Secondary attack rates and determinants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) household transmission in Pakistan: A case-ascertained prospective, longitudinal study.

BACKGROUND: Households are considered ideal settings for studying the transmission dynamics of an infectious disease. METHODS: A prospective study was conducted, based on the World Health Organization FFX protocol from October 2020 to January,2021. Household contacts of laboratory-confirmed index cases were followed up for their symptomatic history, nasal swabs for RT-PCR,and blood samples for anti-SARS CoV-2 antibodies were collected at enrollment and days 7, 14 and 28. We estimated secondary attack rate (SAR), effective household case cluster size and determinants of secondary infection among susceptible household contacts using multivariable logistic regression. RESULTS: We enrolled 77 index cases and their 543 contacts. Out of these, 252 contacts were susceptible at the time of enrollment. There were 77 household clusters, out of which, transmission took place in 20 (25.9%) giving rise to 34 cases. The acquired secondary attack rate (SAR) was 14.0% (95% CI 9.0-18.0). The effective household case cluster size was 0.46 (95%CI 0.33,0.56). Reported symptoms of nausea and vomiting (aOR, 7.9; 95% CI, 1.4-45.5) and fatigue (aOR, 9.3; 95% CI, 3.8-22.7) were associated with SARS-CoV-2 transmission. CONCLUSIONS: We observed a low SARS-CoV-2 secondary attack rate in the backdrop of high seroprevalence and asymptomatic transmission among households in Karachi, Pakistan.

Environmental surveillance for COVID-19 using SARS-CoV-2 RNA concentration in wastewater - a study in District East, Karachi, Pakistan.

Background: Wastewater-based surveillance is used to track the temporal patterns of the SARS-CoV-2 virus in communities. Viral RNA particle detection in wastewater samples can indicate an outbreak within a catchment area. We describe the feasibility of using a sewage network to monitor SARS-CoV-2 trend and use of genomic sequencing to describe the viral variant abundance in an urban district in Karachi, Pakistan. This was among the first studies from Pakistan to demonstrate the surveillance for SARS-CoV-2 from a semi-formal sewage system. Methods: Four sites draining into the Lyari River in District East, Karachi, were identified and included in the current study. Raw sewage samples were collected early morning twice weekly from each site between June 10, 2021 and January 17, 2022, using Bag Mediated Filtration System (BMFS). Secondary concentration of filtered samples was achieved by ultracentrifugation and skim milk flocculation. SARS-CoV-2 RNA concentrations in the samples were estimated using PCR (Qiagen ProMega kits for N1 & N2 genes). A distributed-lag negative binomial regression model within a hierarchical Bayesian framework was used to describe the relationship between wastewater RNA concentration and COVID-19 cases from the catchment area. Genomic sequencing was performed using Illumina iSeq100. Findings: Among the 151 raw sewage samples included in the study, 123 samples (81.5%) tested positive for N1 or N2 genes. The average SARS-CoV-2 RNA concentrations in the sewage samples at each lag (1-14 days prior) were associated with the cases reported for the respective days, with a peak association observed on lag day 10 (RR: 1.15; 95% Credible Interval: 1.10-1.21). Genomic sequencing showed that the delta variant dominated till September 2022, while the omicron variant was identified in November 2022. Interpretation: Wastewater-based surveillance, together with genomic sequencing provides valuable information for monitoring the community temporal trend of SARS-CoV-2. Funding: PATH, Bill & Melinda Gates Foundation, and Global Innovation Fund.

Building up a genomic surveillance platform for SARS-CoV-2 in the middle of a pandemic: a true North-South collaboration.

