Households are an important location for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, especially during periods where travel and work was restricted to essential ...services. We aimed to assess the association of close-range contact patterns with SARS-CoV-2 transmission.
We deployed proximity sensors for two weeks to measure face-to-face interactions between household members after SARS-CoV-2 was identified in the household, in South Africa, 2020 - 2021. We calculated duration, frequency and average duration of close range proximity events with SARS-CoV-2 index cases. We assessed the association of contact parameters with SARS-CoV-2 transmission using mixed effects logistic regression accounting for index and household member characteristics.
We included 340 individuals (88 SARS-CoV-2 index cases and 252 household members). On multivariable analysis, factors associated with SARS-CoV-2 acquisition were index cases with minimum C
value <30 (aOR 10.6 95%CI 1.4-80.1) vs >35, and female contacts (aOR 2.4 95%CI 1.2-4.8). No contact parameters were associated with acquisition (aOR 1.0-1.1) for any of the duration, frequency, cumulative time in contact or average duration parameters.
We did not find an association between close-range proximity events and SARS-CoV-2 household transmission. Our findings may be due to study limitations, that droplet-mediated transmission during close-proximity contacts play a smaller role than airborne transmission of SARS-CoV-2 in the household, or due to high contact rates in households.
Wellcome Trust (Grant number 221003/Z/20/Z) in collaboration with the Foreign, Commonwealth and Development Office, United Kingdom.
A resurgence of Hib in the UK between 1999 and 2002 was partly attributed to the use of poorly immunogenic combination vaccines, including an acellular pertussis component with no booster dose.2 In ...their Article in The Lancet Infectious Diseases, Susana Monge and colleagues3 assess the effectiveness of the hexavalent DTPa-HBV-IPV/Hib vaccine in the routine immunisation programme in the Netherlands, to determine whether reduced vaccine effectiveness is contributing to an increase in the incidence of Hib. Before the Hib vaccine became availabile widely, Hib was one of the most common causes of meningitis and pneumonia.4 Hib vaccines were introduced in many high-income countries in the 1990s, but there were delays in their introduction to low-income and middle-income countries.5 Several efforts have aimed to increase global Hib vaccine coverage, including funding of Hib vaccination by Gavi, the Vaccine Alliance, and efforts by the Hib Initiative to generate data to aid evidence-based decisions regarding introduction of the Hib vaccine into routine immunisation programmes. Ian Boddy/Science Photo Library CC and AvG have received grants from the US Centers for Disease Control and Prevention, Gates Foundation, and Sanofi, and non-financial support from Sanofi and Parexel.
Background
Estimates of the disease burden associated with different respiratory viruses are severely limited in low‐ and middle‐income countries, especially in Africa.
Methods
We estimated ...age‐specific numbers and rates of medically and non‐medically attended influenza‐like illness (ILI) and severe respiratory illness (SRI) that were associated with influenza, respiratory syncytial virus (RSV), rhinovirus, human metapneumovirus, adenovirus, enterovirus and parainfluenza virus types 1–3 after adjusting for the attributable fraction (AF) of virus detection to illness in South Africa during 2013–2015. The base rates were estimated from five surveillance sites and extrapolated nationally.
Results
The mean annual rates per 100,000 population were 51,383 and 4196 for ILI and SRI, respectively. Of these, 26% (for ILI) and 46% (for SRI) were medically attended. Among outpatients with ILI, rhinovirus had the highest AF‐adjusted rate (7221), followed by influenza (6443) and adenovirus (1364); whereas, among inpatients with SRI, rhinovirus had the highest AF‐adjusted rate (400), followed by RSV (247) and influenza (130). Rhinovirus (9424) and RSV (2026) had the highest AF‐adjusted rates among children aged <5 years with ILI or SRI, respectively, whereas rhinovirus (757) and influenza (306) had the highest AF‐adjusted rates among individuals aged ≥65 years with ILI or SRI, respectively.
Conclusions
There was a substantial burden of ILI and SRI in South Africa during 2013–2015. Rhinovirus and influenza had a prominent disease burden among patients with ILI. RSV and influenza were the most prominent causes of SRI in children and the elderly, respectively.
ABSTRACT
Background
Identifying children at risk for severe COVID‐19 disease from severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) may guide future mitigation interventions. Using ...sentinel surveillance data, we aimed to identify risk factors for SARS‐CoV‐2–associated hospitalisation among patients aged ≤ 18 years with respiratory illness.
