Is It Possible to Test for Viral Infectiousness?: The Use Case of (SARS-CoV-2)

Identifying and managing individuals with active or chronic disease, implementing appropriate infection control measures, and mitigating the spread of the COVID-19 pandemic highlighted the need for tests of infectiousness. The gold standard for assessing infectiousness has been the recovery of infectious virus in cell culture. Using cycle threshold values, antigen testing, and SARS-CoV-2, replication intermediate strands were used to assess infectiousness, with many limitations. Infectiousness can be influenced by host factors (eg, preexisting immune responses) and virus factors (eg, evolution).

Molecular insights into the adaptive evolution of SARS-CoV-2 spike protein

The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has substantially damaged the global economy and human health. The spike (S) protein of coronaviruses plays a pivotal role in viral entry by binding to host cell receptors. Additionally, it acts as the primary target for neutralizing antibodies in those infected and is the central focus for currently utilized or researched vaccines. During the virus's adaptation to the human host, the S protein of SARS-CoV-2 has undergone significant evolution. As the COVID-19 pandemic has unfolded, new mutations have arisen and vanished, giving rise to distinctive amino acid profiles within variant of concern strains of SARS-CoV-2. Notably, many of these changes in the S protein have been positively selected, leading to substantial alterations in viral characteristics, such as heightened transmissibility and immune evasion capabilities. This review aims to provide an overview of our current understanding of the structural implications associated with key amino acid changes in the S protein of SARS-CoV-2. These research findings shed light on the intricate and dynamic nature of viral evolution, underscoring the importance of continuous monitoring and analysis of viral genomes. Through these molecular-level investigations, we can attain deeper insights into the virus's adaptive evolution, offering valuable guidance for designing vaccines and developing antiviral drugs to combat the ever-evolving viral threats.

A biomechanical model of a vehicle passenger in the sagittal plane

Musculoskeletal biomechanical models have wide applications in ergonomics, rehabilitation, and injury estimation. Their use can be extended to enable quantitatively explaining and estimating ride comfort for a vehicle's passenger. A biomechanical model of the upper body in the sagittal plane is constructed, which allows for curved motion to simulate the propagation of disturbance energy within a seated passenger aboard a moving vehicle. The dynamic predictions of the model are validated against experimental results within the literature. Frequency responses show that within the vehicular frequency range, the L4L5 and the L5S1 discs in the lower lumbar region are susceptible to the highest vibration transmission. It was also found that vibration transmission is maximized at around 4.5 Hz. The model provides analytical and geometric intuition into the motion of the various segments of the upper body using a few simple geometric assumptions and can be employed to develop a quantitative ride-comfort metric, such that the most comfortable ride would be that which would induce the least internal motion within the passenger model.

Relevance of the Entry by Fusion at the Cytoplasmic Membrane vs. Fusion After Endocytosis in the HIV and SARS-Cov-2 Infections

HIV-1 and SARS-Cov-2 fuse at the cell surface or at endosomal compartments for entry into target cells; entry at the cell surface associates to productive infection, whereas endocytosis of low pH-independent viruses may lead to virus inactivation, slow replication, or alternatively, to productive infection. Endocytosis and fusion at the cell surface are conditioned by cell type-specific restriction factors and the presence of enzymes required for activation of the viral fusogen. Whereas fusion with the plasma membrane is considered the main pathway to productive infection of low pH-independent entry viruses, endocytosis is also productive and may be the main route of the highly efficient cell-to-cell dissemination of viruses. Alternative receptors, membrane cofactors, and the presence of enzymes processing the fusion protein at the cell membrane, determine the balance between fusion and endocytosis in specific target cells. Characterization of the mode of entry in particular cell culture conditions is desirable to better assess the effect of neutralizing and blocking agents and their mechanism of action. Whatever the pathway of virus internalization, production of the viral proteins into the cells can lead to the expression of the viral fusion protein on the cell surface; if this protein is able to induce membrane fusion at physiological pH, it promotes the fusion of the infected cell with surrounding uninfected cells, leading to the formation of syncytia or heterokaryons. Importantly, particular membrane proteins and lipids act as cofactors to support fusion. Virus-induced cell-cell fusion leads to efficient virus replication into fused cells, cell death, inflammation, and severe disease.

Mutations in HA and PA affect the transmissibility of H7N9 avian influenza virus in chickens

Low pathogenic (LP) H7N9 avian influenza virus (AIV) emerged in 2013 and had spread widely over several months in China, experienced a noteworthy reduction in isolation rate in poultry and human since 2017. Here, we examined the transmission of H7N9 viruses to better understand viral spread and dissemination mechanisms. Three out of four viruses (2013-2016) could transmit in chickens through direct contact, and airborne transmission was confirmed in the JT157 (2016) virus. However, we did not detect the transmission of the two 2017 viruses, WF69 and AH395, through either direct or airborne exposure. Molecular analysis of genome sequence of two viruses identified eleven mutations located in viral proteins (except for matrix protein), such as PA (K362R and S364N) and HA (D167N, H7 numbering), etc. We explored the genetic determinants that contributed to the difference in transmissibility of the viruses in chickens by generating a series of reassortants in the JT157 background. We found that the replacement of HA gene in JT157 by that of WF69 abrogated the airborne transmission in recipient chickens, whereas the combination of HA and PA replacement led to the loss of airborne and direct contact transmission. Failure with contact transmission of the viruses has been associated with the emergence of the mutations D167N in HA and K362R and S364N in PA. Furthermore, the HA D167N mutation significantly reduced viral attachment to chicken lung and trachea tissues, while mutations K362R and S364N in PA reduced the nuclear transport efficiency and the PA protein expression levels in both cytoplasm and nucleus of CEF cells. The D167N substitution in HA reduced the H7N9 viral acid stability and avian-like receptor binding, while enhanced human-like receptor binding. Further analysis revealed these mutants grew poorly in vitro and in vivo. To conclude, H7N9 AIVs that contain mutations in the HA and PA protein reduced the viral transmissibility in chicken, and may pose a reduced threat for poultry but remain a heightened public health risk.

Association between ozone and influenza transmissibility in China

BACKGROUND

Common air pollutants such as ozone (O3), sulfur dioxide (SO2), nitrogen dioxide (NO2), and particulate matter play significant roles as influential factors in influenza-like illness (ILI). However, evidence regarding the impact of O3 on influenza transmissibility in multi-subtropical regions is limited, and our understanding of the effects of O3 on influenza transmissibility in temperate regions remain unknown.

METHODS

We studied the transmissibility of influenza in eight provinces across both temperate and subtropical regions in China based on 2013 to 2018 provincial-level surveillance data on influenza-like illness (ILI) incidence and viral activity. We estimated influenza transmissibility by using the instantaneous reproduction number ([Formula: see text]) and examined the relationships between transmissibility and daily O3 concentrations, air temperature, humidity, and school holidays. We developed a multivariable regression model for [Formula: see text] to quantify the contribution of O3 to variations in transmissibility.

RESULTS

Our findings revealed a significant association between O3 and influenza transmissibility. In Beijing, Tianjin, Shanghai and Jiangsu, the association exhibited a U-shaped trend. In Liaoning, Gansu, Hunan, and Guangdong, the association was L-shaped. When aggregating data across all eight provinces, a U-shaped association was emerged. O3 was able to accounted for up to 13% of the variance in [Formula: see text]. O3 plus other environmental drivers including mean daily temperature, relative humidity, absolute humidity, and school holidays explained up to 20% of the variance in [Formula: see text].

CONCLUSIONS

O3 was a significant driver of influenza transmissibility, and the association between O3 and influenza transmissibility tended to display a U-shaped pattern.

Chronicling the 3-year evolution of the COVID-19 pandemic: analysis of disease management, characteristics of major variants, and impacts on pathogenicity

Announced on December 31, 2019, the novel coronavirus arising in Wuhan City, Hubei Province resulted in millions of cases and lives lost. Following intense tracking, coronavirus disease 2019 (COVID-19) was declared a pandemic by the World Health Organization (WHO) in 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the cause of COVID-19 and the continuous evolution of the virus has given rise to several variants. In this review, a comprehensive analysis of the response to the pandemic over the first three-year period is provided, focusing on disease management, development of vaccines and therapeutics, and identification of variants. The transmissibility and pathogenicity of SARS-CoV-2 variants including Alpha, Beta, Gamma, Delta, and Omicron are compared. The binding characteristics of the SARS-CoV-2 spike protein to the angiotensin-converting enzyme 2 (ACE2) receptor and reproduction numbers are evaluated. The effects of major variants on disease severity, hospitalisation, and case-fatality rates are outlined. In addition to the spike protein, open reading frames mutations are investigated. We also compare the pathogenicity of SARS-CoV-2 with SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Overall, this study highlights the strengths and weaknesses of the global response to the pandemic, as well as the importance of prevention and preparedness. Monitoring the evolution of SARS-CoV-2 is critical in identifying and potentially predicting the health outcomes of concerning variants as they emerge. The ultimate goal would be a position in which existing vaccines and therapeutics could be adapted to suit new variants in as close to real-time as possible.