Next-generation sequencing technology has revolutionised pathogen surveillance over the last two decades. However, the benefits are not equitably distributed, with developing countries lagging far behind in acquiring the required technology and analytical capacity. Recent declines in the cost associated with sequencing-equipment and running consumables have created an opportunity for broader adoption. During the COVID-19 pandemic, rapid diagnostics development and DNA sequencing revolutionised the ability to diagnose and sequence SARS-CoV-2 rapidly. Socioeconomic inequalities substantially impact the ability to sequence SARS-CoV-2 strains and undermine a developing country's pandemic preparedness. Low- and middle-income countries face additional challenges in establishing, maintaining and expanding genomic surveillance. We present our experience of establishing a genomic surveillance system at the Aga Khan University, Karachi, Pakistan. Despite being at a leading health sciences research institute in the country, we encountered significant challenges. These were related to collecting standardised contextual data for SARS-CoV-2 samples, procuring sequencing reagents and consumables, and challenges with library preparation, sequencing and submission of high-quality SARS-CoV-2 genomes. Several technical roadblocks ensued during the implementation of the genomic surveillance framework, which were resolved in collaboration with our partners. High-quality genome sequences were then deposited on open-access platforms per the best practices. Subsequently, these efforts culminated in deploying Pakistan's first SARS-CoV-2 phyllo surveillance map as a Nextstrain build. Our experience offers lessons for the successful development of Genomic Surveillance Infrastructure in resource-limited settings struck by a pandemic.

Pediatric Critical Care-Associated Parental Traumatic Stress: Beyond the First Year.

OBJECTIVES: Perform a longitudinal analysis of parental traumatic stress up to 30 months after PICU discharge. DESIGN: Prospective observational cohort study. SETTING: Two tertiary care children's hospitals with mixed medical/surgical/cardiac PICUs. SUBJECTS: Parents of patients unexpectedly admitted to the PICU. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Two hundred sixty-five parents of 188 children were enrolled. Of the 195 parents who completed the 3-9-month assessments, 29 (14.8%) met posttraumatic stress disorder (PTSD) qualification on the PTSD Symptom Scale Interview for Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition. Multivariable analysis showed parents who met acute stress disorder (ASD) qualification (odds ratio [OR] 8.01; 95% CI 2.64-24.3), parents of children with Pediatric Overall Performance Category score of severe or coma at discharge (OR 5.21; 95% CI 1.65-16.4), parents who had concerns for their child's permanent injury (OR 1.82; 95% CI 1.36-2.43), and parents who reported increased knowledge of child illness during admission (OR 1.82; 95% CI 1.13-2.93) had increased odds of developing parental PTSD. Of the 175 parents (66%) who completed the 18-30-month assessments, 22 (12.5%) met PTSD qualification. Multivariable analysis showed parents who met ASD qualification (OR 4.19; 95% CI 1.12-15.7), parents who had a history of a family member or themselves being admitted to ICU (OR 6.51; 95% CI 1.43-29.6), and parents who had concerns of child's susceptibility to death post discharge (OR 1.58; 95% CI 1.19-2.09) had increased odds of developing parental PTSD. At 18-30 months post discharge, parents who met the PTSD qualification were more likely to report a decrease in household income following discharge (OR 9.23; 95% CI 1.71-49.9). CONCLUSIONS: Parental PTSD remains a significant morbidity of PICU admission for a subgroup of parents greater than 18 months post admission. Identifiable risk factors will inform the development of targeted interventions.

Acute Stress in Parents of Patients Admitted to the Pediatric Intensive Care Unit: A Two-Center Cross-Sectional Observational Study.

OBJECTIVE: To examine medical and psychosocial risk factors associated with the development of acute stress in parents of patients unexpectedly admitted to the PICU. DESIGN: Cross-sectional observational study. SETTING: Two tertiary care children's hospitals with mixed medical/surgical/cardiac PICU. PATIENTS: Parents of patients unexpectedly admitted to the PICU. INTERVENTION: None. MEASUREMENTS AND MAIN RESULTS: 265 parents of 188 children were enrolled of whom 49 parents (18%) met ASD qualification and 108 (41%) parents developed ASD symptoms as determined by the ASDS-5 scale. Risk factors making parents likely to meet ASD qualification include parents from area served by Penn State (p < 0.001), prior psychiatric illness (p < 0.01), and female gender (p < 0.05), while graduating college was protective (p < 0.05). In the multivariate analysis, parents from area served by Penn State (OR 3.00 (1.49-6.05) p < 0.01) and parents with prior psychiatric illness (OR 2.16 (1.03-4.52) p < 0.05) were associated with ASD qualification. Parents who graduated college or had prior medical problems were not significant.Risk factors making parents more likely to develop ASD symptoms (significant symptoms that do not meet ASD qualification) include patients with higher PRISM-III scores (p < 0.01), patients receiving cardiovascular support (p < 0.05), parents with a history of prior physical/sexual abuse (p < 0.01), parental involvement in the past with a major disaster/accident (p < 0.01), a family member admitted to an ICU in the past (p < 0.05) and preexisting parental psychiatric/medical disorders (p < 0.001). In a multivariate analysis, prior parental psychiatric disorder (OR 4.11 (1.80-6.42) p < 0.001), history of parental abuse (OR 3.11 (1.14-5.08) p < 0.05), and parental prior medical problem (OR 2.03 (1.01-3.05) p < 0.05) were associated with the development of ASD symptoms. However, PRISM-III score and prior involvement in major disaster were not significant. CONCLUSIONS: A combination of psychosocial parental risk factors and patient factors were associated with acute stress in parents. Further studies evaluating targeted hospital interventions towards parents most at-risk are needed.

