Quantifying the presymptomatic transmission of COVID-19 in the USA.

The emergence of many presymptomatic hidden transmission events significantly complicated the intervention and control of the spread of COVID-19 in the USA during the year 2020. To analyze the role that presymptomatic infections play in the spread of this disease, we developed a state-level metapopulation model to simulate COVID-19 transmission in the USA in 2020 during which period the number of confirmed cases was more than in any other country. We estimated that the transmission rate (i.e., the number of new infections per unit time generated by an infected individual) of presymptomatic infections was approximately 59.9% the transmission rate of reported infections. We further estimated that {at any point in time the} average proportion of infected individuals in the presymptomatic stage was consistently over 50% of all infected individuals. Presymptomatic transmission was consistently contributing over 52% to daily new infections, as well as consistently contributing over 50% to the effective reproduction number from February to December. Finally, non-pharmaceutical intervention targeting presymptomatic infections was very effective in reducing the number of reported cases. These results reveal the significant contribution that presymptomatic transmission made to COVID-19 transmission in the USA during 2020, as well as pave the way for the design of effective disease control and mitigation strategies.

Does the resumption of international tourism heighten COVID-19 transmission?

Reopening countries also carries the risk of another wave of infections in many parts of the world, raising the question of whether we are ready to reopen our countries. This study examines the impact of reopening countries to receive foreign tourists on the spread of COVID-19 in 2022, encompassing 83 countries worldwide. We employ spatial quantile models capable of analyzing the spatial impact of tourism on the spread of the virus at different quantile levels. The research categorizes countries into three groups: low infection rate (10th-30th quantiles), moderate infection rate (40th-60th quantiles), and high infection rate (70th-90th quantiles). This allows for a more comprehensive and detailed comparison of the impacts. Additionally, considering the spatial dimension enables the explanation of both the direct and indirect effects of tourists on the country itself and neighboring countries. The findings reveal that the number of international tourists has a significant effect on the COVID-19 infection rate, particularly in countries with high initial infection rates. However, countries that effectively controlled their infection rates at a low level could maintain a low infection rate even after reopening to foreign tourists. It is also observed that reopening a country's borders negatively impacts the infection rate of neighboring countries. These important findings imply that governments of highly infected countries should shift their focus towards bolstering their economy by promoting domestic tourism and should delay reopening until the number of infections decreases.

Study of the Vertical Transmission of COVID-19 by Using the World Health Organisation Protocol in a Tertiary Care Hospital in Eastern India.

BACKGROUND: The World Health Organisation (WHO) has established criteria to diagnose vertical transmission in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study aimed to determine the incidence of vertical transmission of SARS-CoV-2 using WHO criteria in a tertiary care centre in eastern India. METHODS: A hospital-based prospective observational study was conducted from June 2021 to February 2022 on women admitted for delivery with a positive nasopharyngeal (NP) swab and a SARS-CoV-2 real-time reverse-transcriptase polymerase chain reaction (RT-PCR) test. Following the delivery, the amniotic fluid (AF) and swab from the placenta were tested for SARS-CoV-2 by the Truenat test. The umbilical cord and maternal blood were analyzed to detect immunoglobulin M (IgM) and immunoglobulin G (IgG). The nasopharyngeal swabs of the newborns were tested for SARS-CoV-2 by RT-PCR. RESULTS: Forty-eight SARS-CoV-2-positive asymptomatic women were included in the study. Twenty-eight (58.3%) were delivered via cesarean section. Preterm delivery occurred in 13 (27.1%) cases. In only one case, vertical transmission was confirmed as the neonate had a positive nasopharyngeal SARS-CoV-2 RT-PCR test and the cord blood was IgM positive (suggesting an immune response in the neonate). The placenta was positive in three cases, and amniotic fluid was positive in two. However, vertical transmission was deemed unlikely in these cases as there was no evidence of immune response or viral persistence according to the WHO criteria. There was one stillbirth, and it tested negative for SARS-CoV-2. CONCLUSION: This study strengthens the evidence of vertical transmission in COVID-19-positive asymptomatic mothers. The data suggest a low transmission rate.

