Case clustering, contact stratification, and transmission heterogeneity of SARS-CoV-2 Omicron BA.5 variants in Urumqi, China: An observational study.

Background: From August to September 2022, Urumqi, the capital of the Xinjiang Uygur Autonomous Region in China, faced its largest COVID-19 outbreak caused by the emergence of the SARS-CoV-2 Omicron BA.5.2 variants. Although the superspreading of COVID-19 played an important role in triggering large-scale outbreaks, little was known about the superspreading potential and heterogeneity in the transmission of Omicron BA.5 variants. Methods: In this retrospective observational, contact tracing study, we identified 1139 laboratory-confirmed COVID-19 cases of Omicron BA.5.2 variants, and 51 323 test-negative close contacts in Urumqi from 7 August to 7 September 2022. By using detailed contact tracing information and exposure history of linked case-contact pairs, we described stratification in contact and heterogeneity in transmission across different demographic strata, vaccine statuses, and contact settings. We adopted beta-binomial models to characterise the secondary attack rate (SAR) distribution among close contacts and modelled COVID-19 transmission as a branching process with heterogeneity in transmission governed by negative binomial models. Results: After the city lockdown, the mean case cluster size decreased from 2.0 (before lockdown) to 1.6, with decreased proportions of contacts in workplace and community settings compared with household settings. We estimated that 14% of the most infectious index cases generated 80% transmission, whereas transmission in the community setting presented the highest heterogeneity, with 5% index cases seeding 80% transmission. Compared with zero, one, and two doses of inactivated vaccine (Sinopharm), index cases with three doses of vaccine had a lower risk of generating secondary cases in terms of the reproduction number. Contacts of female cases, cases with ages 0-17 years, and household settings had relatively higher SAR. Conclusions: In the context of intensive control measures, active case detection, and relatively high vaccine coverage, but with an infection-naive population, our findings suggested high heterogeneity in the contact and transmission risks of Omicron BA.5 variants across different demographic strata, vaccine statuses, and contact settings. Given the rapid evolution of SARS-CoV-2, investigating the distribution of transmission not only helped promote public awareness and preparedness among high-risk groups, but also highlighted the importance of continuously monitoring the transmission characteristics of genetic variants of SARS-CoV-2.

Transmission Characteristics and Inactivated Vaccine Effectiveness Against Transmission of SARS-CoV-2 Omicron BA.5 Variants in Urumqi, China.

Importance: In 2022, Omicron variants circulated globally, and Urumqi, China, experienced a COVID-19 outbreak seeded by Omicron BA.5 variants, resulting in the highest number of infections in the city's record before the exit of the zero COVID-19 strategy. Little was known about the characteristics of Omicron variants in mainland China. Objective: To evaluate transmission characteristics of Omicron BA.5 variants and the effectiveness of inactivated vaccine (mainly BBIBP-CorV) against their transmission. Design, Setting, and Participants: This cohort study was conducted using data from an Omicron-seeded COVID-19 outbreak in Urumqi from August 7 to September 7, 2022. Participants included all individuals with confirmed SARS-CoV-2 infections and their close contacts identified between August 7 and September 7, 2022 in Urumqi. Exposures: A booster dose was compared vs 2 doses (reference level) of inactivated vaccine and risk factors were evaluated. Main Outcomes and Measures: Demographic characteristics, timeline records from exposure to laboratory testing outcomes, contact tracing history, and contact setting were obtained. The mean and variance of the key time-to-event intervals of transmission were estimated for individuals with known information. Transmission risks and contact patterns were assessed under different disease-control measures and in different contact settings. The effectiveness of inactivated vaccine against the transmission of Omicron BA.5 was estimated using multivariate logistic regression models. Results: Among 1139 individuals diagnosed with COVID-19 (630 females [55.3%]; mean [SD] age, 37.4 [19.9] years) and 51 323 close contacts who tested negative for COVID-19 (26 299 females [51.2%]; mean [SD] age, 38.4 [16.0] years), the means of generation interval, viral shedding period, and incubation period were estimated at 2.8 days (95% credible interval [CrI], 2.4-3.5 days), 6.7 days (95% CrI, 6.4-7.1 days), and 5.7 days (95% CrI, 4.8-6.6 days), respectively. Despite contact tracing, intensive control measures, and high vaccine coverage (980 individuals with infections [86.0%] received ≥2 doses of vaccine), high transmission risks were found in household settings (secondary attack rate, 14.7%; 95% CrI, 13.0%-16.5%) and younger (aged 0-15 years; secondary attack rate, 2.5%; 95% CrI, 1.9%-3.1%) and older age (aged >65 years; secondary attack rate, 2.2%; 95% CrI, 1.5%-3.0%) groups. Vaccine effectiveness against BA.5 variant transmission for the booster-dose vs 2 doses was 28.9% (95% CrI, 7.7%-45.2%) and 48.5% (95% CrI, 23.9%-61.4%) for 15-90 days after booster dose. No protective outcome was detected beyond 90 days after the booster dose. Conclusions and Relevance: This cohort study revealed key transmission characteristics of SARS-CoV-2 as they evolved, as well as vaccine effectiveness against variants. These findings suggest the importance of continuously evaluating vaccine effectiveness against emerging SARS-CoV-2 variants.

