Antigenic diversity and dengue disease risk

Many pathogens continuously change their protein structure in response to immune-driven selection, resulting in weakened protection. In addition, for some pathogens such as dengue virus, poorly targeted immunity is associated with increased risk of severe disease, through a mechanism known as antibody-dependent enhancement. However, it remains a mystery whether the antigenic distance between an individual's first infection and subsequent exposures dictate disease risk, explaining the observed large-scale differences in dengue hospitalisations across years. Here we develop an inferential framework that combines detailed antigenic and genetic characterisation of viruses, and hospitalised cases from 21 years of surveillance in Bangkok, Thailand to identify the role of the antigenic profile of circulating viruses in determining disease risk. We find that the risk of hospitalisation depends on both the specific order of infecting serotypes and the antigenic distance between an individual's primary and secondary infections, with risk maximised at intermediate antigenic distances. These findings suggest immune imprinting helps determine dengue disease risk, and provides a pathway to monitor the changing risk profile of populations and to quantifying risk profiles of candidate vaccines.

Testing Frequency Matters: An Evaluation of the Diagnostic Performance of a Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Rapid Antigen Test in US Correctional Facilities

BACKGROUND

The Centers for Disease Control and Prevention recommends serial rapid antigen assay collection within congregate facilities. Although modeling and observational studies from communities and long-term care facilities have shown serial collection provides adequate sensitivity and specificity, the accuracy within correctional facilities remains unknown.

METHODS

Using Connecticut Department of Correction data from 21 November 2020 to 15 June 2021, we estimated the accuracy of a rapid assay, BinaxNOW (Abbott), under 3 collection strategies: single test collection and serial collection of 2 and 3 tests separated by 1-4 days. The sensitivity and specificity of the first (including single), second, and third serially collected BinaxNOW tests were estimated relative to RT-PCRs collected ≤1 day of the BinaxNOW test. The accuracy metrics of the testing strategies were then estimated as the sum (sensitivity) and product (specificity) of tests in each strategy.

RESULTS

Of the 13 112 residents who contributed ≥1 BinaxNOW test during the study period, 3825 contributed ≥1 RT-PCR paired BinaxNOW test. In relation to RT-PCR, the 3-rapid-antigen-test strategy had a sensitivity of 95.9% (95% CI: 93.6-97.5%) and specificity of 98.3% (95% CI: 96.7-99.1%). The sensitivities of the 2- and 1-rapid-antigen-test strategies were 88.8% and 66.8%, and the specificities were 98.5% and 99.4%, respectively. The sensitivity was higher among symptomatic residents and when RT-PCRs were collected before BinaxNOW tests.

CONCLUSIONS

We found serial antigen test collection resulted in high diagnostic accuracy. These findings support serial collection for outbreak investigation, screening, and when rapid detection is required (such as intakes or transfers).

Structural factors contributing to SARS-CoV-2 infection risk in the urban slum setting.. [PMID: 35194620 PMCID: PMC8863166 DOI: 10.1101/2022.02.13.22270856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Background

The structural environment of urban slums, including physical, demographic and socioeconomic attributes, renders inhabitants more vulnerable to SARS-CoV-2 infection. Yet, little is known about the specific determinants that contribute to high transmission within these communities.

Methods and findings

We performed a serosurvey of an established cohort of 2,035 urban slum residents from the city of Salvador, Brazil between November 2020 and February 2021, following the first COVID-19 pandemic wave in the country. We identified high SARS-CoV-2 seroprevalence (46.4%, 95% confidence interval [CI] 44.3–48.6%), particularly among female residents (48.7% [95% CI 45.9–51.6%] vs. 43.2% [95% CI 39.8–46.6%] among male residents), and among children (56.5% [95% CI 52.3–60.5%] vs. 42.4% [95% CI 39.9–45.0%] among adults). In multivariable models that accounted for household-level clustering, the odds ratio for SARS-CoV-2 seropositivity among children was 1.96 (95% CI 1.42–2.72) compared to adults aged 30–44 years. Adults residing in households with children were more likely to be seropositive; this effect was particularly prominent among individuals with age 30–44 and 60 years or more. Women living below the poverty threshold (daily per capita household income <$1.25) and those who were unemployed were more likely to be seropositive.