Epidemic dynamics with time-varying transmission risk reveal the role of disease stage-dependent infectiousness

A key characteristic of acute communicable diseases is the infectiousness that varies over time as the infection dynamics evolve within a host, which influences the risk of transmission in different stages of the disease. Despite the evidence of time-varying transmission risk, most dynamic models of epidemics assume a constant transmission rate during the infectious period. Recent work has shown the difference in epidemic dynamics when this assumption is relaxed and different transmission rates are used by discretizing the infectious period into multiple sub-periods. Here, we develop an age-structured model to integrate a continuous time-varying transmission risk, based on an established correlation between the viral dynamics and infectiousness profile. Taking into account the natural history and parameter estimates of COVID-19 caused by the original strain of SARS-CoV-2, we demonstrate the difference in temporal epidemic dynamics when a continuous time-varying transmission probability is used as compared to multiple constant transmission probabilities. Our results show a significant difference between the incidence curves in terms of the magnitude and peak time, even when the reproduction number and total number of infections are the same for continuous and discrete transmission probabilities. Finally, we demonstrate the spurious outcome of preventing an epidemic through the isolation of infectious individuals when constant transmission probabilities are used, highlighting the importance of integrating a continuous time-dependent transmission parameter in dynamic models. These findings suggest a more cautious interpretation of model outcomes, especially those that are intended to evaluate the effectiveness of interventions and inform policy decisions for disease mitigation strategies.

Epidemiological characteristics and transmissibility of HPV infection: A long-term retrospective study in Hokkien Golden Triangle, China, 2013-2021

OBJECTIVE

Multiple human papillomavirus (HPV)-associated diseases have put a significant disease burden on the world. Therefore, we conducted a study to explore the epidemiological characteristics of HPV and the transmissibility of its genotypes.

METHODS

HPV testing data was collected from Hospital. A transmission dynamics model of HPV was constructed to simulate and compare the transmissibility of different HPV genotypes, which was quantitatively described by the basic reproduction number (R0).

RESULTS

The collected HPV subjects were mainly from Xiamen City, Zhangzhou City and Quanzhou City, together, they are known as the Hokkien golden triangle. There were variations in the distribution of HPV infections by age groups. Among all HPV genotypes, 13 of them had R0 > 1, with 10 of them being high-risk types. The top five were HPV56, 18, 58, 52 and 53, among which, HPV56, 18, 58 and 42 were of high risk, whereas HPV53 was not, and the R0 values for the five were 3.35 (CI: 0.00-9.99), 3.20 (CI: 0.00-6.46), 3.19 (CI: 1.27-6.94), 3.19 (CI: 1.01-8.42) and 2.99 (CI: 0.00-9.39), respectively. In addition, HPV52 had R0 > 1 for about 51 months, which had the longest duration.

CONCLUSION

Most high-risk HPV types in the Hokkien golden triangle could transmit among the population. Therefore, there is a need of further optimization for developing HPV vaccines and better detection methods in the region.

A comparative study on epidemiological characteristics, transmissibility, and pathogenicity of three COVID-19 outbreaks caused by different variants

OBJECTIVES

The Omicron BA.2 variant is probably the main epidemic strain worldwide at present. Comparing the epidemiological characteristics, transmissibility, and influencing factors of SARS-CoV-2, the results obtained in this paper will help to provide theoretical support for disease control.

METHODS

This study was a historical information analysis, using the R programming language and SPSS 24.0 for statistical analysis. The Geoda and Arc GIS were used for spatial autocorrelation analysis.

RESULTS

Local spatial autocorrelations of the incidence rate were observed in Delta and Omicron BA.1 outbreaks, whereas Omicron BA.2 outbreaks showed a random distribution in incidence rate. The time-dependent reproduction number of Delta, Omicron BA.1, and Omicron BA.2 were 3.21, 4.29, and 2.96, respectively, and correspondingly, the mean serial interval were 4.29 days (95% confidence interval [CI]: 0.37-8.21), 3.84 days (95% CI: 0-8.37), and 2.77 days (95% CI: 0-5.83). The asymptomatic infection rate of cases in Delta, Omicron BA.1, and Omicron BA.2 outbreaks were 21.71%, 6.25%, and 4.35%, respectively.

CONCLUSION

The Omicron BA.2 variant had the greatest serial interval, transmissibility, and transmission speed, followed by BA.1, and then Delta. Compared with Delta and Omicron BA.1 variants, the Omicron BA.2 variant may be less pathogenic and more difficult to control than Omicron BA.1 and Delta.

Increased viral load in patients infected with severe acute respiratory syndrome coronavirus 2 Omicron variant in the Republic of Korea

BACKGROUND

Coronavirus disease 2019 (COVID-19) has been declared a global pandemic owing to the rapid spread of the causative agent, severe acute respiratory syndrome coronavirus 2. Its Delta and Omicron variants are more transmissible and pathogenic than other variants. Some debates have emerged on the mechanism of variants of concern. In the COVID-19 wave that began in December 2021, the Omicron variant, first reported in South Africa, became identifiable in most cases globally. The aim of this study was to provide data to inform effective responses to the transmission of the Omicron variant.

METHODS

The Delta variant and the spike protein D614G mutant were compared with the Omicron variant. Viral loads from 5 days after symptom onset were compared using epidemiological data collected at the time of diagnosis.

RESULTS

The Omicron variant exhibited a higher viral load than other variants, resulting in greater transmissibility within 5 days of symptom onset.

CONCLUSION

Future research should focus on vaccine efficacy against the Omicron variant and compare trends in disease severity associated with its high viral load.

Association of climatic variables with risk of transmission of influenza in Guangzhou, China, 2005-2021

BACKGROUND

Climatic variables constitute important extrinsic determinants of transmission and seasonality of influenza. Yet quantitative evidence of independent associations of viral transmissibility with climatic factors has thus far been scarce and little is known about the potential effects of interactions between climatic factors on transmission.

OBJECTIVE

This study aimed to examine the associations of key climatic factors with risk of influenza transmission in subtropical Guangzhou.

METHODS

Influenza epidemics were identified over a 17-year period using the moving epidemic method (MEM) from a dataset of N = 295,981 clinically- and laboratory-confirmed cases of influenza in Guangzhou. Data on eight key climatic variables were collected from China Meteorological Data Service Centre. Generalized additive model combined with the distributed lag non-linear model (DLNM) were developed to estimate the exposure-lag-response curve showing the trajectory of instantaneous reproduction number (R_t) across the distribution of each climatic variable after adjusting for depletion of susceptible, inter-epidemic effect and school holidays. The potential interaction effects of temperature, humidity and rainfall on influenza transmission were also examined.

RESULTS

Over the study period (2005-21), 21 distinct influenza epidemics with varying peak timings and durations were identified. Increasing air temperature, sunshine, absolute and relative humidity were significantly associated with lower R_t, while the associations were opposite in the case of ambient pressure, wind speed and rainfall. Rainfall, relative humidity, and ambient temperature were the top three climatic contributors to variance in transmissibility. Interaction models found that the detrimental association between high relative humidity and transmissibility was more pronounced at high temperature and rainfall.

CONCLUSION

Our findings are likely to help understand the complex role of climatic factors in influenza transmission, guiding informed climate-related mitigation and adaptation policies to reduce transmission in high density subtropical cities.

Association of public health and social measures on the hand-foot-mouth epidemic in South Korea

BACKGROUND

School based-measures such as school closure and school holidays have been considered a viable intervention during the hand-foot-mouth disease (HFMD) epidemic. The aim of this study was to explore the association of nationwide public health and social measures (PHSMs) including planned school vacation on the transmissibility and attack rate of the HFMD epidemic in South Korea.

METHODS

In this study, we used Korean national surveillance data on HFMD from 2014 to 2019 to estimate the temporal changes in HFMD transmissibility (instantaneous reproductive number, Rt). Furthermore, to assess the changes in the HFMD attack rate, we used a stochastic transmission model to simulate the HFMD epidemic with no school vacation and nationwide PHSMs in 2015 South Korea.

RESULTS

We found that school vacations and 2015 PHSMs were associated with the reduced Rt by 2-7 % and 13 %, respectively. Model projections indicated school vacations and 2015 PHSMs were associated with reduced HFMD attack rate by an average of 1.10 % (range: 0.38-1.51 %).