Assessing the impact of booster vaccination on diphtheria transmission: Mathematical modeling and risk zone mapping.

The COVID-19 pandemic caused significant disruptions in the healthcare system, affecting vaccinations and the management of diphtheria cases. As a consequence of these disruptions, numerous countries have experienced a resurgence or an increase in diphtheria cases. West Java province in Indonesia is identified as one of the high-risk areas for diphtheria, experiencing an upward trend in cases from 2021 to 2023. To analyze the situation, we developed an SIR model, which integrated DPT and booster vaccinations to determine the basic reproduction number, an essential parameter for infectious diseases. Through spatial analysis of geo-referenced data, we identified hotspots and explained diffusion in diphtheria case clusters. The calculation of R0 resulted in an R0 = 1.17, indicating the potential for a diphtheria outbreak in West Java. To control the increasing cases, one possible approach is to raise the booster vaccination coverage from the current 64.84% to 75.15%, as suggested by simulation results. Furthermore, the spatial analysis revealed that hot spot clusters were present in the western, central, and southern regions, posing a high risk not only in densely populated areas but also in rural regions. The diffusion pattern of diphtheria clusters displayed an expansion-contagious pattern. Understanding the rising trend of diphtheria cases and their geographic distribution can offer crucial insights for government and health authorities to manage the number of diphtheria cases and make informed decisions regarding the best prevention and intervention strategies.

Analysis of the transplacental transmission of SARS CoV-2 virus and antibody transfer according to the gestational age at maternal infection.

To quantify transplacental transmission of SARS-CoV-2 virus and antibody transfer in pregnant women and their newborns according to the gestational age at maternal infection. A prospective observational multicenter study including pregnant women with a positive RT-PCR or a positive serology for SARS-CoV-2 and compatible symptoms, from April to December 2020, in 11 French maternities. The study was designed to obtain a systematic collection of mother-infant dyad's samples at birth. SARS-CoV-2 viral load was measured by RT-PCR. IgG and IgM antibodies against the SARS-CoV-2 spike protein were measured by enzyme-linked immunosorbent assay. Antibody concentrations and transplacental transfer ratios were analyzed according to the gestational age at maternal infection. The primary outcome was the rate of SARS CoV-2 materno-fetal transmission at birth. The secondary outcome was the quantification of materno-fetal antibody transfer. Maternal and neonatal outcomes at birth were additionally assessed. Among 165 dyads enrolled, one congenital infection was confirmed {n = 1 (0.63%) IC95% [0.02%; 3.48%]}. The average placental IgG antibody transfer ratio was 1.27 (IC 95% [0.69-2.89]). The transfer ratio increased with increasing time between the onset of maternal infection and delivery (P Value = 0.0001). Maternal and neonatal outcomes were reassuring. We confirmed the very low rate of SARS-CoV-2 transplacental transmission (< 1%). Maternal antibody transfer to the fetus was more efficient when the infection occurred during the first and second trimester of pregnancy.

Public holidays increased the transmission of COVID-19 in Japan, 2020-2021: a mathematical modelling study.

OBJECTIVES: Although the role of specific holidays in modifying transmission dynamics of infectious diseases has received some research attention, the epidemiological impact of public holidays on the transmission of coronavirus disease 2019 (COVID-19) remains unclear. METHODS: To assess the extent of increased transmission frequency during public holidays, we collected COVID-19 incidence and mobility data in Hokkaido, Tokyo, Aichi, and Osaka from February 15, 2020 to September 30, 2021. Models linking the estimated effective reproduction number (Rt) with raw or adjusted mobility, public holidays, and the state of emergency declaration were developed. The best-fit model included public holidays as an essential input variable, and was used to calculate counterfactuals of Rt in the absence of holidays. RESULTS: During public holidays, on average, Rt increased by 5.71%, 3.19%, 4.84%, and 24.82% in Hokkaido, Tokyo, Aichi, and Osaka, respectively, resulting in a total increase of 580 (95% confidence interval [CI], 213 to 954), 2,209 (95% CI, 1,230 to 3,201), 1,086 (95% CI, 478 to 1,686), and 5,211 (95% CI, 4,554 to 5,867) cases that were attributable to the impact of public holidays. CONCLUSIONS: Public holidays intensified the transmission of COVID-19, highlighting the importance of considering public holidays in designing appropriate public health and social measures in the future.

