By August, 2021, South Africa had been affected by three waves of SARS-CoV-2; the second associated with the beta variant and the third with the delta variant. Data on SARS-CoV-2 burden, ...transmission, and asymptomatic infections from Africa are scarce. We aimed to evaluate SARS-CoV-2 burden and transmission in one rural and one urban community in South Africa.
We conducted a prospective cohort study of households in Agincourt, Mpumalanga province (rural site) and Klerksdorp, North West province (urban site) from July, 2020 to August, 2021. We randomly selected households for the rural site from a health and sociodemographic surveillance system and for the urban site using GPS coordinates. Households with more than two members and where at least 75% of members consented to participate were eligible. Midturbinate nasal swabs were collected twice a week from household members irrespective of symptoms and tested for SARS-CoV-2 using real-time RT-PCR (RT-rtPCR). Serum was collected every 2 months and tested for anti-SARS-CoV-2 antibodies. Main outcomes were the cumulative incidence of SARS-CoV-2 infection, frequency of reinfection, symptomatic fraction (percent of infected individuals with ≥1 symptom), the duration of viral RNA shedding (number of days of SARS-CoV-2 RT-rtPCR positivity), and the household cumulative infection risk (HCIR; number of infected household contacts divided by the number of susceptible household members).
222 households (114 at the rural site and 108 at the urban site), and 1200 household members (643 at the rural site and 557 at the urban site) were included in the analysis. For 115 759 nasal specimens from 1200 household members (follow-up 92·5%), 1976 (1·7%) were SARS-CoV-2-positive on RT-rtPCR. By RT-rtPCR and serology combined, 749 of 1200 individuals (62·4% 95% CI 58·1–66·4) had at least one SARS-CoV-2 infection episode, and 87 of 749 (11·6% 9·4–14·2) were reinfected. The mean infection episode duration was 11·6 days (SD 9·0; range 4–137). Of 662 RT-rtPCR-confirmed episodes (>14 days after the start of follow-up) with available data, 97 (14·7% 11·9–17·9) were symptomatic with at least one symptom (in individuals aged <19 years, 28 7·5% of 373 episodes symptomatic; in individuals aged ≥19 years, 69 23·9% of 289 episodes symptomatic). Among 222 households, 200 (90·1% 85·3–93·7) had at least one SARS-CoV-2-positive individual on RT-rtPCR or serology. HCIR overall was 23·9% (195 of 817 susceptible household members infected 95% CI 19·8–28·4). HCIR was 23·3% (20 of 86) for symptomatic index cases and 23·9% (175 of 731) for asymptomatic index cases (univariate odds ratio OR 1·0 95% CI 0·5–2·0). On multivariable analysis, accounting for age and sex, low minimum cycle threshold value (≤30 vs >30) of the index case (OR 5·3 2·3–12·4) and beta and delta variant infection (vs Wuhan-Hu-1, OR 3·3 1·4–8·2 and 10·4 4·1–26·7, respectively) were associated with increased HCIR. People living with HIV who were not virally supressed (≥400 viral load copies per mL) were more likely to develop symptomatic illness when infected with SAR-CoV-2 (OR 3·3 1·3–8·4), and shed SARS-CoV-2 for longer (hazard ratio 0·4 95% CI 0·3–0·6) compared with HIV-uninfected individuals.
In this study, 565 (85·3%) SARS-CoV-2 infections were asymptomatic and index case symptom status did not affect HCIR, suggesting a limited role for control measures targeting symptomatic individuals. Increased household transmission of beta and delta variants was likely to have contributed to successive waves of SARS-CoV-2 infection, with more than 60% of individuals infected by the end of follow-up.
US CDC, South Africa National Institute for Communicable Diseases, and Wellcome Trust.