CONCLUSIONS

PHSMs likely have a larger association with reduced HFMD transmissibility than school-based measures alone (i.e. school vacations). Preventive measures targeting preschoolers could be considered as potential options for reducing the future burden of HFMD.

A comparison of transmissibility of SARS-CoV-2 variants of concern

BACKGROUND

The World Health Organization (WHO) has currently detected five Variants of Concern of SARS-CoV-2 having the WHO labels of 'Alpha', 'Beta', 'Gamma', 'Delta' and 'Omicron'. We aimed to assess and compare the transmissibility of the five VOCs in terms of basic reproduction number, time-varying reproduction number and growth rate.

METHODS

Publicly available data on the number of analyzed sequences over two-week windows for each country were extracted from covariants.org and GISAID initiative database. The ten countries which reported the highest number of analyzed sequences for each of the five variants were included in the final dataset and was analyzed using R language. The epidemic curves for each variant were estimated utilizing the two-weekly discretized incidence data using local regression (LOESS) models. The basic reproduction number was estimated with the exponential growth rate method. The time-varying reproduction number was calculated for the estimated epidemic curves by the ratio of the number of new infections generated at time step t to the total infectiousness of infected individuals at time t, using the EpiEstim package.

RESULTS

The highest R0 for the variants Alpha (1.22), Beta (1.19), Gamma (1.21), Delta (1.38) and Omicron (1.90) were reported from Japan, Belgium, the United States, France and South Africa, respectively. Nine out of ten epidemic curves with the highest estimated growth rates and reproduction numbers were due to the Omicron variant indicating the highest transmissibility.

CONCLUSIONS

The transmissibility was highest in the Omicron variant followed by Delta, Alpha, Gamma and Beta respectively.

Discrepancy in the transmissibility of multidrug-resistant Mycobacterium tuberculosis in urban and rural areas in China

The fitness of multidrug-resistant tuberculosis (MDR-TB) is thought to be an important determinant of a strain's ability to be transmitted and cause outbreaks. Studies in the laboratory have demonstrated that MDR-TB strains have reduced fitness but the relative transmissibility of MDR-TB versus drug-susceptible (DS) TB strains in human populations remains unresolved. We used data on genomic clustering from our previous molecular epidemiological study in Songjiang (2011-2020) and Wusheng (2009-2020), China, to compare the relative transmissibility of MDR-TB versus DS-TB. Genomic clusters were defined with a threshold distance of 12-single-nucleotide-polymorphisms and the risk for MDR-TB clustering was analyzed by logistic regression. In total, 2212 culture-positive pulmonary TB patients were enrolled in Songjiang and 1289 in Wusheng. The clustering rates of MDR-TB and DS-TB strains were 19.4% (20/103) and 26.3% (509/1936), respectively in Songjiang, and 43.9% (29/66) and 26.0% (293/1128) in Wusheng. The risk of MDR-TB clustering was 2.34 (95% CI 1.38-3.94) times higher than DS-TB clustering in Wusheng and 0.64 (95% CI 0.38-1.06) times lower in Songjiang. Neither lineage 2, compensatory mutations nor rpoB S450L were significantly associated with MDR-TB transmission, and katG S315T increased MDR-TB transmission only in Wusheng (OR 5.28, 95% CI 1.42-19.21). MDR-TB was not more transmissible than DS-TB in either Songjiang or Wusheng. It appears that the different transmissibility of MDR-TB in Songjiang and Wusheng is likely due to differences in the quality of the local TB control programs. These results suggest that the most effective way to control MDR-TB is by improving local TB control programs.

The global dynamic transmissibility of COVID-19 and its influencing factors: an analysis of control measures from 176 countries

OBJECTIVE

To summarise the dynamic characteristics of COVID-19 transmissibility; To analyse and quantify the effect of control measures on controlling the transmissibility of COVID-19; To predict and compare the effectiveness of different control measures.

METHODS

We used the basic reproduction number ([Formula: see text]) to measure the transmissibility of COVID-19, the transmissibility of COVID-19 and control measures of 176 countries and regions from January 1, 2020 to May 14, 2022 were included in the study. The dynamic characteristics of COVID-19 transmissibility were summarised through descriptive research and a Dynamic Bayesian Network (DBN) model was constructed to quantify the effect of control measures on controlling the transmissibility of COVID-19.

RESULTS

The results show that the spatial transmissibility of COVID-19 is high in Asia, Europe and Africa, the temporal transmissibility of COVID-19 increases with the epidemic of Beta and Omicron strains. Dynamic Bayesian Network (DBN) model shows that the transmissibility of COVID-19 is negatively correlated with control measures. Restricting population mobility has the strongest effect, nucleic acid testing (NAT) has a strong effect, and vaccination has the weakest effect.

CONCLUSION

Strict control measures are essential for controlling the COVID-19 outbreak; Restricting population mobility and nucleic acid testing (NAT) have significant impacts on controlling the COVID-19 transmissibility, while vaccination has no significant impact. In light of these findings, future control measures may include the widespread use of new NAT technology and the promotion of booster immunization.

The reproduction rate of severe acute respiratory syndrome coronavirus 2 different variants recently circulated in human: a narrative review

SARS-COV-2 is responsible for the current worldwide pandemic, which started on December 2019 in Wuhan, China. On March 2020 World Health Organization announced COVID-19 as the new pandemic. Some SARS-COV-2 variants have increased transmissibility, cause more severe disease (e.g., increased hospitalizations or deaths), are resistant to antibodies produced by the previous infection or vaccination, and there is more difficulty in treatment and diagnosis of them. World Health Organization considered them as SARS-CoV-2 variants of concern. The introductory reproduction rate (R₀) is an epidemiologic index of the transmissibility of the virus, defined as the average number of persons infected by the virus after known contact with an infectious person in a susceptible population. An R₀ > 1 means that the virus is spreading exponentially, and R₀ < 1, means that the outbreak is subsiding. In various studies, the estimated R and VOC growth rates were reported to be greater than the ancestral strains. However, it was also a low level of concordance between the estimated Rt of the same variant in different studies. It is because the R of a variant not only dependent on the biological and intrinsic factors of the virus but also several parameters can affect the R0, including the duration of contagiousness and the likelihood of infection per contact. Evaluation of changes in SARS-CoV-2 has shown that the rate of human-to-human transmission of this virus has increased. Like other viruses with non-human sources which succeeded in surviving in the human population, SARS-CoV-2 has gradually adapted to the human population, and its ability to transmit from human to human has increased. Of course, due to the continuous changes in this virus, it is crucial to survey the rate of transmission of the virus over time.

Possibility of mpox viral transmission and control from high-risk to the general population: a modeling study

BACKGROUND

Mpox is an emerging infectious disease that is now a global hazard. The strategies for preventing and controlling mpox should be further investigated in terms of transmission characteristics, infection risk among different populations, and ideal therapeutic approaches.

METHODS

A multi-group dynamic model was used to quantify the transmissibility of mpox. We further analyzed the transmission risk from men who have sex with men (MSM) to non-MSM and evaluated the effects of three intervention measures, including community-based prevention, early detection, and vaccination.

RESULTS

The median value of effective reproduction number (R_eff) and probability of contact via a single contact (q) among MSM worldwide is 3.11 (interquartile range [IQR]: 2.82-5.57) and 2.15% (IQR: 1.95-3.84%). We found that the cumulative incidence rate of non-MSM is much lower than that of MSM (< 1/2048) when the possibility of infection (including the percentage of high-risk behaviors of contact degree [C] and q) was lowered to less than 1 in 100,000. When comparing the three intervention measures, if we want to control the cumulative incidence rate to 5.96 × 10^-8 we need to increase the vaccine coverage to 81% or reduce the transmission rate factor (Cq) to 70% or shorten the transmission period to 74%.

CONCLUSIONS

Mpox has high transmissibility in MSM, which required minimize the risk of infection and exposure to high-risk populations. Community prevention and control is the top priority of interventions to contain the spread of mpox.

More or less deadly? A mathematical model that predicts SARS-CoV-2 evolutionary direction

SARS-CoV-2 has caused tremendous deaths globally. It is of great value to predict the evolutionary direction of SARS-CoV-2. In this paper, we proposed a novel mathematical model that could predict the evolutionary trend of SARS-CoV-2. We focus on the mutational effects on viral assembly capacity. A robust coarse-grained mathematical model is constructed to simulate the virus dynamics in the host body. Both virulence and transmissibility can be quantified in this model. A delicate equilibrium point that optimizes the transmissibility can be numerically obtained. Based on this model, the virulence of SARS-CoV-2 might further decrease, accompanied by an enhancement of transmissibility. However, this trend is not continuous; its virulence will not disappear but remains at a relatively stable range. A virus assembly model which simulates the virus packing process is also proposed. It can be explained why a few mutations would lead to a significant divergence in clinical performance, both in the overall particle formation quantity and virulence. This research provides a novel mathematical attempt to elucidate the evolutionary driving force in RNA virus evolution.