Incidence and transmission associated with respiratory viruses in an acute care facility: An observational study.

We estimated the extent of respiratory virus transmission over three pre-COVID-19 seasons. Of 16,273 assays, 22.9% (3,726) detected ≥1 respiratory virus. The frequency of putatively hospital-acquired infection ranged from 6.9% (influenza A/B) to 24.7% (adenovirus). The 176 clusters were most commonly associated with rhinovirus/enterovirus (70) and influenza A/B (62).

Efficacy of facemasks in preventing transmission of COVID-19 in non-healthcare settings: A scoping review.

Background: During the COVID-19 pandemic, an abundance of literature relating to the efficacy of face masks on reducing transmission of COVID-19 in non-healthcare settings emerged. Aim/objective: The aim of this scoping review was to allow the identification of: types of evidence conducted in this area; knowledge gaps and common concepts relating to mask efficacy in non-healthcare settings. Methods: A comprehensive literature search was conducted in PubMed, CINAHL, MEDLINE, Embase and the Irish Management Institute bibliographic database on December 15th, 2021. All types of face masks were included. Of 722 records, 16 were included after full text screening. Findings/results: Themes from an adapted model of Howard et al. framework were used to group results and identify common concepts. The grouped thematic results were then applied to the socio-ecological model. This illustrated the multifactorial elements determining the efficacy of masks themselves while also illustrating how other factors such as individual behaviours, social interactions, settings and national policy can influence the degree of the protective effect. Discussion: The findings from this scoping review indicate that an abundance of experimental literature is available indicating that masks are effective at preventing COVID-19 transmission but their degree of efficacy is impacted by external factors. This review highlights that the quality of the evidence available is low.

Mechanisms of SARS-CoV-2 Placental Transmission.

The widespread occurrence of SARS-CoV-2 infections and the diverse range of symptoms have placed significant strain on healthcare systems worldwide. Pregnancy has also been affected by COVID-19, with an increased risk of complications and unfavorable outcomes for expectant mothers. Multiple studies indicate that SARS-CoV-2 can infiltrate the placenta, breach its protective barrier, and infect the fetus. Although the precise mechanisms of intrauterine transmission remain unclear, factors such as perinatal infection, macrophages, sexual intercourse, and the virus' interaction with host angiotensin-converting enzyme 2 (ACE2) and neuropilin-1 (NRP-1) proteins appear to play a role in this process. The integrity of the placental barrier fluctuates throughout pregnancy and appears to influence the likelihood of fetal transmission. The expression of placental cell receptors, like ACE2, changes during pregnancy and in response to placental damage. However, due to the consistent presence of others, such as NRP-1, SARS-CoV-2 may potentially enter the fetus at different stages of pregnancy. NRP-1 is also found in macrophages, implicating maternal macrophages and Hofbauer cells as potential routes for viral transmission. Our current understanding of SARS-CoV-2's vertical transmission pathways remains limited. Some researchers question the ACE2-associated transmission model due to the relatively low expression of ACE2 in the placenta. Existing studies investigating perinatal transmission and the impact of sexual intercourse have either involved small sample sizes or lacked statistical significance. This review aims to explore the current state of knowledge regarding the potential mechanisms of COVID-19 vertical transmission, identifying areas where further research is needed to fill the gaps in our understanding.

Significance of weather condition, human mobility, and vaccination on global COVID-19 transmission.

