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1.
Open Forum Infect Dis ; 9(12), 2022.
Article in English | PubMed Central | ID: covidwho-2190075

ABSTRACT

Background: Data on risk factors for coronavirus disease 2019 (COVID-19)-associated hospitalization and mortality in high human immunodeficiency virus (HIV) prevalence settings are limited. Methods: Using existing syndromic surveillance programs for influenza-like-illness and severe respiratory illness at sentinel sites in South Africa, we identified factors associated with COVID-19 hospitalization and mortality. Results: From April 2020 through March 2022, severe acute respiratory syndrome coronavirus 2 was detected in 24.0% (660 of 2746) of outpatient and 32.5% (2282 of 7025) of inpatient cases. Factors associated with COVID-19-associated hospitalization included the following: older age (25–44 [adjusted odds ratio {aOR}= 1.8, 95% confidence interval (CI) = 1.1–2.9], 45–64 [aOR = 6.8, 95% CI = 4.2–11.0] and ≥65 years [aOR = 26.6, 95% CI = 14.4–49.1] vs 15–24 years);black race (aOR, 3.3;95% CI, 2.2–5.0);obesity (aOR, 2.3;95% CI, 1.4–3.9);asthma (aOR, 3.5;95% CI, 1.4–8.9);diabetes mellitus (aOR, 5.3;95% CI, 3.1–9.3);HIV with CD4 ≥200/mm3 (aOR, 1.5;95% CI, 1.1–2.2) and CD4 <200/mm3 (aOR, 10.5;95% CI, 5.1–21.6) or tuberculosis (aOR, 12.8;95% CI, 2.8–58.5). Infection with Beta (aOR, 0.5;95% CI, .3–.7) vs Delta variant and being fully vaccinated (aOR, 0.1;95% CI, .1–.3) were less associated with COVID-19 hospitalization. In-hospital mortality was increased in older age (45–64 years [aOR, 2.2;95% CI, 1.6–3.2] and ≥65 years [aOR, 4.0;95% CI, 2.8–5.8] vs 25–44 years) and male sex (aOR, 1.3;95% CI, 1.0–1.6) and was lower in Omicron-infected (aOR, 0.3;95% CI, .2–.6) vs Delta-infected individuals. Conclusions: Active syndromic surveillance encompassing clinical, laboratory, and genomic data identified setting-specific risk factors associated with COVID-19 severity that will inform prioritization of COVID-19 vaccine distribution. Elderly people with tuberculosis or people with HIV, especially severely immunosuppressed, should be prioritized for vaccination.

2.
Open Forum Infectious Diseases ; 9(Supplement 2):S14-S15, 2022.
Article in English | EMBASE | ID: covidwho-2189500

ABSTRACT

Background. Prolonged infection by respiratory viruses has been reported, especially in hospitalized or immunocompromised children. However, little is known of factors contributing to prolonged respiratory viral infection, particularly in asymptomatic and less severe infections. We examined characteristics associated with prolonged viral infection in a community-based birth cohort. Methods. The PREVAIL cohort is a CDC-sponsored two-year birth cohort in Cincinnati, Ohio conducted during 4/2017 to 8/2020. Mid-turbinate nasal swabs were collected weekly from children and tested using the Luminex Respiratory Pathogen Panel. The primary outcome was prolonged viral infection, which was defined as a viral nucleic acid detection lasting 4 or more weeks. Proportions of prolonged viral infections were compared using Fisher's exact test with Holms corrections. Adjusted odds ratios (aOR) and 95% confidence intervals were calculated using a mixed effects logistic regression model while controlling for within-subject clustering, viral species, child age, child sex, symptom status, and coinfection. This analysis was limited to subjects who provided at least 70% of weekly samples. Results. Among 101 children, providing 7871 child-weeks of follow-up, we identified 780 viral infections. The median duration of infection across all respiratory viruses was 1 week, except for bocavirus and coronavirus NL63, each with 2 weeks;40% of bocavirus and >10% of adenovirus, coronavirus NL63, RSV A, human metapneumovirus, and parainfluenza 1 infections were associated with prolonged infection (>4 weeks). No prolonged infections were detected for influenza A or B, coronavirus 229E or HKU1, or parainfluenza 2 or 4 infections. Viral coinfection (aOR=3.1, 95% CI 1.9, 5.0) and female sex (aOR 1.8, 95%CI 1.1, 2.9) were significantly associated with prolonged infection, while symptom status and child age were not. Conclusion. In the PREVAIL cohort, detection of respiratory viruses lasting 4 weeks or longer was common for certain respiratory pathogens and was especially prolonged for bocavirus. Biological factors such as the presence of additional viral infections or child sex may affect the likelihood of prolonged infection. (Figure Presented).

