Protective Effect of Previous Infection and Vaccination Against Reinfection with BA.5 Omicron Subvariant: A Nation-Wide Population-Based Study in Japan (preprint)

Background: The Omicron variant of SARS-CoV-2 was reported to evade immunity derived from vaccination and previous infection. A better understanding of hybrid immunity informs effective infection control strategies. Since the reinfection risk was not well-assessed in East Asia, this study aims to evaluate the risk of infection with Omicron subvariant BA.5 among previously infected individuals in Japan.Methods: All notified cases were extracted from the Japanese national COVID-19 surveillance database including 20,297,335 records up to 25 September 2022. Reinfection with BA.5 was defined as the second infection notified during the BA.5 dominated period. The protective effect of prior infections against reinfections with BA.5 was estimated by applying a case-population design and the protective effect of vaccination was estimated by a multivariable Cox regression adjusting for age, sex, variants of prior infection, and the time since the last vaccination.Findings: Among 19,830,548 SARS-CoV-2 infections, 233,424 (1·2%) were reinfected with BA.5. The protective effect of prior infection with Wuhan, Alpha, Delta, and BA.1/BA.2 against BA.5 reinfection was 46·2% (45·5–47·0), 35·2% (34·2–36·2), 40·6% (39·9–41·2), and 73·9% (73·4–74·4), respectively. The risk of BA.5 reinfection was reduced by 14%, 41%, and 71% by two, three and four doses of vaccination, respectively, compared with one-dose vaccination.Interpretation: The prior infections with Omicron subvariant BA.1/BA.2 protected BA.5 reinfection more than pre-Omicron variants. Increased frequency of vaccination led to more protection from reinfection with BA.5. Up-to-date vaccination may be encouraged to prevent future reinfection among the previously infected population.Funding: RK received funding from the Japan Society for the Promotion of Science (JSPS) KAKENHI (21K17307). MS and TK received the Ministry of Health Labour and Welfare Science Research Grant (23HA2005).Declaration of Interest: The authors declare that they have no conflict of interest.Ethical Approval: No ethical approval was required because this study was conducted for public health purposes using national surveillance data.

Factors associated with father-infant bonding in the COVID-19 pandemic: An internet-based cross-sectional study in Japan (preprint)

The Covid-19 pandemic has forced changes in our lifestyles and affected the relationships between father and infant. The aim of this study was to explore factors associated with father-infant bonding during the Covid-19 pandemic in Japan. This study was a cross-sectional study using a nationwide online survey data. The Japanese version of the Mother-to-Infant Bonding Scale (MIBS) was used for father-infant bonding. The study participants were divided into two groups depending on their partners’ parity. A linear regression model (Gauss-Markov-type) was used for the two groups. A total of 1,055 men were included in the analysis. Of these men, 521 (49.4%) had a partner who was primipara, and 534 (50.6%) had a partner who was multipara. No significant differences were found between the two groups for MIBS-J scores. The fathers’ mental health, relationship with the partner and family members, abusive behavior towards children, wanted pregnancy, and admission history to NICU for the youngest child were associated with father-infant bonding. As for factors related to Covid-19, caring for the child while the partner is at home has a negative impact on bonding, while fear related to infection with Covid-19 has no negative impact on the bonding.

A prospective evaluation of AI-augmented epidemiology to forecast COVID-19 in the USA and Japan (preprint)

The COVID-19 pandemic has highlighted the global need for reliable models of disease spread. We propose an AI-augmented forecast modeling framework that provides daily predictions of the expected number of confirmed COVID-19 deaths, cases and hospitalizations during the following 4 weeks and we present an international, prospective evaluation of our models' performance across all states and counties in the USA and prefectures in Japan. National mean absolute percentage error (MAPE) for predicting COVID-19 associated deaths before and after prospective deployment remained consistently <2% (US) and <10% (Japan). Average statewide (US) and prefecture wide (Japan) MAPE was 6% and 26% respectively (14% when looking at prefectures with more than 10 deaths). We show that our models perform well even during periods of considerable change in population behavior, and that it is robust to demographic differences across different geographic locations. We further demonstrate that our framework provides meaningful explanatory insights with the models accurately adapting to local and national policy interventions. Our framework enables counterfactual simulations, which indicate continuing Non-Pharmaceutical Interventions alongside vaccinations is essential for faster recovery from the pandemic, delaying the application of interventions has a detrimental effect, and allow exploration of the consequences of different vaccination strategies. The COVID-19 pandemic remains a global emergency. In the face of substantial challenges ahead, the approach presented here has the potential to inform critical decisions.