Methods
From April 2020 to March 2022, patients meeting study case definitions were enrolled at four outpatient influenza‐like illness (ILI) and five inpatient severe respiratory infection (SRI) surveillance sites and tested for SARS‐CoV‐2 infection using polymerase chain reaction (PCR). Each ILI clinic shared a catchment area with its corresponding SRI hospital. Potential risk factors for SARS‐CoV‐2–associated hospitalisation were analysed using multivariable logistic regression by comparing inpatient versus outpatient SARS‐CoV‐2 cases.
Results
Of 4688 participants aged ≤ 18 years, 4556 (97%) with complete PCR and HIV data were included in the analysis. Among patients with ILI and SRI, 92/1145 (8%) and 154/3411 (5%) tested SARS‐CoV‐2 positive, respectively. Compared to outpatients, hospitalised SARS‐CoV‐2 cases were associated with age < 6 months (adjusted odds ratio (aOR) 8.0, 95% confidence interval (CI) 2.7–24.0 versus 1–4 years); underlying medical condition other than HIV aOR 5.8, 95% CI 2.3–14.6; laboratory‐confirmed Omicron BA.1/BA.2 or Delta variant (aOR 4.9, 95% CI 1.7–14.2 or aOR 2.8, 95% CI 1.1–7.3 compared to ancestral SARS‐CoV‐2); and respiratory syncytial virus coinfection aOR 6.2, 95% CI 1.0–38.5.
Conclusion
Aligning with previous research, we identified age < 6 months or having an underlying condition as risk factors for SARS‐CoV‐2–associated SRI hospitalisation and demonstrated the potential of sentinel surveillance to monitor COVID‐19 in children.
Background
Economic burden estimates are essential to guide policy‐making for influenza vaccination, especially in resource‐limited settings.
Methods
We estimated the cost, absenteeism, and years of ...life lost (YLL) of medically and non‐medically attended influenza‐associated mild and severe respiratory, circulatory and non‐respiratory/non‐circulatory illness in South Africa during 2013‐2015 using a modified version of the World Health Organization (WHO) worksheet based tool for estimating the economic burden of seasonal influenza. Additionally, we restricted the analysis to influenza‐associated severe acute respiratory illness (SARI) and influenza‐like illness (ILI; subsets of all‐respiratory illnesses) as suggested in the WHO manual.
Results
The estimated mean annual cost of influenza‐associated illness was $270.5 million, of which $111.3 million (41%) were government‐incurred costs, 40.7 million (15%) were out‐of‐pocket expenses, and $118.4 million (44%) were indirect costs. The cost of influenza‐associated medically attended mild illness ($107.9 million) was 2.3 times higher than that of severe illness ($47.1 million). Influenza‐associated respiratory illness costs ($251.4 million) accounted for 93% of the total cost. Estimated absenteeism and YLL were 13.2 million days and 304 867 years, respectively. Among patients with influenza‐associated WHO‐defined ILI or SARI, the costs ($95.3 million), absenteeism (4.5 million days), and YLL (65 697) were 35%, 34%, and 21% of the total economic and health burden of influenza.
Conclusion
The economic burden of influenza‐associated illness was substantial from both a government and a societal perspective. Models that limit estimates to those obtained from patients with WHO‐defined ILI or SARI substantially underestimated the total economic and health burden of influenza‐associated illness.
Purpose
The PHIRST study (Prospective Household cohort study of Influenza, Respiratory Syncytial virus, and other respiratory pathogens community burden and Transmission dynamics in South Africa) ...aimed to estimate the community burden of influenza and respiratory syncytial virus (RSV) including the incidence of infection, symptomatic fraction, and to assess household transmission.
Participants
We enrolled 1684 individuals in 327 randomly selected households in a rural and an urban site over three consecutive influenza and two RSV seasons. A new cohort of households was enrolled each year. Participants were sampled with nasopharyngeal swabs twice‐weekly during the RSV and influenza seasons of the year of enrolment. Serology samples were collected at enrolment and before and after the influenza season annually.
