Amyn Malik

Analysis Group

The emergence of the SARS-CoV-2 Omicron sublineages resulted in increased transmission rates and reduced protection from vaccines. To counteract these effects, multiple booster strategies were used in different countries, although data comparing their efficiency in improving protective immunity remain sparse, especially among vulnerable populations...

Background: Lebanon endured its worst economic and financial crisis in 2020-2021. To minimize the impact of COVID-19 pandemic, it is important to improve the overall COVID-19 vaccination rate. Given that vaccine hesitancy among health care workers (HCWs) affects the general population's decision to be vaccinated, our study assessed COVID-19 vaccin...

Masking, a common SARS-CoV-2 risk mitigation strategy, is controversial for children in educational settings such as childcare. A prospective survey of early childcare workers demonstrated that child masking was associated with a significant reduction in COVID-19 program closure, highlighting potential benefits of child masking in keeping childcare...

Background: Significant data gaps exist for children and adolescents with drug-resistant (DR) TB, particularly from high TB incidence settings. This report provides a descriptive analysis of programmatic outcomes among children and adolescents treated for DR-TB in Pakistan. Methods: We extracted programmatic data from January 2014 to December 20...

Amidst an unprecedented Monkeypox outbreak, we aimed to measure knowledge, attitudes, practices and Monkeypox vaccination intentions among the U.S. adult population. We conducted an online cross-sectional survey, representative of the U.S. adult general public in June 2022. We asked participants whether they would receive a Monkeypox vaccine, if th...

Importance All U.S. states provided Covid-19 vaccine access to frontline healthcare workers first, but after that, states varied in whether they gave earlier access to the elderly, versus the vulnerable with comorbidities, or school employees or essential workers, reflecting the underlying scientific and policy uncertainty. Objective To evaluate i...

Background Clinical pediatric TB diagnosis may lead to over-diagnosis particularly among children with HIV (CHIV). We assessed the performance of monocyte-lymphocyte ratio (MLR) as a diagnostic biomarker and constructed a clinical prediction score to improve specificity of TB diagnosis in CHIV with limited access to microbiologic testing. Methods...

Background: The World Health Organization (WHO) recommends tuberculosis (TB) diagnostic evaluation for children with HIV (CHIV) who have history of TB contact, poor weight gain, cough or fever. These screening criteria were developed based on studies of symptomatic CHIV with incomplete microbiologic confirmation. We performed routine TB microbiolo...

Introduction: Given their central role in supporting children's development, childcare professionals' overall physical and mental health is important. We evaluated the prevalence of chronic diseases, depression, and stress levels during the COVID-19 pandemic among US childcare professionals. Methods: Data were obtained from US childcare professi...

Background The discovery of vaccines significantly reduced morbidity and mortality of infectious diseases and led to the elimination and eradication of some. Development of safe and effective vaccines is a critical step to the control of infectious diseases; however, there is the need to address vaccine hesitancy because of its potential impact on...

Despite a growing focus on the plight of tuberculosis (TB) among children, 56% of the 1.2 million children who develop TB annually are not detected and notified. TB REACH is a platform of the Stop TB Partnership that supports innovative interventions to improve TB case detection and preventative treatment. We present summary findings from 27 TB REA...

SARS-CoV-2 infection can result in the development of a constellation of persistent sequelae following acute disease called post-acute sequelae of COVID-19 (PASC) or Long COVID. Individuals diagnosed with Long COVID frequently report unremitting fatigue, post-exertional malaise, and a variety of cognitive and autonomic dysfunctions; however, the ba...

BACKGROUND: We assessed treatment uptake and completion for 6 months of isoniazid (6H) and 3 months of isoniazid plus rifapentine weekly (3HP) in a programmatic setting in Pakistan.METHODS: All household contacts were clinically evaluated to rule out TB disease. 6H was used for TB preventive treatment (TPT) from October 2016 to April 2017; from May...

While the Monkeypox outbreak is growing, little is known about the general public’s levels of knowledge, their trusted sources of information and attitudes towards a Monkeypox vaccine. In our representative survey of the US general public, we find that almost half the respondents (47%) feel that their knowledge level about Monkeypox is poor or very...