Enhanced pathogenicity and transmissibility of H9N2 avian influenza virus in mammals by hemagglutinin mutations combined with PB2-627K

H9N2 avian influenza viruses (AIVs) circulate globally in poultry and have become the dominant AIV subtype in China in recent years. Previously, we demonstrated that the H9N2 virus (A/chicken/Eastern China/SDKD1/2015) naturally harbors a mammalian-adaptive molecular factor (627K) in the PB2 protein and is weakly pathogenic in mice. Here, we focused on new markers for virulence in mammals. A mouse-adapted H9N2 virus was serially passaged in mice by infecting their lungs. As expected, infected mice showed clinical symptoms and died at passage six. A comparison between the wild-type and mouse-adapted virus sequences identified amino acid substitutions in the hemagglutinin (HA) protein. H9N2 viruses with the T187P ​+ ​M227L double mutation exhibited an increased affinity to human-type (SAα2,6Gal) receptors and significantly enhanced viral attachment to mouse lung tissues, which contributed to enhancing viral replication and virulence in mice. Additionally, HA with the T187P ​+ ​M227L mutation enabled H9N2 viral transmission in guinea pigs via direct contact. AIV pathogenicity in mice is a polygenic trait. Our results demonstrated that these HA mutations might be combined with PB2-627K to significantly increase H9N2 virulence in mice, and this enhanced virulence was achieved in other H9N2 AIVs by generating the same combination of mutations. In summary, our study identified novel key elements in the HA protein that are required for H9N2 pathogenicity in mice and provided valuable insights into pandemic preparedness against emerging H9N2 strains.

Pathogenicity and anti-infection immunity of animal H3N2 and H6N6 subtype influenza virus cross-species infection with tree shrews

Animal influenza viruses can spread across species and pose a fatal threat to human health due to the high pathogenicity and mortality. Animal models are crucial for studying cross-species infection and the pathogenesis of influenza viruses. Tupaia belangeri (tree shrew) has been emerging as an animal model for multiple human virus infections recently because of the close genetic relationship and phylogeny with humans. So far, tree shrew has been reported to be susceptible to human influenza virus subtype H1N1, avian influenza viruses subtype H9N2, subtype H5N1, and subtype H7N9. However, the pathogenicity, infection, and immunity of swine and land avian influenza viruses with low pathogenicity and the potential to jump to humans remain largely unexplored in the tree shrew model. Previously, our team has successfully isolated the newly emerging swine influenza virus subtype H3N2 (A/Swine/GX/NS2783/2010, SW2783) and avian influenza virus subtype H6N6 (A/CK/ZZ/346/2014, ZZ346). In this study, we observed the pathogenicity, immune characteristics, and cross-species infection potential ability of SW2783 and ZZ346 strains in tree shrew model with 50% tissue culture infective dose (TCID₅₀), hematoxylin and eosin (HE) staining, immunohistochemistry (IHC), real-time quantitative PCR (qRT-PCR) and other experimental methods. Both animal-borne influenza viruses had a strong ability on tissue infection in the turbinate and the trachea of tree shrews in vitro, in which SW2783 showed stronger replication ability than in ZZ346. SW2783 and ZZ346 both showed pathogenic ability with infected tree shrews model in vivo without prior adaptive culture, which mainly happened in the upper respiratory tract. However, the infection ability was weak, the clinical symptoms were mild, and the histopathological changes in the respiratory tract were relatively light. Furthermore, innate immune responses and adaptive immunity were observed in the tree shrew model after the infection of SW2783 and ZZ346 strains. We observed that the unadapted SW2783 and ZZ346 virus could transmit among tree shrews by direct contact. We also observed that SW2783 virus could transmit from tree shrews to guinea pigs. These results indicated that both animal-borne influenza viruses could induce similar pathogenicity and immune response to those caused by human-common influenza viruses. Tree shrews may be an excellent animal model for studying the interaction between the influenza virus and the host and the cross-species infection mechanism of the animal influenza virus.

Retrospective analysis of SARS-CoV-2 omicron invasion over delta in French regions in 2021-22: a status-based multi-variant model

BACKGROUND

SARS-CoV-2 is a rapidly spreading disease affecting human life and the economy on a global scale. The disease has caused so far more then 5.5 million deaths. The omicron outbreak that emerged in Botswana in the south of Africa spread around the globe at further increased rates, and caused unprecedented SARS-CoV-2 infection incidences in several countries. At the start of December 2021 the first omicron cases were reported in France.

METHODS

In this paper we investigate the spreading potential of this novel variant relatively to the delta variant that was also in circulation in France at that time. Using a dynamic multi-variant model accounting for cross-immunity through a status-based approach, we analyze screening data reported by Santé Publique France over 13 metropolitan French regions between 1st of December 2021 and the 30th of January 2022. During the investigated period, the delta variant was replaced by omicron in all metropolitan regions in approximately three weeks. The analysis conducted retrospectively allows us to consider the whole replacement time window and compare regions with different times of omicron introduction and baseline levels of variants' transmission potential. As large uncertainties regarding cross-immunity among variants persist, uncertainty analyses were carried out to assess its impact on our estimations.

RESULTS

Assuming that 80% of the population was immunized against delta, a cross delta/omicron cross-immunity of 25% and an omicron generation time of 3.5 days, the relative strength of omicron to delta, expressed as the ratio of their respective reproduction rates, [Formula: see text], was found to range between 1.51 and 1.86 across regions. Uncertainty analysis on epidemiological parameters led to [Formula: see text] ranging from 1.57 to 2.34 on average over the metropolitan French regions, weighted by population size.

CONCLUSIONS

Upon introduction, omicron spread rapidly through the French territory and showed a high fitness relative to delta. We documented considerable geographical heterogeneities on the spreading dynamics. The historical reconstruction of variant emergence dynamics provide valuable ground knowledge to face future variant emergence events.

Omicron variant: Current insights and future directions

The global COVID-19 outbreak has returned with the identification of the SARS-CoV-2 Omicron variant (B.1.1.529) after appearing to be persistently spreading for the more than past two years. In comparison to prior SARS-CoV-2 variants, this new variant revealed a significant amount of mutation. This novel variety may have a greater rate of transmissibility which might impede the effectiveness of current diagnostic equipment as well as vaccination efficacy and also impede immunotherapies (Antibody / monoclonal antibody based). WHO designated B.1.1.529 as a variant of concern on November 26, 2021, identified as Omicron. The Omicron variant transmission method and severity, on the other hand, are well defined. The global spread of Omicron, which has now seized many nations, has resulted in numerous speculations regarding its origin and degree of infectivity. The following sections will go over its potential for transmission, omicron structure, and impact on COVID-19 vaccines, how it is different from delta variant and diagnostics.

Investigating the relationship between interventions, contact patterns, and SARS-CoV-2 transmissibility

BACKGROUND

After a rapid upsurge of COVID-19 cases in Italy during the fall of 2020, the government introduced a three-tiered restriction system aimed at increasing physical distancing. The Ministry of Health, after periodic epidemiological risk assessments, assigned a tier to each of the 21 Italian regions and autonomous provinces. It is still unclear to what extent these different sets of measures altered the number of daily interactions and the social mixing patterns.

METHODS AND FINDINGS

We conducted a survey between July 2020 and March 2021 to monitor changes in social contact patterns among individuals in the metropolitan city of Milan, Italy, which was hardly hit by the second wave of the COVID-19 pandemic. The number of daily contacts during periods characterized by different levels of restrictions was analyzed through negative binomial regression models and age-specific contact matrices were estimated under the different tiers of restrictions. By relying on the empirically estimated mixing patterns, we quantified relative changes in SARS-CoV-2 transmission potential associated with the different tiers. As tighter restrictions were implemented during the fall of 2020, a progressive reduction in the mean number of daily contacts recorded by study participants was observed: from 15.9 % under mild restrictions (yellow tier), to 41.8 % under strong restrictions (red tier). Higher restrictions levels were also found to increase the relative contribution of contacts occurring within the household. The SARS-CoV-2 reproduction number was estimated to decrease by 17.1 % (95 %CI: 1.5-30.1), 25.1 % (95 %CI: 13.0-36.0) and 44.7 % (95 %CI: 33.9-53.0) under the yellow, orange, and red tiers, respectively.