Summary Background 18 500 laboratory-confirmed deaths caused by the 2009 pandemic influenza A H1N1 were reported worldwide for the period April, 2009, to August, 2010. This number is likely to be ...only a fraction of the true number of the deaths associated with 2009 pandemic influenza A H1N1. We aimed to estimate the global number of deaths during the first 12 months of virus circulation in each country. Methods We calculated crude respiratory mortality rates associated with the 2009 pandemic influenza A H1N1 strain by age (0–17 years, 18–64 years, and >64 years) using the cumulative (12 months) virus-associated symptomatic attack rates from 12 countries and symptomatic case fatality ratios (sCFR) from five high-income countries. To adjust crude mortality rates for differences between countries in risk of death from influenza, we developed a respiratory mortality multiplier equal to the ratio of the median lower respiratory tract infection mortality rate in each WHO region mortality stratum to the median in countries with very low mortality. We calculated cardiovascular disease mortality rates associated with 2009 pandemic influenza A H1N1 infection with the ratio of excess deaths from cardiovascular and respiratory diseases during the pandemic in five countries and multiplied these values by the crude respiratory disease mortality rate associated with the virus. Respiratory and cardiovascular mortality rates associated with 2009 pandemic influenza A H1N1 were multiplied by age to calculate the number of associated deaths. Findings We estimate that globally there were 201 200 respiratory deaths (range 105 700–395 600) with an additional 83 300 cardiovascular deaths (46 000–179 900) associated with 2009 pandemic influenza A H1N1. 80% of the respiratory and cardiovascular deaths were in people younger than 65 years and 51% occurred in southeast Asia and Africa. Interpretation Our estimate of respiratory and cardiovascular mortality associated with the 2009 pandemic influenza A H1N1 was 15 times higher than reported laboratory-confirmed deaths. Although no estimates of sCFRs were available from Africa and southeast Asia, a disproportionate number of estimated pandemic deaths might have occurred in these regions. Therefore, efforts to prevent influenza need to effectively target these regions in future pandemics. Funding None.
Background
Scant data are available about global patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread and global epidemiology of early confirmed cases of COVID-19 outside ...mainland China. We describe the global spread of SARS-CoV-2 and characteristics of COVID-19 cases and clusters before the characterisation of COVID-19 as a pandemic.
Cases of COVID-19 reported between Dec 31, 2019, and March 10, 2020 (ie, the prepandemic period), were identified daily from official websites, press releases, press conference transcripts, and social media feeds of national ministries of health or other government agencies. Case characteristics, travel history, and exposures to other cases were abstracted. Countries with at least one case were classified as affected. Early cases were defined as those among the first 100 cases reported from each country. Later cases were defined as those after the first 100 cases. We analysed reported travel to affected countries among the first case reported from each country outside mainland China, demographic and exposure characteristics among cases with age or sex information, and cluster frequencies and sizes by transmission settings.
Among the first case reported from each of 99 affected countries outside of mainland China, 75 (76%) had recent travel to affected countries; 60 (61%) had travelled to China, Italy, or Iran. Among 1200 cases with age or sex information, 874 (73%) were early cases. Among 762 early cases with age information, the median age was 51 years (IQR 35–63); 25 (3%) of 762 early cases occurred in children younger than 18 years. Overall, 21 (2%) of 1200 cases were in health-care workers and none were in pregnant women. 101 clusters were identified, of which the most commonly identified transmission setting was households (76 75%; mean 2·6 cases per cluster range 2–7), followed by non-health-care occupational settings (14 14%; mean 4·3 cases per cluster 2–14), and community gatherings (11 11%; mean 14·2 cases per cluster 4–36).
Cases with travel links to China, Italy, or Iran accounted for almost two-thirds of the first reported COVID-19 cases from affected countries. Among cases with age information available, most were among adults aged 18 years and older. Although there were many clusters of household transmission among early cases, clusters in occupational or community settings tended to be larger, supporting a possible role for physical distancing to slow the progression of SARS-CoV-2 spread.
None.
We measured the immunogenicity of seasonal trivalent inactivated influenza vaccines (IIV3) among older Thai adults and the effect of one-year prior vaccination status on immune responses.
Adults aged ...≥65 years (n = 370) were vaccinated with Southern Hemisphere IIV3 in 2015. Hemagglutination inhibition assays were performed using goose red blood cells on sera collected from the participants at baseline and after 1, 6, and 12 months of vaccination. Prior year vaccination (in 2014) was verified with the national health security office database. We analyzed the associations between prior vaccination and geometric mean titers (GMT) at each time point using generalized linear regression on logged transformed titers, and seroprotection and seroconversion using Log-binomial regression.