Conclusions

During a single wave of the COVID-19 pandemic, cumulative incidence as assessed by serology approached 50% in a Brazilian urban slum population. In contrast to observations from industrialized countries, SARS-CoV-2 incidence was highest among children, as well as women living in extreme poverty. These findings emphasize the need for targeted interventions that provide safe environments for children and mitigate the structural risks posed by crowding and poverty for the most vulnerable residents of urban slum communities.

Change in COVID-19 risk over time following vaccination with CoronaVac: A testnegative case-control study

OBJECTIVE

To estimate the change in odds of covid-19 over time following primary series completion of the inactivated whole virus vaccine, CoronaVac (Sinovac Biotech) in São Paulo state, Brazil.

DESIGN

Test negative case-control study.

SETTING

Community testing for covid-19 in São Paulo state, Brazil.

PARTICIPANTS

Adults aged 18-120 years who were residents of São Paulo state, without a previous laboratory-confirmed covid-19 infection, who received only two doses of CoronaVac, and underwent reverse transcription polymerase chain reaction (RT-PCR) testing for SARS-CoV-2 from 17 January to 30 September 2021.

MAIN OUTCOME MEASURES

RT-PCR-confirmed symptomatic covid-19 and associated hospital admissions and deaths. Cases were pair-matched to test-negative controls by age (in 5-year bands), municipality of residence, healthcare worker (HCW) status, and date of RT-PCR test (±3 days). Conditional logistic regression was adjusted for sex, number of covid-19-associated comorbidities, race, and previous acute respiratory infection.

RESULTS

From 137,820 eligible individuals, 37,929 cases with symptomatic covid-19 and 25,756 test-negative controls with covid-19 symptoms were formed into 37,929 matched pairs. Adjusted odds ratios of symptomatic covid-19 increased with time since series completion, and this increase was greater in younger individuals, and among HCWs compared to non-HCWs. Adjusted odds ratios of covid-19 hospitalisation or death were significantly increased from 98 days since series completion, compared to individuals vaccinated 14-41 days previously: 1.40 (95% confidence interval 1.09 to 1.79) from 98-125 days, 1.55 (1.16 to 2.07) from 126-153 days, 1.56 (1.12 to 2.18) from 154-181 days, and 2.12 (1.39-3.22) from 182 days.

CONCLUSIONS

In the general population of São Paulo state, Brazil, an increase in odds of moderate and severe covid-19 outcomes was observed over time following primary series completion with CoronaVac.

Antigenic evolution of dengue viruses over 20 years

Infection with one of dengue viruses 1 to 4 (DENV1-4) induces protective antibodies against homotypic infection. However, a notable feature of dengue viruses is the ability to use preexisting heterotypic antibodies to infect Fcγ receptor–bearing immune cells, leading to higher viral load and immunopathological events that augment disease. We tracked the antigenic dynamics of each DENV serotype by using 1944 sequenced isolates from Bangkok, Thailand, between 1994 and 2014 (348 strains), in comparison with regional and global DENV antigenic diversity (64 strains). Over the course of 20 years, the Thailand DENV serotypes gradually evolved away from one another. However, for brief periods, the serotypes increased in similarity, with corresponding changes in epidemic magnitude. Antigenic evolution within a genotype involved a trade-off between two types of antigenic change (within-serotype and between-serotype), whereas genotype replacement resulted in antigenic change away from all serotypes. These findings provide insights into theorized dynamics in antigenic evolution.

Outpatient healthcare personnel knowledge and attitudes towards infection prevention measures for protection from respiratory infections

BACKGROUND

Healthcare personnel (HCP) knowledge and attitudes toward infection control measures are important determinants of practices that can protect them from transmission of infectious diseases.

METHODS

Healthcare personnel were recruited from Emergency Departments and outpatient clinics at seven sites. They completed knowledge surveys at the beginning and attitude surveys at the beginning and end of each season of participation. Attitudes toward infection prevention and control measures, especially medical masks and N95 respirators, were compared. The proportion of participants who correctly identified all components of an infection control bundle for seven clinical scenarios was calculated.