Estimation of the serial interval of monkeypox during the early outbreak in 2022.

With increased transmissibility and novel transmission mode, monkeypox poses new threats to public health globally in the background of the ongoing COVID-19 pandemic. Estimates of the serial interval, a key epidemiological parameter of infectious disease transmission, could provide insights into the virus transmission risks. As of October 2022, little was known about the serial interval of monkeypox due to the lack of contact tracing data. In this study, public-available contact tracing data of global monkeypox cases were collected and 21 infector-infectee transmission pairs were identified. We proposed a statistical method applied to real-world observations to estimate the serial interval of the monkeypox. We estimated a mean serial interval of 5.6 days with the right truncation and sampling bias adjusted and calculated the reproduction number of 1.33 for the early monkeypox outbreaks at a global scale. Our findings provided a preliminary understanding of the transmission potentials of the current situation of monkeypox outbreaks. We highlighted the need for continuous surveillance of monkeypox for transmission risk assessment.

Association between temperature variability and global meningitis incidence.

BACKGROUND: Meningitis can cause devastating epidemics and is susceptible to climate change. It is unclear how temperature variability, an indicator of climate change, is associated with meningitis incidence. METHODS: We used global meningitis incidence data along with meteorological and demographic data over 1990-2019 to identify the association between temperature variability and meningitis. We also employed future (2020-2100) climate data to predict meningitis incidence under different emission levels (SSPs: Shared Socioeconomic Pathways). RESULTS: We found that the mean temperature variability increased by almost 3 folds in the past 30 years. The largest changes occurred in Australasia, Tropical Latin America, and Central Sub-Saharan Africa. With a logarithmic unit increase in temperature variability, the overall global meningitis risk increases by 4.8 %. Australasia, Central Sub-Saharan Africa, and High-income North America are the most at-risk regions. Higher statistical differences were identified in males, children, and the elderly population. Compared to high-emission (SSP585) scenario, we predicted a median reduction of 85.8 % in meningitis incidence globally under the low-emission (SSP126) climate change scenario by 2100. CONCLUSION: Our study provides evidence for temperature variability being in association with meningitis incidence, which suggests that global actions are urgently needed to address climate change and to prevent meningitis occurrence.

Analysis of Firearm Violence During the COVID-19 Pandemic in the US.

Importance: In the US, the COVID-19 pandemic intensified some conditions that may contribute to firearm violence, and a recent surge in firearm sales during the pandemic has been reported. However, patterns of change in firearm violence in the first year of the COVID-19 pandemic in the US remain unclear. Objective: To quantify the changes in interpersonal firearm violence associated with the pandemic across all 50 US states and the District of Columbia. Design, Setting, and Participants: This population-based cross-sectional study examined 50 US states and the District of Columbia from January 1, 2016, to February 28, 2021. The COVID-19 pandemic period was defined as between March 1, 2020, and February 28, 2021. Statistical analysis was performed from April to December 2021. Main Outcomes and Measures: A 2-stage interrupted time-series design was used to examine the excess burden of firearm-related incidents, nonfatal injuries, and deaths associated with the pandemic while accounting for long-term trends and seasonality. In the first stage, separate quasi-Poisson regression models were fit to the daily number of firearm events in each state. In the second stage, estimates were pooled using a multivariate meta-analysis. Results: In the US (all 50 states and the District of Columbia) during the pandemic period of March 1, 2020, to February 28, 2021, there were 62 485 identified firearm-related incidents, 40 021 firearm-related nonfatal injuries, and 19 818 firearm-related deaths. The pandemic period was associated with 8138 (95% empirical confidence interval [eCI], 2769-12 948) excess incidents (increase of 15.0% [95% eCI, 4.6%-26.1%]), 10 222 (95% eCI, 8284-11 650) excess nonfatal injuries (increase of 34.3% [95% eCI, 26.1%-41.1%]), and 4381 (95% eCI, 2262-6264) excess deaths (increase of 28.4% [95% eCI, 12.9%-46.2%]). The increase in firearm-related violence was more pronounced from June to October 2020 and in Minnesota and New York State. Conclusions and Relevance: In the US, the first year of the COVID-19 pandemic was associated with an excess burden of firearm-related incidents, nonfatal injuries, and deaths, with substantial temporal and spatial variations.