At baseline, previously vaccinated participants (n = 203) had a significantly higher GMT and seroprotection against all three influenza strains than those previously unvaccinated (n = 167) (all p-values <0.001). Seroprotection rates were similar after one month in both groups for A(H1N1)pdm09 (adjusted risk ratio aRR 1.10, 95% CI 0.97-1.25), and A(H3N2) (aRR 1.08, 95% CI 0.87-1.33), but higher in previously vaccinated persons for B (aRR 1.20, 95% CI 1.08-1.32). At 12 months, 50% or more had seroprotection in previously vaccinated group with no difference between previously vaccinated or unvaccinated persons. Seroconversion was lower in the previously vaccinated group for A(H1N1)pdm09 (aRR 0.62, 95% CI 0.43-0.89), but did not differ between the two groups for A(H3N2) (aRR 0.94, 95% CI 0.69-1.28) and B (aRR 0.85, 95% CI 0.60-1.20).
Influenza vaccination elicited good humoral response in older Thai adults. While seroconversion seemed attenuated in persons previously vaccinated for influenza A(H1N1)pdm09 (the only vaccine strain not to change), this was not apparent for influenza A(H3N2) and B, and prior vaccination was not associated with any inhibition in seroprotection.
On April 15 and April 17, 2009, novel swine-origin influenza A (H1N1) virus (S-OIV) was identified in specimens obtained from two epidemiologically unlinked patients in the United States. The same ...strain of the virus was identified in Mexico, Canada, and elsewhere. We describe 642 confirmed cases of human S-OIV infection identified from the rapidly evolving U.S. outbreak.
Enhanced surveillance was implemented in the United States for human infection with influenza A viruses that could not be subtyped. Specimens were sent to the Centers for Disease Control and Prevention for real-time reverse-transcriptase-polymerase-chain-reaction confirmatory testing for S-OIV.
From April 15 through May 5, a total of 642 confirmed cases of S-OIV infection were identified in 41 states. The ages of patients ranged from 3 months to 81 years; 60% of patients were 18 years of age or younger. Of patients with available data, 18% had recently traveled to Mexico, and 16% were identified from school outbreaks of S-OIV infection. The most common presenting symptoms were fever (94% of patients), cough (92%), and sore throat (66%); 25% of patients had diarrhea, and 25% had vomiting. Of the 399 patients for whom hospitalization status was known, 36 (9%) required hospitalization. Of 22 hospitalized patients with available data, 12 had characteristics that conferred an increased risk of severe seasonal influenza, 11 had pneumonia, 8 required admission to an intensive care unit, 4 had respiratory failure, and 2 died. The S-OIV was determined to have a unique genome composition that had not been identified previously.
A novel swine-origin influenza A virus was identified as the cause of outbreaks of febrile respiratory infection ranging from self-limited to severe illness. It is likely that the number of confirmed cases underestimates the number of cases that have occurred.
Background Seasonal influenza vaccination uptake among young children in Thailand is low despite national recommendation for vaccination. We implemented a knowledge, attitude/perception, and practice ...survey to understand determinants of influenza vaccination in children aged six months to two years. Methods Using a cross-sectional design, we interviewed caregivers of 700 children in seven hospitals using a structured questionnaire to collect information on caregivers' and children's demographic characteristics, and caregivers' knowledge of influenza illness and national vaccine recommendation, attitude/perception toward influenza vaccine, and information sources. We verified children's influenza vaccination status against medical records (vaccinated vs. unvaccinated). Logistic regression was used to examine factors independently associated with children receiving influenza vaccination in the 2018 season using the dataset restricted to only children's parents. Variables associated with vaccination at p-value less than or equal to0.20 were included in subsequent multivariable logistic models. Significant independent determinants of children's influenza vaccination and collinearity of covariates were assessed. The final model was constructed using a stepwise backward elimination approach with variables significant at p-value <0.05 retained in the model. Results During August 2018-February 2019, 700 children's caregivers completed the questionnaire; 61 (9%) were caregivers of vaccinated children. Caregivers of the vaccinated children were statistically more likely to have higher education (61% vs. 38%; p-value<0.01) and to know of influenza illness (93% vs. 76%; p-value = 0.03) than those of the unvaccinated group. Factors associated with children receiving influenza vaccination were identifying healthcare providers as a primary source of information about influenza illness for parents (adjusted odds ratio aOR, 2.8; 95% confidence interval CI, 1.3-6.0), parents' strongly agreeing with the national recommendation for influenza vaccination in young children (aOR, 2.9; 95% CI, 1.5-5.9), using health insurance provided by the government or parent's employer for children's doctor visits (aOR, 2.6; 95% CI, 1.1-6.6), and the children's history of receiving influenza vaccination in the 2017 season or earlier (aOR, 3.2; 95% CI, 1.4-7.8). Conclusion The majority of caregivers of children in this study had knowledge of influenza illness and influenza vaccine. Caregivers reported various sources of information regarding influenza illness and the vaccine, but healthcare providers remained the most trusted source. Children's history of influenza vaccination in prior season(s) was the strongest determinant of children being vaccinated for influenza in the current season.