3.
Nature communications ; 14(1):246, 2023.
Article in English | MEDLINE | ID: covidwho-2185834

ABSTRACT

South Africa was among the first countries to detect the SARS-CoV-2 Omicron variant. However, the size of its Omicron BA.1 and BA.2 subvariants (BA.1/2) wave remains poorly understood. We analyzed sequential serum samples collected through a prospective cohort study before, during, and after the Omicron BA.1/2 wave to infer infection rates and monitor changes in the immune histories of participants over time. We found that the Omicron BA.1/2 wave infected more than half of the cohort population, with reinfections and vaccine breakthroughs accounting for > 60% of all infections in both rural and urban sites. After the Omicron BA.1/2 wave, we found few (< 6%) remained naive to SARS-CoV-2 and the population immunologic landscape is fragmented with diverse infection/immunization histories. Prior infection with the ancestral strain, Beta, and Delta variants provided 13%, 34%, and 51% protection against Omicron BA.1/2 infection, respectively. Hybrid immunity and repeated prior infections reduced the risks of Omicron BA.1/2 infection by 60% and 85% respectively. Our study sheds light on a rapidly shifting landscape of population immunity in the Omicron era and provides context for anticipating the long-term circulation of SARS-CoV-2 in populations no longer naive to the virus.

4.
MMWR - Morbidity & Mortality Weekly Report ; 71(5152):1625-1630, 2022.
Article in English | MEDLINE | ID: covidwho-2204208

ABSTRACT

Monovalent COVID-19 mRNA vaccines, designed against the ancestral strain of SARS-CoV-2, successfully reduced COVID-19-related morbidity and mortality in the United States and globally (1,2). However, vaccine effectiveness (VE) against COVID-19-associated hospitalization has declined over time, likely related to a combination of factors, including waning immunity and, with the emergence of the Omicron variant and its sublineages, immune evasion (3). To address these factors, on September 1, 2022, the Advisory Committee on Immunization Practices recommended a bivalent COVID-19 mRNA booster (bivalent booster) dose, developed against the spike protein from ancestral SARS-CoV-2 and Omicron BA.4/BA.5 sublineages, for persons who had completed at least a primary COVID-19 vaccination series (with or without monovalent booster doses) >=2 months earlier (4). Data on the effectiveness of a bivalent booster dose against COVID-19 hospitalization in the United States are lacking, including among older adults, who are at highest risk for severe COVID-19-associated illness. During September 8-November 30, 2022, the Investigating Respiratory Viruses in the Acutely Ill (IVY) Network assessed effectiveness of a bivalent booster dose received after >=2 doses of monovalent mRNA vaccine against COVID-19-associated hospitalization among immunocompetent adults aged >=65 years. When compared with unvaccinated persons, VE of a bivalent booster dose received >=7 days before illness onset (median = 29 days) against COVID-19-associated hospitalization was 84%. Compared with persons who received >=2 monovalent-only mRNA vaccine doses, relative VE of a bivalent booster dose was 73%. These early findings show that a bivalent booster dose provided strong protection against COVID-19-associated hospitalization in older adults and additional protection among persons with previous monovalent-only mRNA vaccination. All eligible persons, especially adults aged >=65 years, should receive a bivalent booster dose to maximize protection against COVID-19 hospitalization this winter season. Additional strategies to prevent respiratory illness, such as masking in indoor public spaces, should also be considered, especially in areas where COVID-19 community levels are high (4,5).