Background Posterior reversible encephalopathy syndrome (PRES) is relatively uncommon in paediatric patients; however, its pathophysiology remains obscure. Objective The aims of this study were to find an association or correlation between (1) blood pressures and (2) imaging severity and the presence of atypical imaging features in children with P...

In 1995, journalist Gary Taubes published an article in Science titled "Epidemiology faces its limits," which questioned the utility of nonrandomized epidemiologic research and has since been cited more than 1000 times. He highlighted numerous examples of research topics he viewed as having questionable merit. Studies have since accumulated for the...

Background and objective: Chronic kidney disease (CKD) constitutes a major public health challenge, with a global prevalence of 15-74.7 cases /million children. Preventing CKD in children, slowing its progression and management of complications are essential, especially in challenged health systems in low middle income countries (LMIC). We conduct...

Background: Clinical presentation for extrapulmonary tuberculosis (EPTB) in children can be variable and nonspecific, leading to delayed diagnosis, disease and death. We describe the age-specific clinical presentation and identify risk factors for EPTB among children in Pakistan. Methods: In 2015-2016 in 4 facilities in Sindh, Pakistan, children...

Background The relationship between the use of nonpharmaceutical interventions and COVID-19 vaccination among U.S. child care providers remains unknown. If unvaccinated child care providers are also less likely to employ nonpharmaceutical interventions, then a vaccine mandate across child care programs may have larger health and safety benefits. M...

Parental hesitancy poses a serious threat to the success of the COVID-19 childhood vaccination campaign. We investigate whether adults' opinions on childhood vaccination can be influenced via two survey experiments in Italy (n=3,524 participants) and the UK (n=3,066 participants). Respondents were randomly assigned to: a “risk treatment” that highl...

The authors wish to revise the second citation of reference [26] to [27] in the original article main text [...]

Background The aim of this study was to investigate the presence of mediastinal lymphadenopathy in hospitalized Covid-19 patients in a tertiary care hospital in the metropolitan city of Lahore, Pakistan from September 2020 till July 2021. Methods We retrospectively collected data of Covid-19 patients hospitalized from September 2020 till July 2021...

Importance There is no published national research reporting child care professionals’ physical health, depression, or stress during the COVID-19 pandemic. Given their central role in supporting children’s development, child care professionals’ overall physical and mental health is important. Objectives To evaluate the prevalence of chronic diseas...

The recent emergence of the SARS-CoV-2 Omicron variant is raising concerns because of its increased transmissibility and by its numerous spike mutations with potential to evade neutralizing antibodies elicited by COVID-19 vaccines. Here, we evaluated the effects of a heterologous BNT162b2 mRNA vaccine booster on the humoral immunity of participants...

The global fight against tuberculosis (TB) has gained momentum since the adoption of the ‘End TB Strategy’ in 2014 [...]

Objective To apply a cascade-of-care framework to evaluate the effectiveness—by age of the child—of an intensified tuberculosis patient-finding intervention. Design From a prospective screening program at four hospitals in Pakistan (2014–2016) we constructed a care cascade comprising six steps: screened, positive screen, evaluated, diagnosed, star...

Importance: It is not known how effective child masking is in childcare settings in preventing the transmission of SARS-CoV-2. This question is critical to inform health policy and safe childcare practices. Objective: To assess the association between masking children 2 years and older and subsequent childcare closure because of COVID-19. Desig...

As the COVID-19 pandemic surged, lockdowns led to the cancellation of essential health services. As part of our Zero TB activities in Karachi, we adapted our approach to integrate activities for TB and COVID-19 to decrease the impact on diagnosis and linkage to care for TB treatment. We implemented the following: (1) integrated COVID-19 screening a...

The COVID-19 pandemic led to a worldwide lockdown and school closures, which have placed a substantial mental health burden on children and college students. Through a systematic search of the literature on PubMed and Collabovid of studies published January 2020–July 2021, our findings of five studies on children and 16 studies on college students...

Background Cruise ships provide an ideal setting for transmission of SARS-CoV-2, given the socially dense exposure environment. Aim To provide a comprehensive review of COVID-19 outbreaks on cruise ships. Methods PubMed was searched for COVID-19 cases associated with cruise ships between January and October 2020. A list of cruise ships with COVID...