Findings to Date
There were 122 113 potential individual follow‐up visits over the 3 years, and participants were interviewed for 105 783 (87%) of these. Out of 105 683 nasopharyngeal swabs, 1258 (1%) and 1026 (1%) tested positive on polymerase chain reaction (PCR) for influenza viruses and RSV, respectively. Over one third of individuals had PCR‐confirmed influenza each year. Overall, there was influenza transmission to 10% of household contacts of an index case.
Future Plans
Future planned analyses include analysis of influenza serology results and RSV burden and transmission. Households enrolled in the PHIRST study during 2016–2018 were eligible for inclusion in a study of SARS‐CoV‐2 transmission initiated in July 2020. This study uses similar testing frequency to assess the community burden of SARS‐CoV‐2 infection and the role of asymptomatic infection in virus transmission.
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.
Data on neonatal group B streptococcal (GBS) invasive disease burden are needed to refine prevention policies. Differences in surveillance methods and investigating for cases can lead to varying ...disease burden estimates. We compared the findings of laboratory-based passive surveillance for GBS disease across South Africa, and for one of the provinces compared this to a real-time, systematic, clinical surveillance in a population-defined region in Johannesburg, Soweto. Passive surveillance identified a total of 799 early-onset disease (EOD, <7 days age) and 818 LOD (late onset disease, 7-89 days age) cases nationwide. The passive surveillance provincial incidence varied for EOD (range 0.00 to 1.23/1000 live births), and was 0.03 to 1.04/1000 live births for LOD. The passive surveillance rates for Soweto, were not significantly different compared to those from the systematic surveillance (EOD 1.23 95%CI 1.06-1.43 vs. 1.50 95%CI 1.30-1.71, respectively, rate ratio 0.82 95%CI 0.67-1.01; LOD 1.04 95% CI 0.90-1.23 vs. 1.22 95%CI 1.05-1.42, rate ratio 0.85 95% CI 0.68-1.07). A review of the few cases missed in the passive system in Soweto, suggested that missing key identifiers, such as date of birth, resulted in their omission during the electronic data extraction process. Our analysis suggests that passive surveillance provides a modestly lower estimate of invasive GBS rates compared to real time sentinel-site systematic surveillance, however, this is unlikely to be the reason for the provincial variability in incidence of invasive GBS disease in South Africa. This, possibly reflects that invasive GBS disease goes undiagnosed due to issues related to access to healthcare, poor laboratory capacity and varying diagnostic procedures or empiric antibiotic treatment of neonates with suspected sepsis in the absence of attempting to making a microbiological diagnosis. An efficacious GBS vaccine for pregnant women, when available, could be used as a probe to better quantify the burden of invasive GBS disease in low-middle resourced settings such as ours. From our study passive systems are important to monitor trends over time as long as they are interpreted with caution; active systems give better detailed information and will have greater representivity when expanded to other surveillance sites.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections may be underestimated because of limited access to testing. We measured SARS-CoV-2 seroprevalence in South Africa every 2 ...months during July 2020–March 2021 in randomly selected household cohorts in 2 communities. We compared seroprevalence to reported laboratory-confirmed infections, hospitalizations, and deaths to calculate infection–case, infection–hospitalization, and infection–fatality ratios in 2 waves of infection. Post–second wave seroprevalence ranged from 18% in the rural community children <5 years of age, to 59% in urban community adults 35–59 years of age. The second wave saw a shift in age distribution of case-patients in the urban community (from persons 35–59 years of age to persons at the extremes of age), higher attack rates in the rural community, and a higher infection–fatality ratio in the urban community. Approximately 95% of SARS-CoV-2 infections were not reported to national surveillance.
Epidemiological studies of the naturally transformable bacterial pathogen Streptococcus pneumoniae have previously been confounded by high rates of recombination. Sequencing 240 isolates of the PMEN1 ...(Spain²³F-1) multidrug-resistant lineage enabled base substitutions to be distinguished from polymorphisms arising through horizontal sequence transfer. More than 700 recombinations were detected, with genes encoding major antigens frequently affected. Among these were 10 capsule-switching events, one of which accompanied a population shift as vaccine-escape serotype 19A isolates emerged in the USA after the introduction of the conjugate polysaccharide vaccine. The evolution of resistance to fluoroquinolones, rifampicin, and macrolides was observed to occur on multiple occasions. This study details how genomic plasticity within lineages of recombinogenic bacteria can permit adaptation to clinical interventions over remarkably short time scales.
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