5.
Emerg Infect Dis ; 28(13):177-180, 2022.
Article in English | PubMed | ID: covidwho-2162893

ABSTRACT

As COVID-19 cases increased during the first weeks of the pandemic in South Africa, the National Institute of Communicable Diseases requested assistance with epidemiologic and surveillance expertise from the US Centers for Disease Control and Prevention South Africa. By leveraging its existing relationship with the National Institute of Communicable Diseases for >2 months, the US Centers for Disease Control and Prevention South Africa supported data capture and file organization, data quality reviews, data analytics, laboratory strengthening, and the development and review of COVID-19 guidance This case study provides an account of the resources and the technical, logistical, and organizational capacity leveraged to support a rapid response to the COVID-19 pandemic in South Africa.

6.
Open Forum Infectious Diseases ; 8(SUPPL 1):S93, 2021.
Article in English | EMBASE | ID: covidwho-1746772

ABSTRACT

Background. Sharp declines in influenza and respiratory syncytial virus (RSV) circulation across the U.S. have been described during the pandemic in temporal association with community mitigation for control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We aimed to determine relative frequencies of rhinovirus/ enterovirus (RV/EV) and other respiratory viruses in children presenting to emergency departments or hospitalized with acute respiratory illness (ARI) prior to and during the COVID-19 pandemic. Methods. We conducted a multi-center active prospective ARI surveillance study in children as part of the New Vaccine Surveillance Network (NVSN) from December 2016 through January 2021. Molecular testing for RV/EV, RSV, influenza, and other respiratory viruses [i.e., human metapneumovirus, parainfluenza virus (Types 1-4), and adenovirus] were performed on specimens collected from children enrolled children. Cumulative percent positivity of each virus type during March 2020-January 2021 was compared from March-January in the prior seasons (2017-2018, 2018-2019, 2019-2020) using Pearson's chi-squared. Data are provisional. Results. Among 69,403 eligible children, 37,676 (54%) were enrolled and tested for respiratory viruses. The number of both eligible and enrolled children declined in early 2020 (Figure 1), but 4,691 children (52% of eligible) were enrolled and tested during March 2020-January 2021. From March 2020-January 2021, the overall percentage of enrolled children with respiratory testing who had detectable RV/EV was similar compared to the same time period in 2017-2018 and 2019-2020 (Figure 1, Table 1). In contrast, the percent positivity of RSV, influenza, and other respiratory viruses combined declined compared to prior years, (p< 0.001, Figure 1, Table 1). Figure 1. Percentage of Viral Detection Among Enrolled Children Who Received Respiratory Testing, New Vaccine Surveillance Network (NVSN), United States, December 2016 - January 2021 Table 1. Percent of Respiratory Viruses Circulating in March 2020- January 2021, compared to March-January in Prior Years, New Vaccine Surveillance Network (NVSN), United States, March 2017 - January 2021 Conclusion. During 2020, RV/EV continued to circulate among children receiving care for ARI despite abrupt declines in other respiratory viruses within this population. These findings warrant further studies to understand virologic, behavioral, biological, and/or environmental factors associated with this continued RV/EV circulation.

10.
Eurosurveillance ; 26(29):10, 2021.
Article in English | Web of Science | ID: covidwho-1341599

ABSTRACT

Background In South Africa, COVID-19 control measures to prevent SARS-CoV-2 spread were initiated on 16 March 2020. Such measures may also impact the spread of other pathogens, including influenza virus and respiratory syncytial virus (RSV) with implications for future annual epidemics and expectations for the subsequent northern hemisphere winter. Methods We assessed the detection of influenza and RSV through facility-based syndromic surveillance of adults and children with mild or severe respiratory illness in South Africa from January to October 2020, and compared this with surveillance data from 2013 to 2019. Results Facility-based surveillance revealed a decline in influenza virus detection during the regular season compared with previous years. This was observed throughout the implementation of COVID-19 control measures. RSV detection decreased soon after the most stringent COVID-19 control measures commenced;however, an increase in RSV detection was observed after the typical season, following the reopening of schools and the easing of measures. Conclusion COVID-19 non-pharmaceutical interventions led to reduced circulation of influenza and RSV in South Africa. This has limited the country's ability to provide influenza virus strains for the selection of the annual influenza vaccine. Delayed increases in RSV case numbers may reflect the easing of COVID-19 control measures. An increase in influenza virus detection was not observed, suggesting that the measures may have impacted the two pathogens differently. The impact that lowered and/or delayed influenza and RSV circulation in 2020 will have on the intensity and severity of subsequent annual epidemics is unknown and warrants close monitoring.

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