The frequency of SARS-CoV-2 breakthrough infections in fully vaccinated individuals increased with the emergence of the Delta variant, particularly with longer time from vaccine completion. However, whether breakthrough infections lead to onward transmission remains unclear. Here, we conducted a study involving 125 patients comprised of 72 vaccinat...

Background Cruise ships provide an ideal setting for efficient transmission of SARS-CoV- 2 given a socially dense exposure environment. No systematic review of transmission of COVID-19 on cruise ships to date has been completed. Methods MEDLINE was searched in accordance with PRIMSA guidelines for COVID-19 cases associated with cruise ships. A lis...

Objectives: Despite WHO guidelines recommending household contact investigation, and studies showing the impact of active screening, most tuberculosis (TB) programmes in resource-limited settings only carry out passive contact investigation. The cost of such strategies is often cited as barriers to their implementation. However, little data are av...

In the absence of widespread vaccination for COVID-19, governments and public health officials have advocated for the public to wear masks during the pandemic. The decision to wear a mask in public is likely affected by both beliefs about its efficacy and the prevalence of the behavior. Greater mask use in the community may encourage others to foll...

As immunization campaigns are accelerating, understanding how to distribute the scarce doses of vaccines is of paramount importance and a quantitative analysis of the trade-offs involved in domestic-only versus cooperative distribution is still missing. In this study we use a network Susceptible-Infected-Removed (SIR) model to show circumstances un...

Background Healthcare workers’ (HCW) COVID-19 vaccine hesitancy is a threat to any healthcare system. Vaccine hesitancy can increase HCWs’ and patients’ infection risk, while also impacting patients' decision to accept the vaccine. Our study assessed United Arab Emirates’ (UAE) HCWs’ COVID-19 vaccine acceptance. Methods Using purposive sampling, U...

Objectives: Ensuring high coronavirus disease-2019 (COVID-19) vaccine uptake among US child care providers is crucial to mitigating the public health implications of child-staff and staff-child transmission of severe acute respiratory syndrome coronavirus 2; however, the vaccination rate among this group was previously unknown. Methods: To chara...

Widespread acceptance of COVID-19 vaccines is crucial for achieving sufficient immunization coverage to end the global pandemic, yet few studies have investigated COVID-19 vaccination attitudes in lower-income countries, where large-scale vaccination is just beginning. We analyze COVID-19 vaccine acceptance across 15 survey samples covering 10 low-...

SARS-CoV-2 outbreaks have occurred on several nautical vessels, driven by the high-density contact networks on these ships. Optimal strategies for prevention and control that account for realistic contact networks are needed. We developed a network-based transmission model for SARS-CoV-2 on the Diamond Princess outbreak to characterize transmission...

Objectives: Ensuring a high COVID-19 vaccine uptake among U.S. child care providers is crucial to mitigating the public health implications of child-to-staff and staff-to-child transmission of SARS-CoV-2; however, the vaccination rate among this group is unknown. Methods: To characterize the vaccine uptake among U.S. child care providers, we conduc...

Coronavirus disease 2019 (COVID-19) has poorer clinical outcomes in males than in females, and immune responses underlie these sex-related differences. Because immune responses are, in part, regulated by metabolites, we examined the serum metabolomes of COVID-19 patients. In male patients, kynurenic acid (KA) and a high KA-to-kynurenine (K) ratio (...

Objectives The purpose of our study was to assess COVID-19 vaccine acceptance among health care workers (HCW) in the Kingdom of Saudi Arabia (KSA), and identify: 1) vaccine acceptance barriers; 2) demographic differences; and 3) the most trusted COVID-19 sources of information. Methods Between October and December 2020, all registered HCW in the K...

Ascertaining the state of coronavirus outbreaks is crucial for public health decision-making. Absent repeated representative viral test samples in the population, public health officials and researchers alike have relied on lagging indicators of infection to make inferences about the direction of the outbreak and attendant policy decisions. Recentl...

Background Active tuberculosis [TB] during pregnancy adversely affects maternal and neonatal outcomes. We analyzed the results of a pilot project integrating TB screening during antenatal care (ANC) visits in a high TB burden, low-resource setting. Methods We extracted data from the TB screening pilot in obstetrician-gynecologist clinics of 6 tert...

Context: The COVID-19 pandemic has resulted in more than 20 million cases and 350 000 deaths in the United States. With the ongoing media coverage and spread of misinformation, public health authorities need to identify effective strategies and create culturally appropriate and evidence-based messaging that best encourage preventive health behavio...