CONCLUSIONS

Our results give an important quantification of the expected contribution of different restriction levels in shaping social contacts and decreasing the transmission potential of SARS-CoV-2. These estimates can find an operational use in anticipating the effect that the implementation of these tiered restriction can have on SARS-CoV-2 reproduction number under an evolving epidemiological situation.

COVID-19 in Japan, January-March 2020: insights from the first three months of the epidemic

BACKGROUND

Understanding the characteristics and natural history of novel pathogens is crucial to inform successful control measures. Japan was one of the first affected countries in the COVID-19 pandemic reporting their first case on 14 January 2020. Interventions including airport screening, contact tracing, and cluster investigations were quickly implemented. Here we present insights from the first 3 months of the epidemic in Japan based on detailed case data.

METHODS

We conducted descriptive analyses based on information systematically extracted from individual case reports from 13 January to 31 March 2020 including patient demographics, date of report and symptom onset, symptom progression, travel history, and contact type. We analysed symptom progression and estimated the time-varying reproduction number, Rt, correcting for epidemic growth using an established Bayesian framework. Key delays and the age-specific probability of transmission were estimated using data on exposures and transmission pairs.

RESULTS

The corrected fitted mean onset-to-reporting delay after the peak was 4 days (standard deviation: ± 2 days). Early transmission was driven primarily by returning travellers with Rt peaking at 2.4 (95% CrI: 1.6, 3.3) nationally. In the final week of the trusted period (16-23 March 2020), Rt accounting for importations diverged from overall Rt at 1.1 (95% CrI: 1.0, 1.2) compared to 1.5 (95% CrI: 1.3, 1.6), respectively. Household (39.0%) and workplace (11.6%) exposures were the most frequently reported potential source of infection. The estimated probability of transmission was assortative by age with individuals more likely to infect, and be infected by, contacts in a similar age group to them. Across all age groups, cases most frequently onset with cough, fever, and fatigue. There were no reported cases of patients < 20 years old developing pneumonia or severe respiratory symptoms.

CONCLUSIONS

Information collected in the early phases of an outbreak are important in characterising any novel pathogen. The availability of timely and detailed data and appropriate analyses is critical to estimate and understand a pathogen's transmissibility, high-risk settings for transmission, and key symptoms. These insights can help to inform urgent response strategies.

Influenza seasonality and its environmental driving factors in mainland China and Hong Kong

BACKGROUND

Influenza epidemics occur during winter in temperate zones, but have less regular seasonality in the subtropics and tropics. Here we quantified the role of environmental drivers of influenza seasonality in temperate and subtropical China.

METHODS

We used weekly surveillance data on influenza virus activity in mainland China and Hong Kong from 2005 through 2016. We estimated the transmissibility via the instantaneous reproduction number (R_t), a real-time measure of transmissibility, and examined its relationship with different climactic drivers and allowed for the timing of school holidays and the decline in susceptibility in the population as an epidemic progressed. We developed a multivariable regression model for R_t to quantify the contribution of various potential environmental drivers of transmission.

FINDINGS

We found that absolute humidity is a potential driver of influenza seasonality and had a U-shaped association with transmissibility and hence can predict the pattern of influenza virus transmission across different climate zones. Absolute humidity was able to explain up to 15% of the variance in R_t, and was a stronger predictor of R_t across the latitudes. Other climatic drivers including mean daily temperature explained up to 13% of variance in R_t and limited to the locations where the indoor measures of these factors have better indicators of outdoor measures. The non-climatic driver, holiday-related school closures could explain up to 7% of variance in R_t.

INTERPRETATION

A U-shaped association of absolute humidity with influenza transmissibility was able to predict seasonal patterns of influenza virus epidemics in temperate and subtropical locations.

The host-pathogen-environment triad: Lessons learned through the study of the multidrug-resistant Mycobacterium tuberculosis M strain

Multidrug-resistant tuberculosis is one of the major obstacles that face the tuberculosis eradication efforts. Drug-resistant Mycobacterium tuberculosis clones were initially disregarded as a public health threat, because they were assumed to have paid a high fitness cost in exchange of resistance acquisition. However, some genotypes manage to overcome the impact of drug-resistance conferring mutations, retain transmissibility and cause large outbreaks. In Argentina, the HIV-AIDS epidemics fuelled the expansion of the so-called M strain in the early 1990s, which is responsible for the largest recorded multidrug-resistant tuberculosis cluster of Latin America. The aim of this work is to review the knowledge gathered after nearly three decades of multidisciplinary research on epidemiological, microbiological and immunological aspects of this highly successful strain. Collectively, our results indicate that the successful transmission of the M strain could be ascribed to its unaltered virulence, low Th1/Th17 response, a low fitness cost imposed by the resistance conferring mutations and a high resistance to host-related stress. In the early 2000s, the incident cases due to the M strain steadily declined and stabilized in the latest years. Improvements in the management, diagnosis and treatment of multidrug-resistant tuberculosis along with societal factors such as the low domestic and international mobility of the patients affected by this strain probably contributed to the outbreak containment. This stresses the importance of sustaining the public health interventions to avoid the resurgence of this conspicuous multidrug-resistant strain.

Emerging mutation patterns in SARS-CoV-2 variants

There is an urgent need to understand the functional effects of mutations in emerging variants of SARS-CoV-2. Variants of concern (alpha, beta, gamma and delta) acquired four patterns of spike glycoprotein mutations that enhance transmissibility and immune evasion: 1) mutations in the N-terminal domain (NTD), 2) mutations in the Receptor Binding Domain (RBD), 3) mutations at interchain contacts of the spike trimer, and 4) furin cleavage site mutations. Most distinguishing mutations among variants of concern are exhibited in the NTD, localized to sites of high structural flexibility. Emerging variants of interest such as mu, lambda and C.1.2 exhibit the same patterns of mutations as variants of concern. There is a strong likelihood that SARS-CoV-2 variants will continue to emerge with mutations in these defined patterns, thus providing a basis for the development of next line antiviral drugs and vaccine candidates.

The optimal vaccination strategy to control COVID-19: a modeling study in Wuhan City, China

Background

Reaching optimal vaccination rates is an essential public health strategy to control the coronavirus disease 2019 (COVID-19) pandemic. This study aimed to simulate the optimal vaccination strategy to control the disease by developing an age-specific model based on the current transmission patterns of COVID-19 in Wuhan City, China.

Methods

We collected two indicators of COVID-19, including illness onset data and age of confirmed case in Wuhan City, from December 2, 2019, to March 16, 2020. The reported cases were divided into four age groups: group 1, ≤ 14 years old; group 2, 15 to 44 years old; group 3, 44 to 64 years old; and group 4, ≥ 65 years old. An age-specific susceptible-exposed-symptomatic-asymptomatic-recovered/removed model was developed to estimate the transmissibility and simulate the optimal vaccination strategy. The effective reproduction number (R_eff) was used to estimate the transmission interaction in different age groups.

Results

A total of 47 722 new cases were reported in Wuhan City from December 2, 2019, to March 16, 2020. Before the travel ban of Wuhan City, the highest transmissibility was observed among age group 2 (R_eff = 4.28), followed by group 2 to 3 (R_eff = 2.61), and group 2 to 4 (R_eff = 1.69). China should vaccinate at least 85% of the total population to interrupt transmission. The priority for controlling transmission should be to vaccinate 5% to 8% of individuals in age group 2 per day (ultimately vaccinated 90% of age group 2), followed by 10% of age group 3 per day (ultimately vaccinated 90% age group 3). However, the optimal vaccination strategy for reducing the disease severity identified individuals ≥ 65 years old as a priority group, followed by those 45–64 years old.

Conclusions

Approximately 85% of the total population (nearly 1.2 billion people) should be vaccinated to build an immune barrier in China to safely consider removing border restrictions. Based on these results, we concluded that 90% of adults aged 15–64 years should first be vaccinated to prevent transmission in China.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s40249-021-00922-4.

Epidemiological features of COVID-19 patients with prolonged incubation period and its implications for controlling the epidemics in China

BACKGROUND

COVID-19 patients with long incubation period were reported in clinical practice and tracing of close contacts, but their epidemiological or clinical features remained vague.

METHODS

We analyzed 11,425 COVID-19 cases reported between January-August, 2020 in China. The accelerated failure time model, Logistic and modified Poisson regression models were used to investigate the determinants of prolonged incubation period, as well as their association with clinical severity and transmissibility, respectively.