HIV testing by public health centers and municipalities, and new HIV cases during the COVID-19 pandemic in Japan (preprint)

BackgroundDuring the COVID-19 outbreak, medical resources were primarily allocated to COVID-19, which might have reduced facility capacity for HIV testing. Further, people may have opted against HIV testing during this period to avoid COVID-19 exposure. We investigate the influence of the COVID-19 pandemic on HIV testing and its consequences in Japan. MethodsWe analysed quarterly HIV/AIDS-related data from 2015 to the second quarter of 2020 using an anomaly detection approach. The data included the number of consultations that public health centers received, the number of HIV tests performed by public health centers or municipalities, and the number of newly reported HIV cases with and without AIDS diagnosis. As sensitivity analyses, we performed the same analysis for two subgroups: men who have sex with men (MSM) and non-Japanese. FindingsThe number of HIV tests (9,584 vs. 35,908 in the year-before period) and consultations (11,689 vs. 32,565) performed by public health centers significantly declined in the second quarter of 2020, while the proportion of HIV cases with AIDS diagnosis among all HIV cases (36{middle dot}2% vs. 26{middle dot}4%) significantly increased after removing the trend and seasonality effects. The number of HIV cases without AIDS diagnosis numerically decreased (166 vs. 217), although the reduction was not significant. We confirmed similar trend for the MSM and non-Japanese groups. InterpretationThe current HIV testing system including public health centers misses more HIV cases at the early phase of the infection during the pandemic. Given that the clear epidemiological picture of HIV incidence during the pandemic is still uncertain, continuously monitoring the situation as well as securing sufficient test resources using self-test is essential. FundingJapan Society for the Promotion of Science, Japan Science and Technology Agency, Japan Agency for Medical Research and Development. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSBefore this study, we searched PubMed, Medline, and Google Scholar on Oct 12, 2020, for articles investigated the number of HIV test and HIV cases during the COVID-19 pandemic in Japan, using the search terms "novel coronavirus" or "SARS-CoV-2", and "HIV" or "AIDS", and "Japan", with no time restrictions. We found no published work relevant to our study. Added value of this studyDuring the COVID-19 pandemic in Japan, the public health centers and municipalities temporarily suspended facility-based HIV testing to concentrate their limited resources to COVID-19 testing. We investigated the impact of the COVID-19 pandemic on the number of HIV tests in public health centers and municipalities, and on the number of HIV cases with and without AIDS diagnosis. We confirmed that the number of the test declined in the second quarter (April to June) of 2020, and the proportion of HIV with AIDS diagnosis among all HIV cases increased during the same period. Implications of all the available evidenceProviding sufficient HIV testing opportunities even during the pandemic, when facility-based testing is challenging, is necessary for better clinical and public health outcomes. Self-testing and home specimen collection (e.g. dried blood spot or oral fluid test) could be a key to fill the gap between the need for HIV testing and the constraints related to the COVID-19 outbreak.