Prevalence and risk factors of Severe Acute Respiratory Syndrome Coronavirus 2 infection in women and children in peri-urban communities in Pakistan: A prospective cohort study.

Background: Population-based seroepidemiological surveys provide accurate estimates of disease burden. We compare the COVID-19 prevalence estimates from two serial serological surveys and the associated risk factors among women and children in a peri-urban area of Karachi, Pakistan. Methods: The AMANHI-COVID-19 study enrolled women and children between November 2020 and March 2021. Blood samples were collected from March to June 2021 (baseline) and September to December 2021 (follow-up) to test for anti-SARS-CoV-2 antibodies using ROCHE Elecsys®. Participants were visited or called weekly during the study for recording symptoms of COVID-19. We report the proportion of participants with anti-SARS-CoV-2 antibodies and symptoms in each survey and describe infection risk factors using step-wise binomial regression analysis. Results: The adjusted seroprevalence among women was 45.3% (95% confidence interval (CI) = 42.6-47.9) and 82.3% (95% CI = 79.9-84.4) at baseline and follow-up survey, respectively. Among children, it was 18.4% (95% CI = 16.1-20.7) and 57.4% (95% CI = 54.3-60.3) at baseline and follow-up, respectively. Of the women who were previously seronegative, 404 (74.4%) tested positive at the follow-up survey, as did 365 (50.4%) previously seronegative children. There was a high proportion of asymptomatic infection. At baseline, being poorest and lacking access to safe drinking water lowered the risk of infection for both women (risk ratio (RR) = 0.8, 95% CI = 0.7-0.9 and RR = 1.2, 95% CI = 1.1-1.4, respectively) and children (RR = 0.7, 95% CI = 0.5-1.0 and RR = 1.4, 95% CI = 1.0-1.8, respectively). At the follow-up survey, the risk of infection was lower for underweight women and children (RR = 0.4, 95% CI = 0.3-0.7 and RR = 0.7, 95% CI = 0.5-0.8, respectively) and for women in the 30-39 years age group and children who were 24-36 months of age (RR = 0.6, 95% CI = 0.4-0.9 and RR = 0.7, 95% CI = 0.5-0.9, respectively). In both surveys, paternal employment was an important predictor of seropositivity among children (RR = 0.7, 95% CI = 0.6-0.9 and RR = 0.8, 95% CI = 0.7-1.0, respectively). Conclusion: There was a high rate of seroconversion among women and children. Infection was generally mild. Parental education plays an important role in protection of children from COVID-19.

A shorter post-exposure prophylaxis regimen for rabies, Pakistan.

OBJECTIVE: To assess the cost and effectiveness of the two-site, 1-week, intradermal rabies post-exposure prophylaxis regimen recommended by the World Health Organization (WHO) in 2018. METHODS: We compared the number of rabies vaccine and rabies immunoglobulin ampoules consumed at The Indus Hospital in Karachi, Pakistan and their cost before and after implementing WHO's 2018 recommendations. In 2017, patients with suspected rabies-infected bites were treated using the two-site, 4-week, Thai Red Cross regimen, which involved administering four rabies vaccine doses intradermally over 4 weeks and infiltrating immunoglobulin into serious wounds, with the remainder injected into a distant muscle. In 2018, patients received three vaccine doses intradermally over 1 week, with a calculated amount of immunoglobulin infiltrated into wounds only. Remaining immunoglobulin was saved for other patients. The survival of patients bitten by apparently rabid dogs was used as a surrogate for effectiveness. FINDINGS: Despite treating 8.5% more patients in 2018 (5370 patients) than 2017 (4948 patients), 140 fewer ampoules of rabies vaccine and 436 fewer ampoules of rabies immunoglobulin were used, at a cost saving of 4202 United States dollars. Of 56 patients bitten by apparently rabid dogs, 50 were alive at 6-month follow-up. The remaining six patients could not be contacted but did not present to any hospital with rabies. CONCLUSION: The new regimen was more economical than the two-site, 4-week regimen and was equally effective. This regimen is recommended for preventing rabies in countries where the disease is endemic and rabies vaccine and immunoglobulin are in short supply.