RESULTS

The proportion of participants in the medical mask group who reported at least one reason to avoid using medical masks fell from 88.5% on the pre-season survey to 39.6% on the post-season survey (odds ratio [OR] for preseason vs. postseason 0.11, 95% CI 0.10-0.14). Among those wearing N95 respirators, the proportion fell from 87.9% to 53.6% (OR 0.24, 95% CI 0.21-0.28). Participants correctly identified all components of the infection control bundle for 4.9% to 38.5% of scenarios.

CONCLUSIONS

Attitudes toward medical masks and N95 respirators improved significantly between the beginning and end of each season. The proportion of HCP who correctly identified the infection control precautions needed for clinical scenarios was low, but it improved over successive years of participation in the study.

Factors associated with clinical severity in emergency department patients presenting with symptomatic SARS-CoV-2 infection

OBJECTIVE

To measure the association of race, ethnicity, comorbidities, and insurance status with need for hospitalization of symptomatic emergency department patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection.

METHODS

This study is a cohort study of symptomatic patients presenting to a single emergency department (ED) with laboratory-confirmed SARS-CoV-2 infection from March 7-August 9, 2020. We collected patient-level information regarding demographics, insurance status, comorbidities, level of care, and mortality using a structured chart review. We compared characteristics of patients categorized by (1) home discharge, (2) general hospital ward admission, and (3) intensive care unit (ICU) admission or death within 30 days of the index visit. Univariate and multivariable logistic regression analyses were performed to report odds ratios (OR) and 95% confidence intervals (95% CI) between hospital admission versus ED discharge home and between ICU care versus general hospital ward admission.

RESULTS

In total, 994 patients who presented to the ED with symptoms were included in the analysis with 551 (55.4%) patients discharged home, 314 (31.6%) patients admitted to the general hospital ward, and 129 (13.0%) admitted to the ICU or dying. Patients requiring admission were more likely to be Black or to have public insurance (Medicaid and/or Medicare). Patients who were admitted to the ICU or dying were more likely aged ≥ 65 years or male. In multivariable logistic regression, old age, public insurance, diabetes, hypertension, obesity, heart failure, and hyperlipidemia were independent predictors of hospital admission. When comparing those who needed ICU care versus general hospital ward admission in univariate logistic regression, patients with Medicaid (OR 2.4, 95% CI 1.2-4.6), Medicare (OR 4.2, 95% CI 2.1-8.4), Medicaid and Medicare (OR 4.3, 95% CI 2.4-7.7), history of chronic obstructive pulmonary disease (OR 2.2, 95% CI 1.2-4.2), hypertension (OR 1.7, 95% CI 1.1-2.7), and heart failure (OR 2.6, 95% CI 1.4-4.7) were more likely to be admitted into the ICU or die; Black (OR 1.1, 95% CI 0.4-2.9) and Hispanic/Latino (OR 1.0, 95% CI 0.6-1.8) patients were less likely to be admitted into the ICU; however, the associations were not statistically significant. In multivariable logistic regression, old age, male sex, public insurance, and heart failure were independent predictors of ICU care/death.

CONCLUSION

Comorbidities and public insurance are predictors of more severe illness for patients with SARS-CoV-2. This study suggests that the disparities in severity seen in COVID-19 among Black patients may be attributable, in part, to low socioeconomic status and chronic health conditions.

A systematic review of antibody mediated immunity to coronaviruses: antibody kinetics, correlates of protection, and association of antibody responses with severity of disease

The duration and nature of immunity generated in response to SARS-CoV-2 infection is unknown. Many public health responses and modeled scenarios for COVID-19 outbreaks caused by SARSCoV-2 assume that infection results in an immune response that protects individuals from future infections or illness for some amount of time. The timescale of protection is a critical determinant of the future impact of the pathogen. The presence or absence of protective immunity due to infection or vaccination (when available) will affect future transmission and illness severity. The dynamics of immunity and nature of protection are relevant to discussions surrounding therapeutic use of convalescent sera as well as efforts to identify individuals with protective immunity. Here, we review the scientific literature on antibody immunity to coronaviruses, including SARS-CoV-2 as well as the related SARS-CoV-1, MERS-CoV and human endemic coronaviruses (HCoVs). We reviewed 1281 abstracts and identified 322 manuscripts relevant to 5 areas of focus: 1) antibody kinetics, 2) correlates of protection, 3) immunopathogenesis, 4) antigenic diversity and cross-reactivity, and 5) population seroprevalence. While studies of SARS-CoV-2 are necessary to determine immune responses to it, evidence from other coronaviruses can provide clues and guide future research.