The transmission growth rate of infectious diseases, particularly COVID-19, has forced governments to take immediate control decisions. Previous studies have shown that human mobility, weather condition, and vaccination are potential factors influencing virus transmission. This study investigates the contribution of weather conditions, namely temperature and precipitation, human mobility, and vaccination to coronavirus transmission. Three machine learning models: random forest (RF), XGBoost, and neural networks, are applied to predict the confirmed cases based on three aforementioned variables. All models' prediction are evaluated via spatial and temporal analysis. The spatial analysis observes the model performance over countries on certain times. The temporal analysis looks at the model prediction of each country during the specified period. The models' prediction results effectively indicate the transmission trend. The RF model performs best with a coefficient of determination of up to 89%. Meanwhile, all models confirm that vaccination is most significantly associated with COVID-19 cases.

Assessing the effects of SARS-CoV-2 vaccination on the risk of household transmission during delta variant circulation: a population-based data linkage cohort study.

Background: Data on SARS-CoV-2 vaccine effectiveness to reduce transmission of infection in household settings are limited. We examined the effects of SARS-CoV-2 vaccines on Delta variant transmission within households in an infection-naïve population. Methods: This was a population-based data linkage cohort study in the Greater Sydney Metropolitan Area, New South Wales, Australia based on cases observed in June-November 2021. In households with ≥1 confirmed COVID-19 case, we calculated adjusted odds ratios (aOR) and 95% Confidence Intervals (95% CI) for the risk of SARS-CoV-2 transmission, by vaccination status (unvaccinated, partially vaccinated, fully vaccinated, or waning) and type of vaccines (mRNA or vector-based) received by both index cases and household contacts. Findings: In 20,651 households with a single index case, 18,542 of 72,768 (25%) household contacts tested PCR-positive ≤14 days after their respective index case. Household contacts with partial, full, or waning mRNA vaccination had aORs of 0.46 (95% CI 0.40-0.52), 0.36 (95% CI 0.32-0.41) and 0.64 (95% CI 0.51-0.80) compared to unvaccinated contacts, while for vector vaccines the corresponding aORs were 0.77 (95% CI 0.67-0.89), 0.65 (95% CI 0.55-0.76), and 0.64 (95% CI 0.39-1.05). Full mRNA-vaccination in index cases compared to non-vaccination was associated with aORs between 0.09 and 0.21 depending on the vaccination status of household contacts. Interpretation: Full vaccination of household contacts reduced the odds to acquire infection with the SARS-CoV-2 Delta variant in household settings by two thirds for mRNA vaccines and by one third for vector vaccines. For index cases, being fully vaccinated with an mRNA vaccine reduced the odds of onwards transmission by four-fifths compared to unvaccinated index cases. Full vaccination offered stronger protection than partial vaccination, particularly for mRNA vaccines, but with reduced effects when the last vaccination preceded exposure by ≥3 months. Funding: New South Wales Ministry of Health.

Risk of transmission of SARS-CoV-2 on international flights, a retrospective cohort study using national surveillance data in England.

BACKGROUND: It is not yet fully understood to what extent in-flight transmission contributed to the spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). This study aimed to determine the occurrence and extent of SARS-CoV-2 transmission in-flight and assess factors associated with transmission risk to inform future control strategies. METHODS: Retrospective cohort study using data obtained from contact tracing of international flights arriving in England between 02/08/2021-15/10/2021. Transmission risk was estimated by calculating the secondary attack rate (SAR). Univariable and multivariable analyses of the SAR by specific risk factors was undertaken, including: number of in-flight index cases; number of symptomatic index cases; contact vaccination status; flight duration; proximity to the index case(s); contact age. RESULTS: 11,307 index cases linked to 667,849 contacts with 5,289 secondary cases reported. In-flight SAR was 0.79% (95% CI: 0.77-0.81). Increasing numbers of symptomatic cases (when > 4 index cases compared to one index case aOR 1.85; 95% CI: 1.40-2.44) and seating proximity to an index case (seated within compared to outside of two rows OR 1.82; 95% CI: 1.50-2.22) were associated with increased risk of secondary cases. Full vaccination history was protective (aOR 0.52; 95% CI: 0.47-0.57). CONCLUSIONS: This study confirms that in-flight transmission of SARS-CoV-2 occurred. There are factors associated with increased risk of infection. Contact tracing identified exposed persons who subsequently developed infection. A targeted approach to contact tracing passengers with the highest exposure risk could be an effective use of limited public health resources.