COVID-19 Transmission Dynamics Among Close Contacts of Index Patients With COVID-19: A Population-Based Cohort Study in Zhejiang Province, China.

Importance: Much remains unknown about the transmission dynamics of COVID-19. How the severity of the index case and timing of exposure is associated with disease in close contacts of index patients with COVID-19 and clinical presentation in those developing disease is not well elucidated. Objectives: To investigate the association between the timing of exposure and development of disease among close contacts of index patients with COVID-19 and to evaluate whether the severity of the index case is associated with clinical presentation in close contacts who develop COVID-19. Design, Setting, and Participants: This study used a large, population-based cohort of 730 individuals (index patients) who received a diagnosis of COVID-19 in Zhejiang Province, China, from January 8 to July 30, 2020, along with a contact tracing surveillance program. Field workers visited 8852 close contacts of the index patients and evaluated them for COVID-19 through August 2020. A timeline was constructed to characterize different exposure periods between index patients and their contacts. Main Outcomes and Measures: The primary outcome was the attack rate of COVID-19, defined as the total number of new COVID-19 cases diagnosed among contacts of index patients divided by the total number of exposed contacts. A secondary outcome was asymptomatic clinical presentation among infected contacts. Relative risks were calculated to investigate risk factors for COVID-19 among contacts and asymptomatic clinical presentation among infected contacts. Results: Among 8852 close contacts (4679 male contacts [52.9%]; median age, 41 years [interquartile range, 28-54 years]) of 730 index patients (374 male patients [51.2%]; median age, 46 years [interquartile range, 36-56 years]), contacts were at highest risk of COVID-19 if they were exposed between 2 days before and 3 days after the index patient's symptom onset, peaking at day 0 (adjusted relative risk [ARR], 1.3; 95% CI, 1.2-1.5). Compared with being exposed to an asymptomatic index patient, the risk of COVID-19 among contacts was higher when they were exposed to index patients with mild (ARR, 4.0; 95% CI, 1.8-9.1) and moderate (ARR, 4.3; 95% CI, 1.9-9.7) cases of COVID-19. As index case severity increased, infected contacts were less likely to be asymptomatic (exposed to patient with mild COVID-19: ARR, 0.3; 95% CI, 0.1-0.9; exposed to patient with moderate COVID-19: ARR, 0.3; 95% CI, 0.1-0.8). Conclusions and Relevance: This cohort study found that individuals with COVID-19 were most infectious a few days before and after symptom onset. Infected contacts of asymptomatic index patients were less likely to present with COVID-19 symptoms, suggesting that quantity of exposure may be associated with clinical presentation in close contacts.

Estimation of case-fatality rate in COVID-19 patients with hypertension and diabetes mellitus in the New York state: a preliminary report.

Pre-existing health conditions may exacerbate the severity of coronavirus disease 2019 (COVID-19). We aimed to estimate the case-fatality rate (CFR) and rate ratios (RR) for patients with hypertension (HBP) and diabetes mellitus (DM) in the New York state. We obtained the age-specific number of COVID-19 confirmed cases and deaths from public reports provided by the New York State Department of Health, and age-specific prevalence of HBP and DM from the Behavioral Risk Factor Surveillance System 2017. We calculated CFR and RR for COVID-19 patients with HBP and DM based on the reported number of deaths with the comorbidity divided by the expected number of COVID-19 cases with the comorbidity. We performed subgroup analysis by age and calculated the CFR and RR for ages of 18-44, 45-64 and 65+ years, respectively. We found that the older population had a higher CFR, but the elevated RRs associated with comorbidities are more pronounced among the younger population. Our findings suggest that besides the elderly, the young population with comorbidity should also be considered as a vulnerable group.

Estimation of Coronavirus Disease Case-Fatality Risk in Real Time.

We ran a simulation comparing 3 methods to calculate case-fatality risk for coronavirus disease using parameters described in previous studies. Case-fatality risk calculated from these methods all are biased at the early stage of the epidemic. When comparing real-time case-fatality risk, the current trajectory of the epidemic should be considered.