The incubation period of cholera: a systematic review

OBJECTIVES

Recent large cholera outbreaks highlight the need for improved understanding of the pathogenesis and epidemiology of cholera. The incubation period of cholera has important implications for clinical and public health decision-making, yet statements of the incubation period of cholera are often imprecise. Here we characterize the distribution of cholera's incubation period.

METHODS

We conducted a systematic review of the literature for statements of the incubation period of cholera and data that might aid in its estimation. We extracted individual-level data, parametrically estimated the distribution of toxigenic cholera's incubation period, and evaluated evidence for differences between strains.

RESULTS

The incubation period did not differ by a clinically significant margin between strains (except O1 El Tor Ogawa). We estimate the median incubation period of toxigenic cholera to be 1.4 days (95% CI, 1.3-1.6). Five percent of cholera cases will develop symptoms by 0.5 days (95% CI 0.4-0.5), and 95% by 4.4 days (95% CI 3.9-5.0) after infection.

CONCLUSIONS

We recommend that cholera investigations use a recall period of at least five days to capture relevant exposures; significantly longer than recent risk factor studies from the Haitian epidemic. This characterization of cholera's incubation period can help improve clinical and public health practice and advance epidemiologic research.

Models of the impact of dengue vaccines: a review of current research and potential approaches

Vaccination reduces transmission of pathogens directly, by preventing individual infections, and indirectly, by reducing the probability of contact between infected individuals and susceptible ones. The potential combined impact of future dengue vaccines can be estimated using mathematical models of transmission. However, there is considerable uncertainty in the structure of models that accurately represent dengue transmission dynamics. Here, we review models that could be used to assess the impact of future dengue immunization programmes. We also review approaches that have been used to validate and parameterize models. A key parameter of all approaches is the basic reproduction number, R(0), which can be used to determine the critical vaccination fraction to eliminate transmission. We review several methods that have been used to estimate this quantity. Finally, we discuss the characteristics of dengue vaccines that must be estimated to accurately assess their potential impact on dengue virus transmission.

DNA adducts of heterocyclic amines: formation, removal and inhibition by dietary components

The dietary mutagens 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) are carcinogenic in rodents. In F344 rats PhIP induces mammary tumors in females and colon tumors in males, while IQ induces tumors principally in the liver, Zymbal gland and intestines. In CDF1 mice, IQ induces liver, lung and forestomach tumors. We have evaluated the dynamics of formation, removal and inhibition of PhIP- and IQ-DNA adducts in these rodents. After bolus doses (50 mg/kg, by gavage) of IQ or PhIP, both IQ- and PhIP-DNA adducts were removed rapidly from both target and nontarget organs, while after 3-4 weeks of feeding IQ or PhIP (0.01-0.04%) adduct removal was much slower. Gavaging of male F344 rats with PhIP (0.1-1000 micrograms/kg/day) for 23 days resulted in accumulation of PhIP-DNA adducts in various organs, but adducts were detectable only at 100 or 1000 micrograms/kg/day. Urinary excretion of unchanged PhIP was a constant proportion (1.6-2.1%) of the daily dose over the entire dose range and was independent of duration of exposure. When weanling female F344 rats were exposed to dietary PhIP (0.01-0.04%) for 1-4 weeks, the presence of either conjugated linoleic acid (CLA; 0.1-1.0%) or indole-3-carbinol (13C; 0.1%) in the diet inhibited PhIP-DNA adduct formation (58-99%) in various organs, including the mammary gland and the colon. Similarly, the inclusion of 0.075% 4-ipomeanol (IPO) in the diet of male CDF1 mice exposed for 3 weeks to dietary IQ (0.01%) resulted in inhibition of IQ-DNA adduct formation (30-59%) in the target organs (liver, lungs, stomach) but not in a number of other organs. It is concluded that (1) the rate of PhIP- and IQ-DNA adduct removal depends on the dose and frequency of administration, (2) urinary PhIP may be a good biomarker of recent PhIP exposure and (3) CLA, I3C and IPO are potential chemopreventive agents against PhIP- or IQ-induced tumors in rodents.