Severe congenital chorioretinitis caused by congenital lymphocytic choriomeningitis virus infection.

PURPOSE: To describe a case of congenital lymphocytic choriomeningitis virus (LCMV), a potentially severe and under-diagnosed etiology of congenital chorioretinitis. OBSERVATIONS: A 5-month old boy presented with esotropia. Examination revealed light perception vision in the right eye and normal fixation and following behavior in the left eye, and a 50PD esotropia with full versions. The external, anterior segment, and pupil exams were normal. Fundus examination demonstrated slightly pale optic nerves, numerous geographic atrophic and hyperpigmented lesions along the vascular arcades in both eyes that extended into the fovea of the right eye. Head computed tomography (CT) imaging demonstrated bilateral cerebral volume loss with consequential ex vacuo dilation of the lateral ventricles and scattered intracranial calcifications. Serum IgG and IgM titers for toxoplasmosis, rubella, cytomegalovirus (CMV), herpes simplex virus (HSV), syphilis, and zika were all negative. Upon communication of negative TORCHS titers, the mother recalled a severe rat infestation of their home during the pregnancy. A LCMV antibody titer was then ordered and which resulted positive for IgG antibodies. CONCLUSIONS AND IMPORTANCE: Congenital LCMV infection is an under-recognized cause of congenital chorioretinitis.

Serial population-based serosurveys for COVID-19 in two neighbourhoods of Karachi, Pakistan.

OBJECTIVE: To determine population-based estimates of coronavirus disease 2019 (COVID-19) in a densely populated urban community of Karachi, Pakistan. METHODS: Three cross-sectional surveys were conducted in April, June and August 2020 in low- and high-transmission neighbourhoods. Participants were selected at random to provide blood for Elecsys immunoassay for detection of anti-severe acute respiratory syndrome coronavirus-2 antibodies. A Bayesian regression model was used to estimate seroprevalence after adjusting for the demographic characteristics of each district. RESULTS: In total, 3005 participants from 623 households were enrolled in this study. In Phase 2, adjusted seroprevalence was estimated as 8.7% [95% confidence interval (CI) 5.1-13.1] and 15.1% (95% CI 9.4-21.7) in low- and high-transmission areas, respectively, compared with 0.2% (95% CI 0-0.7) and 0.4% (95% CI 0-1.3) in Phase 1. In Phase 3, it was 12.8% (95% CI 8.3-17.7) and 21.5% (95% CI 15.6-28) in low- and high-transmission areas, respectively. The conditional risk of infection was 0.31 (95% CI 0.16-0.47) and 0.41 (95% CI 0.28-0.52) in low- and high-transmission neighbourhoods, respectively, in Phase 2. Similar trends were observed in Phase 3. Only 5.4% of participants who tested positive for COVID-19 were symptomatic. The infection fatality rate was 1.66%, 0.37% and 0.26% in Phases 1, 2 and 3, respectively. CONCLUSION: Continuing rounds of seroprevalence studies will help to improve understanding of secular trends and the extent of infection during the course of the pandemic.

Low Frequency of Lymph Node Metastases in Patients in the United States With Early-stage Gastric Cancers That Fulfill Japanese Endoscopic Resection Criteria.