RESULT

Among local cases, 268 (10.2%) had a prolonged incubation period of > 14 days, which was more frequently seen among elderly patients, those residing in South China, with disease onset after Level I response measures administration, or being exposed in public places. Patients with prolonged incubation period had lower risk of severe illness (OR_adjusted = 0.386, 95% CI: 0.203-0.677). A reduced transmissibility was observed for the primary patients with prolonged incubation period (50.4, 95% CI: 32.3-78.6%) than those with an incubation period of ≤14 days.

CONCLUSIONS

The study provides evidence supporting a prolonged incubation period that exceeded 2 weeks in over 10% for COVID-19. Longer monitoring periods than 14 days for quarantine or persons potentially exposed to SARS-CoV-2 should be justified in extreme cases, especially for those elderly.

The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study

OBJECTIVES

Recently emerging SARS-CoV-2 variants have been associated with an increased rate of transmission within the community. We sought to determine whether this also resulted in increased transmission within hospitals.

METHODS

We collected viral sequences and epidemiological data of patients with community and healthcare associated SARS-CoV-2 infections, sampled from 16th November 2020 to 10th January 2021, from nine hospitals participating in the COG-UK HOCI study. Outbreaks were identified using ward information, lineage and pairwise genetic differences between viral sequences.

RESULTS

Mixed effects logistic regression analysis of 4184 sequences showed healthcare-acquired infections were no more likely to be identified as the Alpha variant than community acquired infections. Nosocomial outbreaks were investigated based on overlapping ward stay and SARS-CoV-2 genome sequence similarity. There was no significant difference in the number of patients involved in outbreaks caused by the Alpha variant compared to outbreaks caused by other lineages.

CONCLUSIONS

We find no evidence to support it causing more nosocomial transmission than previous lineages. This suggests that the stringent infection prevention measures already in place in UK hospitals contained the spread of the Alpha variant as effectively as other less transmissible lineages, providing reassurance of their efficacy against emerging variants of concern.

Does temperature matter for COVID-19 transmissibility? Evidence across Pakistani provinces

The outbreak of novel coronavirus (COVID-19) has become a global concern that is deteriorating environmental quality and damaging human health. Though some researchers have investigated the linkage between temperature and COVID-19 transmissibility across different geographical locations and over time, yet these studies are scarce. This study aims to bridge this gap using daily temperature and COVID-19 cases (transmissibility) by employing grey incidence analysis (GIA) models (i.e., Deng's grey incidence analysis (DGIA), the absolute degree GIA (ADGIA), the second synthetic degree GIA (SSDGIA), the conservative (maximin) model) and correlation analysis. Data on temperature are accessed from the NASA database, while the data on COVID-19 cases are collected from the official website of the government of Pakistan. Empirical results reveal the existence of linkages between temperature and COVID-19 in all Pakistani provinces. These linkages vary from a relatively stronger to a relatively weaker linkage. Based on calculated weights, the strength of linkages is ranked across provinces as follows: Gilgit Baltistan (0.715301) > Baluchistan (0.675091) > Khyber Pakhtunkhwa (0.619893) > Punjab (0.619286) > Sindh (0.601736). The disparity in the strength of linkage among provinces is explained by the discrepancy in the intensity of temperature. Besides, the diagrammatic correlation analysis shows that temperature is inversely linked to COVID-19 cases (per million persons) over time, implying that low temperatures are associated with high COVID-19 transmissibility and vice versa. This study is among the first of its kind to consider the linkages between temperature and COVID-19 transmissibility for a tropical climate country (Pakistan) using the advanced GIA models. Research findings provide an up-to-date glimpse of the outbreak and emphasize the need to raise public awareness about the devastating impacts of the COVID-19. The educational syllabus should provide information on the causes, signs, and precautions of the pandemic. Additionally, individuals should practice handwashing, social distancing, personal hygiene, mask-wearing, and the use of hand sanitizers to ensure a secure and supportive atmosphere for preventing and controlling the current pandemic.

Does temperature matter for COVID-19 transmissibility? Evidence across Pakistani provinces

The outbreak of novel coronavirus (COVID-19) has become a global concern that is deteriorating environmental quality and damaging human health. Though some researchers have investigated the linkage between temperature and COVID-19 transmissibility across different geographical locations and over time, yet these studies are scarce. This study aims to bridge this gap using daily temperature and COVID-19 cases (transmissibility) by employing grey incidence analysis (GIA) models (i.e., Deng's grey incidence analysis (DGIA), the absolute degree GIA (ADGIA), the second synthetic degree GIA (SSDGIA), the conservative (maximin) model) and correlation analysis. Data on temperature are accessed from the NASA database, while the data on COVID-19 cases are collected from the official website of the government of Pakistan. Empirical results reveal the existence of linkages between temperature and COVID-19 in all Pakistani provinces. These linkages vary from a relatively stronger to a relatively weaker linkage. Based on calculated weights, the strength of linkages is ranked across provinces as follows: Gilgit Baltistan (0.715301) > Baluchistan (0.675091) > Khyber Pakhtunkhwa (0.619893) > Punjab (0.619286) > Sindh (0.601736). The disparity in the strength of linkage among provinces is explained by the discrepancy in the intensity of temperature. Besides, the diagrammatic correlation analysis shows that temperature is inversely linked to COVID-19 cases (per million persons) over time, implying that low temperatures are associated with high COVID-19 transmissibility and vice versa. This study is among the first of its kind to consider the linkages between temperature and COVID-19 transmissibility for a tropical climate country (Pakistan) using the advanced GIA models. Research findings provide an up-to-date glimpse of the outbreak and emphasize the need to raise public awareness about the devastating impacts of the COVID-19. The educational syllabus should provide information on the causes, signs, and precautions of the pandemic. Additionally, individuals should practice handwashing, social distancing, personal hygiene, mask-wearing, and the use of hand sanitizers to ensure a secure and supportive atmosphere for preventing and controlling the current pandemic.

Impact of Sterilization Methods on the Seeding Ability of Human Tau Proteopathic Seeds

The protein tau, when misfolded in neurodegenerative diseases, has several prion-like properties including being able to spread by cell-to-cell transfer, induce templated seeding, and exist in distinct conformational strains. These properties of transmission may present health hazards when lesion-containing biospecimens are used in research and neuropathology laboratories. We evaluated the impact standard sterilization and cleaning methods have on the capacity of tau seeds to induce aggregation. We employed a previously developed, highly sensitive FRET-based biosensor assay to assess remnant tau seeding after exposure to these procedures. For tau species derived from human Alzheimer disease tissue (brain homogenate and sarkosyl-insoluble fibrils), both autoclaving and incubation in 90.6% formic acid were sufficient to reduce tau bioactivity. By contrast, boiling was not always effective in completely blocking bioactivity in the seeding assay. Notably, only formic acid incubation was able to produce a similar reduction in tissue from a P301L mutant tau mouse model of tauopathy. Our study highlights nuances in methods for inactivation of tau seeding which may support adapted tissue processing procedures, especially in research settings. These findings also highlight the importance of universal precautions when handling human neuropathological and research laboratory materials.

Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome

Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2 pathogen, has led to waves of global pandemic claiming lives and posing a serious threat to public health and social cum physical interactions. To evaluate the mutational landscape and conserved regions in the genome of the causative pathogen, we analysed 7213 complete SARS-CoV-2 protein sequences mined from the Global Initiative on Sharing All Influenza Data (GISAID) repository from infected patients across all regions on the EpiCov web interface. Regions of origin and the corresponding number of sequences mined are as follows: Asia – 2487; Oceania – 2027; Europe – 1240; Africa – 717; South America – 391; and North America – 351. High recurrent mutations, namely: T265I in non-structural protein 2 (nsp2), L3606F in nsp6, P4715L in RNA-dependent RNA polymerase (RdRp), D614G in spike glycoprotein, R203K and G204R in nucleocapsid phosphoprotein and Q57H in ORF3a with well-conserved envelope and membrane proteins, 3CLpro and spike S2 domains across regions were observed. Comparative analyses of the viral sequences reveal the prevalence P4715L and D614G mutations as the most recurrent and concurrent in Africa (97.20%), Europe (89.83%) and moderately in Asia (61.60%). Mutation rates are central to viral transmissibility, evolution and virulence, which help them to invade host immunity and develop drug resistance. Based on the foregoing, it is important to understand the mutational spectra of SARS-CoV-2 genome across regions. This will help in identifying specific genomic sites as potential targets for drug design and vaccine development, monitoring the spread of the virus and unraveling its evolution, virulence and transmissibility.

