chance of isolating the virus. Our data reveals essential parameters to consider from specimen collection over storage to culturing technique for optimal chance of isolating SARS-CoV-2 and accurately estimating patient contagiousness.

Size and duration of COVID-19 clusters go along with a high SARS-CoV-2 viral load: A spatio-temporal investigation in Vaud state, Switzerland

To understand the geographical and temporal spread of SARS-CoV-2 during the first documented wave of infection in the state of Vaud, Switzerland, we analyzed clusters of positive cases using the precise residential location of 33,651 individuals tested (RT-PCR) between January 10 and June 30, 2020. We used a prospective Poisson space-time scan statistic (SaTScan) and a Modified Space-Time Density-Based Spatial Clustering of Application with Noise (MST-DBSCAN) to identify both space-time and transmission clusters, and estimated cluster duration, transmission behavior (emergence, growth, reduction, etc.) and relative risk. For each cluster, we computed the number of individuals, the median age of individuals and their viral load. Among the 1684 space-time clusters identified, 457 (27.1%) were significant (p ≤ 0.05), such that they harbored a higher relative risk of infection within the cluster than compared to regions outside the cluster. Clusters lasted a median of 11 days (IQR 7-13) and included a median of 12 individuals per cluster (IQR 5-20). The majority of significant clusters (n = 260; 56.9%) had at least one person with an extremely high viral load (>1 billion copies/ml). Those clusters were considerably larger (median of 17 infected individuals, p < 0.001) than clusters with individuals showing a viral load below 1 million copies/ml (median of three infected individuals). The highest viral loads were found in clusters with the lowest average age group considered in the investigation, while clusters with the highest average age had low to middle viral load. In 20 significant clusters, the viral load of the three first cases was below 100,000 copies/ml, suggesting that subjects with fewer than 100,000 copies/ml may still be contagious. Notably, the dynamics of transmission clusters made it possible to identify three diffusion zones, which predominantly differentiated between rural and urban areas, the latter being more prone to persistence and expansion, which may result in the emergence of new clusters nearby. The use of geographic information is key for public health decision makers in mitigating the spread of the SARS-CoV-2 virus. This study suggests that early localization of clusters may help implement targeted protective measures limiting the spread of the virus.

The low contagiousness and new A958D mutation of SARS-CoV-2 in children: An observational cohort study

AIMS

To explore the contagiousness and new SARS-CoV-2 mutations in pediatric COVID-19.

METHODS

This cohort study enrolled all pediatric patients admitted to 8 hospitals in Zhejiang Province of China between 21 January and 29 February 2020, their family members and close-contact classmates. Epidemiological, demographic, clinical and laboratory data were collected. Bioinformatics was used to analyze the features of SARS-CoV-2. Individuals were divided into 3 groups by the first-generation case: Groups 1 (unclear), 2 (adult), and 3 (child). The secondary attack rate (SAR) and R₀ were compared among the groups.

RESULTS

The infection rate among 211 individuals was 64% (135/211). The SAR in Groups 2 and 3 was 71% (73/103) and 3% (1/30), respectively; the median R₀ in Groups 2 and 3 was 2 (range: 1-8) and 0 (range: 0-1), respectively. Compared with adult cases, the SAR and R₀ of pediatric cases were significantly lower (p<0.05). We obtained SARS-CoV-2 sequences from the same infant's throat and fecal samples at a two-month interval and found that the new spike protein A958D mutation detected in the stool improved thermostability theoretically.

CONCLUSIONS

Children have lower ability to spread SARS-CoV-2. The new A958D mutation is a potential reason for its long residence in the intestine.

Oral and laryngeal HPV infection: Incidence, prevalence and risk factors, with special regard to concurrent infection in head, neck and genitals

This review focuses on the importance of oral and laryngeal HPV infection which is present in majority of sexually active individuals at least once in their lifetime. Despite testing, still little is known about prevalence rates, determinants and, especially, the concurrent HPV infection in head and neck, and genitals. The purpose of this review is to clarify some issues of oral HPV incidence, prevalence, and to demonstrate the difficulties in identification of asymptomatic oral HPV carriers. The main premise to take up this topic is the high and still increasing risk for development of oropharyngeal cancer, and potential benefit from screening strategies, education programs and HPV vaccination. Transmission of HPV to the oral cavity and oropharynx is hypothesized to occur mainly through sexual contact. The exposure of oropharyngeal mucosa to HPV infection with consequence of increased risk for oropharyngeal carcinoma depends on specific sexual behavior. Male gender, older age, race or ethnicity, oral hygiene and current cigarette smoking are independently associated with any prevalent oral HPV infection.