Germicidal efficacy of continuous and pulsed ultraviolet-C radiation on pathogen models and SARS-CoV-2.

Ultraviolet radiation's germicidal efficacy depends on several parameters, including wavelength, radiant exposure, microbial physiology, biological matrices, and surfaces. In this work, several ultraviolet radiation sources (a low-pressure mercury lamp, a KrCl excimer, and four UV LEDs) emitting continuous or pulsed irradiation were compared. The greatest log reductions in E. coli cells and B. subtilis endospores were 4.1 ± 0.2 (18 mJ cm-2) and 4.5 ± 0.1 (42 mJ cm-2) with continuous 222 nm, respectively. The highest MS2 log reduction observed was 2.7 ± 0.1 (277 nm at 3809 mJ cm-2). Log reductions of SARS-CoV-2 with continuous 222 nm and 277 nm were ≥ 3.4 ± 0.7, with 13.3 mJ cm-2 and 60 mJ cm-2, respectively. There was no statistical difference between continuous and pulsed irradiation (0.83-16.7% [222 nm and 277 nm] or 0.83-20% [280 nm] duty rates) on E. coli inactivation. Pulsed 260 nm radiation (0.5% duty rate) at 260 nm yielded significantly greater log reduction for both bacteria than continuous 260 nm radiation. There was no statistical difference in SARS-CoV-2 inactivation between continuous and pulsed 222 nm UV-C radiation and pulsed 277 nm radiation demonstrated greater germicidal efficacy than continuous 277 nm radiation. Greater radiant exposure for all radiation sources was required to inactivate MS2 bacteriophage. Findings demonstrate that pulsed irradiation could be more useful than continuous UV radiation in human-occupied spaces, but threshold limit values should be respected. Pathogen-specific sensitivities, experimental setup, and quantification methods for determining germicidal efficacy remain important factors when optimizing ultraviolet radiation for surface decontamination or other applications.

The impact of changes in opioid dependency treatment upon COVID-19 transmission in Sydney, Australia: a retrospective longitudinal observational study.

BACKGROUND: In April 2020, in response to the COVID-19 public health emergency, South Eastern Sydney Local Health District (SESLHD) Drug and Alcohol services modified their delivery of opioid dependency treatment (ODT) to reduce spread of COVID-19 and maintain continuity of care by increasing use of takeaway doses (TADs), transferring clients to local community pharmacies for dosing and encouraging the use of long-acting depot buprenorphine (LADB) which enabled once a month dosing. METHODS: This study was a retrospective longitudinal case-control study conducted from August 1st, to November 30th, 2021. Eligible clients were those admitted for treatment with SESLHD ODT Services prior to August 1st,2021 and who remained in treatment beyond November 30th, 2021. COVID-19 diagnoses were determined by a COVID-19 PCR and extracted from the electronic Medical Records (eMR) Discern Reporting Portal. Demographic, clinical and dosing related data were collected from eMR and the Australian Immunisation Register (AIR). RESULTS: Clients attending SESLHD ODT services had significantly greater odds of acquiring COVID-19 than the NSW adult population at large (OR: 13.63, 95%CI: 9.64,18.88). Additionally, amongst SESLHD ODT clients, being of Aboriginal and Torres Strait Islander origin was associated with greater odds of acquiring COVID-19 (OR = 2.18, CI: 1.05,4.53); whilst being employed (OR = 0.06, CI:0.01,0.46), receiving doses at pharmacy (OR = 0.43, CI: 0.21,0.89), and being vaccinated (OR = 0.12, CI: 0.06,0.26) were associated with lower odds. Every additional day of attendance required for dosing was associated with a 5% increase in odds of acquiring COVID-19 (OR = 1.05, CI: 1.02,1.08). CONCLUSIONS: Clients attending SESLHD ODT services are significantly more likely to acquire COVID-19 than the NSW population at large. Promoting vaccination uptake, transferring clients to pharmacy, and reducing the frequency of dosing (by use of takeaway doses or long-acting depot buprenorphine) are all potential methods to reduce this risk.