Acute lower respiratory infections (ALRI) are a leading cause of morbidity and mortality globally, with most ALRI deaths occurring in children in developing countries. Computational models can be ...used to test the efficacy of respiratory infection prevention interventions, but require data on social mixing patterns, which are sparse in developing countries. We describe social mixing patterns among a rural community in northern India. During October 2015-February 2016, trained field workers conducted cross-sectional face-to-face standardized surveys in a convenience sample of 330 households in Faridabad District, Haryana State, India. Respondents were asked about the number, duration, and setting of social interactions during the previous 24 hours. Responses were compared by age and gender. Among the 3083 residents who were approached, 2943 (96%) participated, of whom 51% were male and the median age was 22 years (interquartile range (IQR) 9-37). Respondents reported contact (defined as having had a face-to-face conversation within 3 feet, which may or may not have included physical contact) with a median of 17 (IQR 12-25) people during the preceding 24 hours. Median total contact time per person was 36 person-hours (IQR 26-52). Female older children and adults had significantly fewer contacts than males of similar age (Kruskal-Wallis χ2 = 226.59, p<0.001), but spent a longer duration in contact with young children (Kruskal-Wallis χ2 = 27.26, p<0.001), suggesting a potentially complex pattern of differential risk of infection between genders. After controlling for household size and day of the week, respondent age was significantly associated with number and duration of contacts. These findings can be used to model the impact of interventions to reduce lower respiratory tract infections in India.
For public health research such as vaccine uptake or effectiveness assessments, self-reported coronavirus disease 2019 (COVID-19) vaccination status may be a more efficient measure than verifying ...vaccination status from medical records if agreement between sources is high. We assessed agreement between self-reported and medical record-documented COVID-19 vaccination status among pregnant individuals followed in a cohort during August 2020-October 2021. At end of pregnancy, participants completed questionnaires about COVID-19 vaccine receipt during pregnancy; staff verified vaccination status using medical records. Agreement was assessed between self-reported and medical record vaccination status using Cohen's kappa. There was high agreement between self-reported and medical record vaccination status (Kappa coefficient=0.94, 95% CI 0.91-0.98), suggesting that self-report may be acceptable for ascertaining COVID-19 vaccination status during pregnancy.
Abstract
Background
To date, no study has examined influenza vaccine effectiveness (IVE) against laboratory-confirmed influenza-associated hospitalizations during pregnancy.
Methods
The Pregnancy ...Influenza Vaccine Effectiveness Network (PREVENT) consisted of public health or healthcare systems with integrated laboratory, medical, and vaccination records in Australia, Canada (Alberta and Ontario), Israel, and the United States (California, Oregon, and Washington). Sites identified pregnant women aged 18 through 50 years whose pregnancies overlapped with local influenza seasons from 2010 through 2016. Administrative data were used to identify hospitalizations with acute respiratory or febrile illness (ARFI) and clinician-ordered real-time reverse transcription polymerase chain reaction (rRT-PCR) testing for influenza viruses. Overall IVE was estimated using the test-negative design and adjusting for site, season, season timing, and high-risk medical conditions.
Results
Among 19450 hospitalizations with an ARFI discharge diagnosis (across 25 site-specific study seasons), only 1030 (6%) of the pregnant women were tested for influenza viruses by rRT-PCR. Approximately half of these women had pneumonia or influenza discharge diagnoses (54%). Influenza A or B virus infections were detected in 598/1030 (58%) of the ARFI hospitalizations with influenza testing. Across sites and seasons, 13% of rRT-PCR-confirmed influenza-positive pregnant women were vaccinated compared with 22% of influenza-negative pregnant women; the adjusted overall IVE was 40% (95% confidence interval = 12%–59%) against influenza-associated hospitalization during pregnancy.
Conclusion
Between 2010 and 2016, influenza vaccines offered moderate protection against laboratory-confirmed influenza-associated hospitalizations during pregnancy, which may further inform the benefits of maternal influenza vaccination programs.
In this retrospective study of hospitals in Australia, Canada, Israel, and the United States from 2010 to 2016, influenza vaccines were 40% effective in preventing laboratory-confirmed influenza-associated hospitalizations during pregnancy.
PDF