Validation in rats of two biomarkers of exposure to the food-borne carcinogen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP): PhIP-DNA adducts and urinary PhIP

2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP)-DNA adducts in white blood cells and tissues and unmetabolized PhIP in urine were validated as biomarkers of exposure in male Fischer-344 rats treated with daily PhIP doses ranging from 1 to 0.0001 mg/kg. At the end of the 23 day treatment period all rats were killed and their blood and 10 tissues were collected for isolation of DNA and analysis of PhIP-DNA adducts by 32P-postlabeling and alkaline hydrolysis with GC/MS. PhIP-DNA adducts could be detected only in animals receiving 1 or 0.1 mg/kg/day, with highest adduct levels in the pancreas, heart and kidneys. There was a good correlation (r = 0.77, P < 0.005) between the two methods of analysis, with average adduct levels determined by 32P-postlabeling approximately 1.4 times higher than those determined by alkaline hydrolysis with GC/MS. PhIP-DNA adducts accumulated in most tissues, especially in the liver, kidneys, heart and pancreas, with lower levels in the white blood cells, small intestine, stomach, colon and cecum. Using GC/MS levels of unmetabolized PhIP were measurable in four weekly 24 h urine samples even at 0.0001 mg/kg/day, a dose comparable with reported human dietary exposure. A linear dose-response was obtained for excretion of unmetabolized PhIP across the range of doses, with approximately 1.8% of the dose excreted daily, largely independent of the number of doses. No PhIP was detected in the urine of untreated rats. If it can be shown that a constant percentage of PhIP is excreted unchanged in human urine, irrespective of dose, as has been found with the rat, measurement of urinary PhIP could be used as an accurate measure of dietary exposure to this amine in man.

Inhibitory effect of dietary 4-ipomeanol on DNA adduct formation by the food mutagen 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) in male CDF1 mice

The food mutagen 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) is carcinogenic in the CDF1 mouse liver, lungs and stomach. IQ is activated to its ultimate carcinogenic form by N-hydroxylation, catalyzed principally by hepatic microsomal cytochrome P450IA2, and further esterification, resulting in the formation of N-(deoxyguanosin-8-yl)-IQ and other adducts. The furanoterpenoid 4-ipomeanol (IPO) is a naturally occurring pneumotoxin which exerts its specific toxicity in Clara cells of the lung after activation by microsomal cytochrome P450. Because IPO is activated in the liver by a cytochrome P450IA2 enzyme, we evaluated IPO as a possible chemopreventive agent by assessing its ability to inhibit IQ-DNA adduct formation in the CDF1 mouse. Mice were put on an AIN-76A diet with or without 0.075% IPO from day 0 to 54. IQ (0.01%) was added to the diets from day 22 to 41 and animals were killed (four animals/time point) on days 42, 44, 46, 48, 50 and 54. Blood (for white blood cell isolation), liver, lungs, stomach, small intestine, cecum, colon, kidneys, spleen and heart were collected for analysis of IQ-DNA adducts by 32P-post-labeling. During the 12 day period after cessation of IQ exposure (days 42-54) IQ-DNA adduct formation was significantly inhibited in the liver (33.6-46.4%), lungs (29.9-58.6%), stomach (33.2-51.5%) and white blood cells (24.5-63.7%), but not in the other organs. Except in the colon, adduct removal from organs during days 42-54 was relatively slow (36.0-81.9% of day 42 levels remaining on day 54, 9.4-16.7% in the colon), but the presence of IPO in the diet did not influence the rate of adduct removal. Measurement of hepatic microsomal ethoxyresorufin deethylase, an activity specific for cytochrome P450IA isozymes, showed that the enzyme could be inhibited (14.1-68.1%) by IPO (0.05-10.0 mM) in vitro. It is concluded that IPO inhibits IQ-DNA adduct formation in target organs of the CDF1 mouse and that IPO may act by inhibiting N-hydroxylation of IQ. It is therefore possible that IPO may be a candidate chemopreventive agent against IQ-induced carcinogenesis.