Significance Early in the US COVID-19 epidemic, Americans spent substantially more time at home to reduce cases. Disentangling voluntary from policy-induced behavioral changes is critical for governments grappling with relaxing or renewing restrictions. We estimate the number of additional reported cases that would have been needed to elicit a volu...

Background As vaccination campaigns are deployed worldwide, addressing vaccine hesitancy is of critical importance to ensure sufficient immunization coverage. We analyzed COVID-19 vaccine acceptance across 15 samples covering ten low- and middle- income countries (LMICs) in Asia, Africa, and South America, and two higher income countries (Russia an...

Background: The coronavirus disease 2019 (COVID-19) pandemic continues to adversely impact the United States socially, culturally, and economically. The purpose of this study was to understand the relationship between COVID-19 county death rates, risk perception, and US adults' voluntary behaviors-particularly physical distancing. Methods: Data...

In the absence of widespread vaccination for COVID-19, governments and public health officials have advocated for the public to wear masks during the pandemic. The decision to wear a mask in public is likely affected by both beliefs about its efficacy and the prevalence of the behavior. Greater mask use in the community may encourage others to foll...

In Karachi, Pakistan, a South Asian megacity with a high prevalence of tuberculosis (TB) and low HIV prevalence, we assessed the effectiveness of fluoroquinolone-based preventive therapy for drug-resistant (DR) TB exposure. During February 2016–March 2017, high-risk household contacts of DR TB patients began a 6-month course of preventive therapy w...

Background Shorter regimens for tuberculosis prevention can improve completion rates and protection against developing active tuberculosis disease after tuberculosis exposure. We aimed to assess the safety and feasibility of 1 month of daily isoniazid and rifapentine (1HP) in children and adolescents in a low-resource setting in south Asia with low...

In Karachi, Pakistan, a South Asian megacity with a high prevalence of tuberculosis (TB) and low HIV prevalence, we assessed the effectiveness of fluoroquinolone-based preventive therapy for drug-resistant (DR) TB exposure. During February 2016–March 2017, high-risk household contacts of DR TB patients began a 6-month course of preventive therapy w...

Background Every year, about 239 000 children die from tuberculosis (TB), despite availability of highly effective regimens. Few studies have evaluated predictors for poor treatment outcomes in children treated for TB. Methods We assessed predictors of unsuccessful TB treatment outcomes in a prospective cohort of children diagnosed by an intensifi...

In a matched case-control study in Pakistan, we found that quantified tuberculosis (TB) exposure using a 10-point score is associated with prevalent TB disease in pediatric household contacts. A 1 unit increase in TB exposure score increased the odds of TB disease by 44% (conditional odds ratio: 1.44, 95% confidence interval: 1.33-1.56). Collecting...

As the clinical trials for COVID-19 vaccine progress, understanding how to distribute the initially scarce doses is of paramount importance and a quantitative analysis of the trade-offs involved in domestic-only versus cooperative distribution is still missing. In this study we use a network Susceptible-Infected-Removed (SIR) model to show under wh...

Background Successful delivery and completion of tuberculosis preventive treatment delivery is necessary for tuberculosis elimination. Shorter preventive treatment regimens currently have higher medication costs, but patients spend less time in care and are more likely to complete treatment. It is unknown how economic costs of successful delivery d...

Recent reports have suggested that there may be dermatologic manifestations of COVID‐19. We searched 12 databases for peer‐reviewed or pre‐print published studies until July 15, 2020, for this PRISMA‐compliant review (CRD42020182050). We used the Oxford Center for Evidence‐Based Medicine Levels of Evidence to facilitate data synthesis. From 86 retr...

Objective Central to the debate over school and child care reopening is whether children are efficient COVID-19 transmitters and likely to increase community spread when programs reopen. We compared COVID-19 outcomes in child care providers who continued to provide direct in-person child care during the first three months of the U.S. COVID-19 pande...

We measured severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA concentrations in primary sewage sludge in the New Haven, Connecticut, USA, metropolitan area during the Coronavirus Disease 2019 (COVID-19) outbreak in Spring 2020. SARS-CoV-2 RNA was detected throughout the more than 10-week study and, when adjusted for time lags, tracke...