Age-specific transmission dynamics of SARS-CoV-2 during the first 2 years of the pandemic.

During its first 2 years, the SARS-CoV-2 pandemic manifested as multiple waves shaped by complex interactions between variants of concern, non-pharmaceutical interventions, and the immunological landscape of the population. Understanding how the age-specific epidemiology of SARS-CoV-2 has evolved throughout the pandemic is crucial for informing policy decisions. In this article, we aimed to develop an inference-based modeling approach to reconstruct the burden of true infections and hospital admissions in children, adolescents, and adults over the seven waves of four variants (wild-type, Alpha, Delta, and Omicron BA.1) during the first 2 years of the pandemic, using the Netherlands as the motivating example. We find that reported cases are a considerable underestimate and a generally poor predictor of true infection burden, especially because case reporting differs by age. The contribution of children and adolescents to total infection and hospitalization burden increased with successive variants and was largest during the Omicron BA.1 period. However, the ratio of hospitalizations to infections decreased with each subsequent variant in all age categories. Before the Delta period, almost all infections were primary infections occurring in naive individuals. During the Delta and Omicron BA.1 periods, primary infections were common in children but relatively rare in adults who experienced either reinfections or breakthrough infections. Our approach can be used to understand age-specific epidemiology through successive waves in other countries where random community surveys uncovering true SARS-CoV-2 dynamics are absent but basic surveillance and statistics data are available.

Transmission potential of mpox in mainland China, June-July 2023: estimating reproduction number during the initial phase of the epidemic.

Despite reporting very few mpox cases in early 2023, mainland China observed a surge of over 500 cases during the summer. Amid ambiguous prevention strategies and stigma surrounding mpox transmission, the epidemic silently escalated. This study aims to quantify the scale of the mpox epidemic and assess the transmission dynamics of the virus by estimating the effective reproduction number (Re) during its early phase. Publicly available data were aggregated to obtain daily mpox case counts in mainland China, and the Re value was estimated using an exponential growth model. The mean Re value was found to be 1.57 (95% credible interval [1.38-1.78]), suggesting a case doubling time of approximately 2 weeks. This estimate was compared with Re values from 16 other countries' national outbreaks in 2022 that had cumulative case count exceeding 700 symptomatic cases by the end of that year. The Re estimates for these outbreaks ranged from 1.13 for Portugal to 2.31 for Colombia. The pooled mean Re was 1.49 (95% credible interval [1.32-1.67]), which aligns closely with the Re for mainland China. These findings underscore the need for immediate and effective control measures including targeted vaccination campaigns to mitigate the further spread and impact of the epidemic.

A tale of lockdown policies on the transmission of COVID-19 within and between Chinese cities: A study based on heterogeneous treatment effect.

During the early outbreak phase of COVID-19 in China, lockdowns prevailed as the only available policy tools to mitigate the spread of infection. To evaluate the impact of lockdown policies in the context of the first phase of COVID-19 pandemic, we leverage data on daily confirmed cases per million people and related characteristics of a large set of cities. The study analyzed 369 Chinese cities, among which 188 implemented lockdowns of varying severity levels from January 23 to March 31, 2020. We use nationwide Baidu Mobility data to estimate the impact of lockdown policies on mitigating COVID-19 cases through reducing human mobility. We adopt a heterogeneous treatment effect model to quantify the effect of lockdown policies on containing confirmed case counts. Our results suggest that lockdowns substantially reduced human mobility, and larger reduction in mobility occurred within-city compared to between-city. The COVID-19 daily confirmed cases per million people decreased by 9% - 9.2% for every ten-percentage point fall in within-city travel intensity in t+7 timeframe. We also find that one city's lockdowns can effectively reduce the spillover cases of the traveler's destination cities. We find no evidence that stricter lockdowns are more effective at mitigating COVID-19 risks. Our findings provide practical insights about the effectiveness of NPI during the early outbreak phase of the unprecedented pandemic.

Ontology-based taxonomical analysis of experimentally verified natural and laboratory human coronavirus hosts and its implication for COVID-19 virus origination and transmission.