Removal of DNA adducts of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) in the male Fischer-344 rat

The food mutagen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) is carcinogenic in the male Fischer-344 rat, affecting principally the colon. PhIP-DNA adducts may play a role in the initiation of the carcinogenic process. We have evaluated the formation and persistence of PhIP-DNA adducts in the colon, circulating white blood cells (WBC) and several other non-target organs of the male Fischer-344 rat. Young adult male animals were given a single dose of PhIP (50 mg/kg) by gavage. Animals were killed 1, 2, 6, 12, 16 or 20 days after dosing (4 animals/time point) and their liver, lungs, stomach, small intestine, cecum, colon, kidneys, WBC, heart and spleen were removed for isolation of DNA and assay of PhIP-DNA adducts by 32P-postlabeling. For interorgan comparisons of cell turnover, rats were given a single i.p. dose of [methyl-3H]thymidine, after which DNA was isolated at the same time intervals as for adduct analysis and its sp. act. (d.p.m. 3H/100 micrograms) was determined. In all organs up to three adducts could be isolated and the adduct pattern was the same in each case. On day 1, total adduct levels were highest in the colon (the target organ), followed by the spleen, cecum, small intestine, stomach, liver, kidneys, lungs, WBC and heart. Rates of adduct removal were similar in the colon, spleen, cecum, liver, lungs, stomach and small intestine, with day 16 and day 20 levels falling to < 16% of those on day 1; rates of removal were slower in the heart and kidneys (52.0 and 30.3% of day 1 values remaining on day 16 respectively). Adducts in WBC increased at first (day 2) and decreased thereafter to virtually non-detectable levels on days 16 and 20. Heart adducts on days 2-12 increased slightly or remained as high as those on day 1, then decreased to lower levels on days 16 and 20 (53.0 and 28.7% of day 1 levels respectively). There was no preferential removal or persistence of any individual adduct in WBC or in any of the organs. On days 1 and 2, the sp. act. of intestinal DNA (small intestine, cecum and colon) was > 30-fold higher than that in several other organs, including the liver. These sp. act. decreased to the low sp. act. of the liver on day 20. It is concluded that the rates of adduct removal from the intestines are more likely to be related to cell turnover of epithelial cells than to enzymatic repair.(ABSTRACT TRUNCATED AT 400 WORDS)

Accumulation of DNA adducts of 2-amino-3-methylimidazo[4,5-f] quinoline (IQ) in tissues and white blood cells of the Fischer-344 rat after multiple oral dosing

The genotoxic effect of an environmental chemical may be estimated from the concentration of its DNA adducts in peripheral white blood cells (WBCs). The food mutagen 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) is carcinogenic in the Fischer-344 rat, affecting principally the liver, small intestine and large intestine. In the present study we have determined whether DNA adducts of IQ are present in circulating WBCs of rats after single or multiple oral doses of IQ and how these adducts are related to those in internal organs. Male Fischer-344 rats received IQ as an oral dose (5 or 50 mg/kg, starting on day 0) by daily gavage (1, 8 or 15 days of treatment). Using 32P-postlabeling assays, IQ-DNA adducts were isolated and quantitated in organs and WBCs on days 1, 8 and 15. Adduct patterns in WBCs were qualitatively similar to those in the organs and adduct formation was highest in the liver, followed by the lungs, kidneys, stomach, large intestine, WBC and small intestine. Accumulation of adducts occurred in all organs and in WBCs in a dose- and time-dependent manner. For all organs, IQ-DNA adduct formation was strongly correlated with those in WBCs. It is concluded that IQ-DNA adducts in WBCs are qualitatively and quantitatively directly related to those in internal organs, independent of the target organ specificity of the carcinogenic effect of IQ.