[Contagiousness and secondary attack rate of 2019 novel coronavirus based on cluster epidemics of COVID-19 in Guangzhou]

Objective: To analyze the contagiousness and secondary attack rate of 2019 novel coronavirus in cluster epidemics in Guangzhou and provide evidence for the prevention and control of COVID-19. Methods: All the individuals identified to be infected with 2019-nCoV in Guangzhou, including confirmed cases and asymptomatic cases, were included and classified as imported cases and local cases. The first case of each cluster epidemic was defined as index case, and the number of subsequent infections was calculated to evaluate the contagiousness and secondary attack rate of 2019 novel coronavirus in the shortest incubation period of 1-3 days. Results: As of 18 February, 2020, a total of 349 cases of 2019-nCoV infection, including 339 confirmed cases (97.13%) and 10 asymptomatic cases (2.87%) were reported in Guangzhou. There were 68 clusters involving 217 2019-nCoV infection cases (210 confirmed cases and 7 asymptomatic cases). The median number of subsequent infections caused by an index case in a cluster epidemic was 3, among which 2 were confirmed cases and 1 was asymptomatic cases, respectively. The average number of contagiousness was 2.18 in shorted incubation period of 1-3 days (The average number of infected cases were 2.18 cases by the index case in a cluster epidemic), the average infection number in family members was 1.86, and the infection ratio of family member transmission was 85.32% (1.86/2.18). The secondary attack rate in close contacts with shortest incubation period of 1-3 days was 17.12%-18.99%, the secondary attack rate in family members was 46.11%-49.56%. Conclusions: The cluster epidemic of COVID-19 in Guangzhou mainly occurred in families, the contagiousness was high. It is necessary to strengthen the prevention and control to reduce the community transmission of COVID-19.

Religiosity and Beliefs About the Transmission of Cancer, Chemotherapy, and Radiation Through Physical Contact in Saudi Arabia

We examined relationships between religiosity and Saudi cancer patients' beliefs about the spread of cancer, chemotherapy, and radiation therapy through close physical contact. Surveyed were 64 patients seen in university oncology clinics. Assessed were beliefs about the spread of cancer and its treatments, along with religious, demographic, social, psychological, and cancer-related characteristics. Greater religiosity was related to older age, non-Saudi nationality, less anxiety, earlier cancer stage, and greater time since initial diagnosis. Non-significant trends suggested that religious practices were associated with less, but intrinsic religious beliefs with more concern about contagiousness, although the findings were limited by low statistical power.

Coupling effects on turning points of infectious diseases epidemics in scale-free networks

Background

Pandemic is a typical spreading phenomenon that can be observed in the human society and is dependent on the structure of the social network. The Susceptible-Infective-Recovered (SIR) model describes spreading phenomena using two spreading factors; contagiousness (β) and recovery rate (γ). Some network models are trying to reflect the social network, but the real structure is difficult to uncover.

Methods

We have developed a spreading phenomenon simulator that can input the epidemic parameters and network parameters and performed the experiment of disease propagation. The simulation result was analyzed to construct a new marker VRTP distribution. We also induced the VRTP formula for three of the network mathematical models.

Results

We suggest new marker VRTP (value of recovered on turning point) to describe the coupling between the SIR spreading and the Scale-free (SF) network and observe the aspects of the coupling effects with the various of spreading and network parameters. We also derive the analytic formulation of VRTP in the fully mixed model, the configuration model, and the degree-based model respectively in the mathematical function form for the insights on the relationship between experimental simulation and theoretical consideration.

Conclusions

We discover the coupling effect between SIR spreading and SF network through devising novel marker VRTP which reflects the shifting effect and relates to entropy.