Transmission Risk of SARS-CoV-2 Before and After Symptom Onset of the Infector

An outbreak of COVID-19 occurred in Ueda City, Nagano prefecture, Japan with a population of 150,000. Because the residents were a population naïve to COVID-19 and many of them had only one chance of exposure, careful epidemiological investigation could reveal attack rates among close contacts on the specific date of exposure. We identified 89 cases and 328 close contacts. Among the close contacts, 114 had only one chance of exposure to their 20 index cases. During the follow-up period, 17 of them tested positive for SARS-CoV-2 (Overall attack rate 15%) after the exposure to 6 infectors. The median number of close contacts was 5.5 (range 2-14) for the 6 infectors. Attack rates among those close contacts were 13% (1/8), 20% (2/5), 33% (2/6), 50% (1/2), 64% (4/9 and 5/5) and 100% (2/2). Transmission risk of SARS-CoV-2 seems to peak one day before symptom onset, and it was at similar level two days before (16%) and on the day (20%) of symptom onset. A multidisciplinary approach is needed to control the COVID-19 outbreak in addition to investigation which started after the case identification.

Estimating COVID-19 cases infected with the variant alpha (VOC 202012/01): an analysis of screening data in Tokyo, January-March 2021

Background

In Japan, a part of confirmed patients’ samples have been screened for the variant of concern (VOC), including the variant alpha with N501Y mutation. The present study aimed to estimate the actual number of cases with variant alpha and reconstruct the epidemiological dynamics.

Methods

The number of cases with variant alpha out of all PCR confirmed cases was estimated, employing a hypergeometric distribution. An exponential growth model was fitted to the growth data of variant alpha cases over fourteen weeks in Tokyo.

Results

The weekly incidence with variant alpha from 18–24 January 2021 was estimated at 4.2 (95% confidence interval (CI): 0.7, 44.0) cases. The expected incidence in early May ranged from 420–1120 cases per week, and the reproduction number of variant alpha was on the order of 1.5 even under the restriction of contact from January-March, 2021, Tokyo.

Conclusions

The variant alpha was predicted to swiftly dominate COVID-19 cases in Tokyo, and this has actually occurred by May 2021. Devising the proposed method, any country or location can interpret the virological sampling data.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12976-021-00146-x.

Emerging SARS-CoV-2 variants of concern and potential intervention approaches

The major variant of concerns (VOCs) have shared mutations in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike proteins, mostly on the S1 unit and resulted in higher transmissibility rate and affect viral virulence and clinical outcome. The spike protein mutations and other non-structural protein mutations in the VOCs may lead to escape approved vaccinations in certain extend. We will discuss these VOC mutations and discuss the need for combination therapeutic strategies targeting viral cycle and immune host responses.

Feasibility of controlling hepatitis E in Jiangsu Province, China: a modelling study

BACKGROUND

Hepatitis E, an acute zoonotic disease caused by the hepatitis E virus (HEV), has a relatively high burden in developing countries. The current research model on hepatitis E mainly uses experimental animal models (such as pigs, chickens, and rabbits) to explain the transmission of HEV. Few studies have developed a multi-host and multi-route transmission dynamic model (MHMRTDM) to explore the transmission feature of HEV. Hence, this study aimed to explore its transmission and evaluate the effectiveness of intervention using the dataset of Jiangsu Province.

METHODS

We developed a dataset comprising all reported HEV cases in Jiangsu Province from 2005 to 2018. The MHMRTDM was developed according to the natural history of HEV cases among humans and pigs and the multi-transmission routes such as person-to-person, pig-to-person, and environment-to-person. We estimated the key parameter of the transmission using the principle of least root mean square to fit the curve of the MHMRTDM to the reported data. We developed models with single or combined countermeasures to assess the effectiveness of interventions, which include vaccination, shortening the infectious period, and cutting transmission routes. The indicator, total attack rate (TAR), was adopted to assess the effectiveness.

RESULTS

From 2005 to 2018, 44 923 hepatitis E cases were reported in Jiangsu Province. The model fits the data well (R2 = 0.655, P < 0.001). The incidence of the disease in Jiangsu Province and its cities peaks are around March; however, transmissibility of the disease peaks in December and January. The model showed that the most effective intervention was interrupting the pig-to-person route during the incidence trough of September, thereby reducing the TAR by 98.11%, followed by vaccination (reducing the TAR by 76.25% when the vaccination coefficient is 100%) and shortening the infectious period (reducing the TAR by 50.05% when the infectious period is shortened to 15 days).

CONCLUSIONS

HEV could be controlled by interrupting the pig-to-person route, shortening the infectious period, and vaccination. Among these interventions, the most effective was interrupting the pig-to-person route.

Smoking cessation in tuberculosis patients and the risk of tuberculosis infection in child household contacts

BACKGROUND

While previous studies have shown that cigarette smoking increases the infectiousness of tuberculosis patients, the impact of smoking cessation on tuberculosis transmissibility has not been evaluated.

DESIGN/METHODS

Between 2009 and 2012, we enrolled 4,500 tuberculosis patients and followed 14,044 household contacts in Lima, Peru. Tuberculosis patients were classified into four categories: never smoked, quit in the distant past (stopped smoking >2 months prior to time of diagnosis), recently quit (stopped smoking ≤2 months prior to time of diagnosis), and active smokers. We used a modified Poisson generalized estimating equation to assess the risk of tuberculosis infection of child contacts at enrollment and by six months of follow-up.

RESULTS

In total, 1,371 (76.8%) child contacts were exposed to patients who had never smoked, 211 (11.8%) were exposed to distant quitters, 155 (8.7%) were exposed to recent quitters, and 49 (2.7%) were exposed to active smokers. Compared to child contacts of index patients who had never smoked, child contacts of recent quitters had a similar risk of tuberculosis infection at enrollment (adjusted risk ratio [aRR], 0.81, 95% CI, 0.50-1.32) and by six months of follow-up (aRR, 0.76, 95% CI, 0.51-1.13); child contacts of recent quitters had a significantly reduced risk of tuberculosis infection compared to contacts of active smokers (enrollment aRR, 0.45, 95% CI, 0.24-0.87; 6-month follow-up aRR, 0.48, 95% CI, 0.29-0.79).

CONCLUSIONS

Our results show that the adverse effects of smoking on the transmissibility of tuberculosis are significantly reduced shortly after quitting smoking, reinforcing the importance of smoking cessation interventions in tuberculosis control.

SARS-CoV-2 variants combining spike mutations and the absence of ORF8 may be more transmissible and require close monitoring

The SARS-CoV-2 Variant of Concern 202012/01 (VOC-202012/01) emerged in southeast England and rapidly spread worldwide. This variant is believed to be more transmissible, with all attention being given to its spike mutations. However, VOC-202012/01 has also a mutation (Q27stop) that truncates the ORF8, a likely immune evasion protein. Removal of ORF8 changes the clinical outset of the disease, which may affect the virus transmissibility. Here I provide a detailed analysis of all reported ORF8-deficient lineages found in the background of relevant spike mutations, identified among 231,433 SARS-CoV-2 genomes. I found 19 ORF8 nonsense mutations, most of them occurring in the 5' half of the gene. The ORF8-deficient lineages were rare, representing 0.67% of sequenced genomes. Nevertheless, I identified two clusters of related sequences that emerged recently and spread in different countries. The widespread D614G spike mutation was found in most ORF-deficient lineages. Although less frequent, HV69-70del and L5F spike mutations occurred in the background of six different ORF8 nonsense mutations. I also confirmed that VOC-202012/01 is the ORF8-deficient variant with more spike mutations reported to date, although other variants could have up to six spike mutations, some of putative biological relevance. Overall, these results suggest that monitoring ORF8-deficient lineages is important for the progression of the COVID-19 pandemic, particularly when associated with relevant spike mutations.

Predicted impacts of government policies and actions on the SARS-CoV-2 disease in the northwestern Himalayan region, India

AIM

The outbreak of the new coronavirus pandemic (SARS-CoV-2) was initiated in December 2019, and within a couple of months it became a global health emergency. Given the importance to assess the evolution and transmissibility of SARS-CoV-2 and to forecast the next scenario of the pandemic, mainly in countries with limited healthcare systems, we estimated the reproductive number (R0) of SARS-CoV-2 in Jammu and Kashmir (J&K), India, and a possible scenario for this pandemic in the region.

SUBJECT AND METHODS

We estimated the reproductive number (R0) of SARS-CoV-2 in its first outbreak stage in the northwestern region of Himalaya, India, and we also predicted new daily cases for the next 90 days using different R0, testing a plausible end of the SARS-CoV-2 outbreak.