To fully understand COVID-19, it is critical to study all possible hosts of SARS-CoV-2 (the pathogen of COVID-19). In this work, we collected, annotated, and performed ontology-based taxonomical analysis of all the reported and verified hosts for all human coronaviruses including SARS-CoV, MERS-CoV, SARS-CoV-2, HCoV-229E, HCoV-NL63, HCoV-OC43, and HCoV-HKU1. A total of 37 natural hosts and 19 laboratory animal hosts of human coronaviruses were identified based on experimental evidence. Our analysis found that all the verified susceptible natural and laboratory animals belong to therian mammals. Specifically, these 37 natural therian hosts include one wildlife marsupial mammal (i.e., Virginia opossum) and 36 Eutheria mammals (a.k.a. placental mammals). The 19 laboratory animal hosts are also classified as therian mammals. The mouse models with genetically modified human ACE2 or DPP4 were more susceptible to virulent human coronaviruses with clear symptoms, suggesting the critical role of ACE2 and DPP4 to coronavirus virulence. Coronaviruses became more virulent and adaptive in the mouse hosts after a series of viral passages in the mice, providing clue to the possible coronavirus origination. The Huanan Seafood Wholesale Market animals identified early in the COVID-19 outbreak were also systematically analyzed as possible COVID-19 hosts. To support knowledge standardization and query, the annotated host knowledge was modeled and represented in the Coronavirus Infectious Disease Ontology (CIDO). Based on our and others' findings, we further propose a MOVIE model (i.e., Multiple-Organism viral Variations and Immune Evasion) to address how viral variations in therian animal hosts and the host immune evasion might have led to dynamic COVID-19 pandemic outcomes.

SARS-CoV-2 Delta and Omicron community transmission networks as added value to contact tracing.

OBJECTIVES: Calculations of SARS-CoV-2 transmission networks at a population level have been limited. Networks that estimate infections between individuals and whether this results in a mutation, can be a way to evaluate fitness of a mutational clone by how much it expands in number as well as determining the likelihood a transmission results in a new variant. METHODS: Australian Delta and Omicron SARS-CoV-2 sequences were downloaded from GISAID. Transmission networks of infection between individuals were estimated using a novel mathematical method. RESULTS: Many of the sequences were identical, with clone sizes following power law distributions driven by negative binomial probability distributions for both the number of infections per individual and the number of mutations per transmission (median 0.74 nucleotide changes for Delta and 0.71 for Omicron). Using these distributions, an agent-based model was able to replicate the observed clonal network structure, providing a basis for more detailed COVID-19 modelling. Possible recombination events, tracked by insertion/deletion (indel) patterns, were identified for each variant in these outbreaks. CONCLUSIONS: This modelling approach reveals key transmission characteristics of SARS-CoV-2 and may complement traditional contact tracing. This methodology can also be applied to other diseases as genetic sequencing of viruses becomes more commonplace.

Environmental microbiome in the home and daycare settings during the COVID-19 pandemic, and potential risk of non-communicable disease in children.

An exposure to diverse microbial population early in life is important for the development of immunity against various non-communicable diseases including asthma, childhood leukaemia and other cancers. Social mixing in daycare settings helps with exposure to a variety of microbes. However, social isolation and a high emphasis on workplace hygiene during the COVID pandemic may have affected children's exposure to diverse microbiota. The structure of microbial communities and their role in developing immunity to various diseases are not well understood. In this study, we investigated the structure of microbial communities in daycare and home settings during the pandemic. Interestingly, microbial diversity was relatively higher in dust samples collected from homes, with human-associated taxa being more prevalent compared to those from daycare settings. Environmental microbes were more abundant in dust samples from daycare providers. These results potentially suggest that cleaning practices during the pandemic may have influenced the diversity and microbial abundance of the daycare samples. Several bacterial taxa detected in both the environments are known to induce anti-inflammatory and immunomodulatory responses, conferring protection from various diseases. Therefore, exposure to diverse microbial population in early childhood may play an important role in developing immunity against various non-communicable and infectious diseases.