Evaluation of China's Hubei Control Strategy for COVID-19 Epidemic: An Observational Study (preprint)

Background: To fight against COVID-19, many policymakers are wavering on stricter public health interventions. However, relying on these measures but different strategies, both in and out of China’s Hubei province basically contained the epidemic in late February 2020. This study aimed to assess the response process and estimate time-varying effect of Hubei control strategy to provide insights for intervention design and implementation.Methods: We retrospectively compared the spread and control of COVID-19 between China’s Hubei (excluding Wuhan) and non-Hubei areas using data that includes case reports, human mobility, and public health interventions from 1 January to 29 February, 2020. The static and dynamic risk assessment models were developed to statistically investigate the effect trends of Hubei control strategy on case growth after adjusting importation risk and response timing with non-Hubei strategy as a contrast.Results: The analysis detected much higher but differential importation risk in Hubei. The response timing largely coincided with the importation risk in non-Hubei areas, but Hubei areas showed an opposite pattern. A careful and comprehensive comparison showed that Hubei control strategy implemented interventions characterized by unprecedentedly strict and ‘monitored’ self-quarantine at home, while non-Hubei strategy included physical distancing measures to reduce contact among individuals within or between populations. In contrast with non-Hubei control strategy, Hubei strategy showed a much higher, non-linear and gradually diminishing protective effect with at least 3 times fewer cases.Conclusions: A risk-based control strategy is crucial to design an effective response for COVID-19 control. Our study demonstrates that the stricter Hubei strategy can achieve much better control effectiveness. These findings highlight the health benefits of precise and differentiated strategies informed by constant monitoring of outbreak risk and policy impacts. 

Estimating the basic reproduction number of COVID-19 in Wuhan, China / 中华流行病学杂志

Objective@#The number of confirmed and suspected cases of the COVID-19 in Hubei province is still increasing. However, the estimations of the basic reproduction number of COVID-19 varied greatly across studies. The objectives of this study are 1) to estimate the basic reproduction number (R0) of COVID-19 reflecting the infectiousness of the virus and 2) to assess the effectiveness of a range of controlling intervention.@*Method@#The reported number of daily confirmed cases from January 17 to February 8, 2020 in Hubei province were collected and used for model fit. Four methods, the exponential growth (EG), maximum likelihood estimation (ML), sequential Bayesian method (SB) and time dependent reproduction numbers (TD), were applied to estimate the R0.@*Result@#Among the four methods, the EG method fitted the data best. The estimated R0 was 3.49 (95% CI: 3.42-3.58) by using EG method. The R0 was estimated to be 2.95 (95%CI: 2.86-3.03) after taking control measures.@*Conclusion@#In the early stage of the epidemic, it is appropriate to estimate R0 using the EG method. Meanwhile, timely and effective control measures were warranted to further reduce the spread of COVID-19.

Estimation of the epidemic properties of the 2019 novel coronavirus: A mathematical modeling study (preprint)

Background The 2019 novel Coronavirus (COVID-19) emerged in Wuhan, China in December 2019 and has been spreading rapidly in China. Decisions about its pandemic threat and the appropriate level of public health response depend heavily on estimates of its basic reproduction number and assessments of interventions conducted in the early stages of the epidemic. Methods We conducted a mathematical modeling study using five independent methods to assess the basic reproduction number (R0) of COVID-19, using data on confirmed cases obtained from the China National Health Commission for the period 10th January to 8th February. We analyzed the data for the period before the closure of Wuhan city (10th January to 23rd January) and the post-closure period (23rd January to 8th February) and for the whole period, to assess both the epidemic risk of the virus and the effectiveness of the closure of Wuhan city on spread of COVID-19. Findings Before the closure of Wuhan city the basic reproduction number of COVID-19 was 4.38 (95% CI: 3.63-5.13), dropping to 3.41 (95% CI: 3.16-3.65) after the closure of Wuhan city. Over the entire epidemic period COVID-19 had a basic reproduction number of 3.39 (95% CI: 3.09-3.70), indicating it has a very high transmissibility. Interpretation COVID-19 is a highly transmissible virus with a very high risk of epidemic outbreak once it emerges in metropolitan areas. The closure of Wuhan city was effective in reducing the severity of the epidemic, but even after closure of the city and the subsequent expansion of that closure to other parts of Hubei the virus remained extremely infectious. Emergency planners in other cities should consider this high infectiousness when considering responses to this virus.