RESULTS

Our results showed a considerable increase in the number of cases, but with a tendency to asymptote. Anantnag, Bandipora, Baramulla, Shopian, and Srinagar districts showed more than 100 cases and Kulgam and Kathua districts showed strong growth of the number of cases from the beginning of May, without a tendency to normalization. The estimated R0 for the J&K region was 1.041; but by decreasing the RO by 10, 25, and 50%, we observed a great decrease in the daily number of new cases, especially by decreasing by 50%.

CONCLUSION

In this study, we indicate positive effects of the preventive measures, such as lockdown and social distancing, taken in the J&K region, showing a stabilization of the growth curves of new cases of SARS-CoV-2, which tends to a strong decrease over time as the R0 decreases.

SARS-CoV-2 variants lacking ORF8 occurred in farmed mink and pangolin

The SARS-CoV-2 Variant of Concern 202012/01 (VOC-202012/01) is rapidly spreading worldwide owing to its substantial transmission advantage. The variant has changes in critical sites of the spike protein with potential biological significance. Moreover, VOC-202012/01 has a mutation that inactivates the ORF8 protein, whose absence can change the clinical features of the infection. Why VOC-202012/01 is more transmissible remains unclear, but spike mutations and ORF8 inactivation stand out by their known phenotypic effects. Here I show that variants combining relevant spike mutations and the absence of ORF8 occurred in SARS-CoV-2 and related viruses circulating in other host species. A truncated ORF8 (Q23stop) occurred in a SARS-CoV-2-related virus from a pangolin seized in China in 2017, also with several mutations in critical spike sites. Strikingly, I found that variants without ORF8 (E19stop) and with the N501T spike mutation circulated in farmed mink and humans from Denmark. Although with differences to VOC-202012/01, the identification of these variants highlights the danger of having reservoirs of SARS-CoV-2 and related viruses where more transmissible variants may occur and spill over to humans.

Evaluating the effectiveness of measures to control the novel coronavirus disease 2019 in Jilin Province, China

BACKGROUND

Based on differences in populations and prevention and control measures, the spread of new coronary pneumonia in different countries and regions also differs. This study aimed to calculate the transmissibility of coronavirus disease 2019 (COVID-19), and to evaluate the effectiveness of measures to control the disease in Jilin Province, China.

METHODS

The data of reported COVID-19 cases were collected, including imported and local cases from Jilin Province as of March 14, 2019. A Susceptible-Exposed-Infectious-Asymptomatic-Recovered/Removed (SEIAR) model was developed to fit the data, and the effective reproduction number (Reff) was calculated at different stages in the province. Finally, the effectiveness of the measures was assessed.

RESULTS

A total of 97 COVID-19 infections were reported in Jilin Province, among which 45 were imported infections (including one asymptomatic infection) and 52 were local infections (including three asymptomatic infections). The model fit the reported data well (R2 = 0.593, P < 0.001). The Reff of COVID-19 before and after February 1, 2020 was 1.64 and 0.05, respectively. Without the intervention taken on February 1, 2020, the predicted cases would have reached a peak of 177,011 on October 22, 2020 (284 days from the first case). The projected number of cases until the end of the outbreak (on October 9, 2021) would have been 17,129,367, with a total attack rate of 63.66%. Based on the comparison between the predicted incidence of the model and the actual incidence, the comprehensive intervention measures implemented in Jilin Province on February 1 reduced the incidence of cases by 99.99%. Therefore, according to the current measures and implementation efforts, Jilin Province can achieve good control of the virus's spread.

CONCLUSIONS

COVID-19 has a moderate transmissibility in Jilin Province, China. The interventions implemented in the province had proven effective; increasing social distancing and a rapid response by the prevention and control system will help control the spread of the disease.

Risk of Transmissibility From Neurodegenerative Disease-Associated Proteins: Experimental Knowns and Unknowns

Recent studies in animal models demonstrate that certain misfolded proteins associated with neurodegenerative diseases can support templated misfolding of cognate native proteins, to propagate across neural systems, and to therefore have some of the properties of classical prion diseases like Creutzfeldt-Jakob disease. The National Institute of Aging convened a meeting to discuss the implications of these observations for research priorities. A summary of the discussion is presented here, with a focus on limitations of current knowledge, highlighting areas that appear to require further investigation in order to guide scientific practice while minimizing potential exposure or risk in the laboratory setting. The committee concluded that, based on all currently available data, although neurodegenerative disease-associated aggregates of several different non-prion proteins can be propagated from humans to experimental animals, there is currently insufficient evidence to suggest more than a negligible risk, if any, of a direct infectious etiology for the human neurodegenerative disorders defined in part by these proteins. Given the importance of this question, the potential for noninvasive human transmission of proteopathic disorders is deserving of further investigation.

Sensitivity analysis of the infection transmissibility in the UK during the COVID-19 pandemic

The coronavirus (COVID-19) outbreak started in December 2019 and rapidly spread around the world affecting millions of people. With the growth of infection rate, many countries adopted different policies to control the spread of the disease. The UK implemented strict rules instructing individuals to stay at home except in some special circumstances starting from 23 March 2020. Accordingly, this study focuses on sensitivity analysis of transmissibility of the infection as the effects of removing restrictions, for example by returning different occupational groups to their normal working environment and its effect on the reproduction number in the UK. For this reason, available social contact matrices are adopted for the population of UK to account for the average number of contacts. Different scenarios are then considered to analyse the variability of total contacts on the reproduction number in the UK as a whole and each of its four nations. Our data-driven retrospective analysis shows that if more than 38.5% of UK working-age population return to their normal working environment, the reproduction number in the UK is expected to be higher than 1. However, analysis of each nation, separately, shows that local reproduction number in each nation may be different and requires more adequate analysis. Accordingly, we believe that using statistical methods and historical data can provide good estimation of local transmissibility and reproduction number in any region. As a consequence of this analysis, efforts to reduce the restrictions should be implemented locally via different control policies. It is important that these policies consider the social contacts, population density, and the occupational groups that are specific to each region.

Transmissibility of asymptomatic COVID-19: Data from Japanese clusters

Background

The epidemiological importance of asymptomatic individuals who would never develop illness, compared to those who eventually develop symptoms, has yet to be fully clarified.

Methods

The very first cluster data in Tokyo and Kanagawa (n = 36) were analyzed. Movement of all close contact was restricted for 14 days and they underwent laboratory testing with polymerase chain reaction. The reproduction numbers of symptomatic and asymptomatic cases were estimated.

Results

The reproduction number for symptomatic cases was estimated to be 1.2 (95% confidence interval (CI): 0.5–2.9). The relative infectiousness of asymptomatically infected cases was estimated to be 0.27 (95% CI: 0.03–0.81) of symptomatic cases.

Conclusion

The relative transmissibility of asymptomatic cases is limited. Observing clusters starting with symptomatic transmission might be sufficient for the control.

Could the ambient higher temperature decrease the transmissibility of COVID-19 in China?

BACKGROUND

Existing literatures demonstrated that meteorological factors could be of importance in affecting the spread patterns of the respiratory infectious diseases. However, how ambient temperature may influence the transmissibility of COVID-19 remains unclear.

OBJECTIVES

We explore the association between ambient temperature and transmissibility of COVID-19 in different regions across China.

METHODS

The surveillance data on COVID-19 and meteorological factors were collected from 28 provincial level regions in China, and estimated the instantaneous reproductive number (R_t). The generalized additive model was used to assess the relationship between mean temperature and R_t.

RESULTS

There were 12,745 COVID-19 cases collected in the study areas. We report the associated effect of temperature on R_t is likely to be negative but not of statistical significance, which holds for most Chinese regions.

CONCLUSIONS

We found little statistical evidence for that the higher temperature may reduce the transmissibility of COVID-19. Since intensive control measures against the COVID-19 epidemics were implemented in China, we acknowledge this may impact the underlying effect size estimation, and thus cautiousness should be taken when interpreting our findings.

Vibration transmissibility and apparent mass changes from vertical whole-body vibration exposure during stationary and propelled walking

Whole-Body Vibration (WBV) is an occupational hazard affecting employees working with transportation, construction or heavy machinery. To minimize vibration-induced pathologies, ISO identified WBV exposure limits based on vibration transmissibility and apparent mass studies. The ISO guidelines do not account for variations in posture or movement. In our study, we measured the transmissibility and apparent mass at the mouth, lower back, and leg of participants during stationary and propelled walking. Stationary walking transmissibility was significantly higher at the lumbar spine and bite bar at 5 and 10 Hz compared to all higher frequencies while the distal tibia was lower at 5 Hz compared to 10 and 15 Hz. Propelled walking transmissibility was significantly higher at the bite bar and knee at 2 Hz than all higher frequencies. These results vary from previously published transmissibility values for static participants, showing that ISO standards should be adjusted for active workers.