BACKGROUND & AIMS: In the West, early gastric cancer is increasingly managed with endoscopic resection (ER). This is, however, based on the assumption that the low prevalence and risk of lymph node metastases observed in Asian patients is applicable to patients in the United States. We sought to evaluate the frequency of and factors associated with metastasis of early gastric cancers to lymph nodes, and whether the Japanese ER criteria are applicable to patients in the US. METHODS: We performed a retrospective study of 176 patients (mean age 68.5 years; 59.1% male; 58.5% white) who underwent surgical resection with lymph node dissection of T1 and Tis gastric adenocarcinomas, staged by pathologists, at 7 tertiary care centers in the US from January 1, 1999, through December 31, 2016. The frequency of lymph node metastases and associated risk factors were determined. RESULTS: The mean size of gastric adenocarcinomas was 23.0 ± 16.6 mm-most were located in the lower-third of the stomach (67.0%), invading the submucosa (55.1%), and moderately differentiated (31.3%). Lymphovascular invasion was observed in 18.2% of lesions. Overall, 20.5% of patients had lymph node metastases. Submucosal invasion (odds ratio, 3.9; 95% CI, 1.4-10.7) and lymphovascular invasion (odds ratio, 4.6; 95% CI, 1.8-12.0) were independently associated with increased risk of metastasis to lymph nodes. The frequency of lymph node metastases among patients fulfilling standard and expanded Japanese criteria for ER were 0 and 7.5%, respectively. CONCLUSIONS: The frequency of lymph node metastases among patients with early gastric cancer in a US population is higher than that of published Asian series. However, early gastric cancer lesions that meet the Japanese standard criteria for ER are associated with negligible risk of metastasis to lymph nodes, so ER can be recommended for definitive therapy. Expanded criteria cancers appear to have a higher risk of metastasis to lymph nodes, so ER may be considered for select cases.

A New Method for Prediction of Dental Arch Perimeter.

PURPOSE: Dental arch length, width, and perimeter are considered to be important for the diagnosis and treatment of orthodontic cases. This study aimed to utilize dental arch width and length to create an equation for predicting dental arch perimeter. MATERIALS AND METHODS: Sixty-seven pairs of study models for patients with normal occlusion who received dental treatment were included in this study. Dental arch width at the level of the canines, first premolars, and first molars, in addition to dental arch length and perimeter, were measured using a digital vernier with 0.01mm accuracy. Data were subjected to step-wise regression analysis to determine the major predictors of arch perimeters and develop regression equations for both arches. The predicted arch perimeters were compared with the actual measured values using paired sample t-test. RESULTS: For both arches, the perimeter showed a direct, moderate to strong, highly significant correlation with the length and width measurements. Findings from step-wise regression analysis indicated that there was a strong correlation between arch perimeter and the inter-canine width and arch length, which explained 67.7% of the variation in arch perimeter in the maxillary arch. In the mandibular arch, inter-molar width, inter-canine width, and arch length explained 55.1% of the variation in the dental arch perimeter. The arch perimeter values predicted from the developed equations were not significantly different from the actual values that were measured. CONCLUSION: New regression equations based on dental arch width and length at the level of the premolars, molars, and canines were developed to predict dental arch perimeters for both the mandibular and maxillary arches.

Pretreatment Predictors of Response to PegIFN-RBV Therapy in Egyptian Patients with HCV Genotype 4.

BACKGROUND: Egypt has the highest prevalence of a difficult to treat chronic hepatitis C virus (HCV), genotype 4. Pretreatment factors could guide individualization of therapy which aids in treatment optimization and interleukin IL28B gene polymorphism has been shown to closely relate to HCV treatment response. Polymorphisms in genes encoding inhibitors of T-cell response, which have role in disease progression as Programmed Cell Death 1 (PD-1), and Cytotoxic T-Lymphocytes Antigen-4 (CTLA-4), could be candidate markers predicting treatment response. METHODS: This cohort study consisted of 200 chronic HCV genotype 4 infected patients treated with PegIFN α-2a and RBV in 2 hepatology centers. Genotyping of the polymorphisms in the IL28B gene region (rs12979860), PD1.3 (rs11568821) and CTLA-4 (rs231775) was performed on DNA collected from each patient using TaqMan® genotyping assay. Groups were classified according to response into sustained virological responders (SVR), or non-responders (NR). A multivariate logistic regression analysis was used to identify potential markers, host pretreatment clinical and viral predictive factors including viral load, insulin resistance, and alpha fetoprotein (AFP) related to treatment response. RESULTS: Our results showed that in a multivariate analyses IL28B C/C genotype was the most significant predictor for SVR (OR = 10.86; p<0.0001) followed by AFP (OR = 0.915; p = 0.001) then CTLA-4/G genotypes (OR = 1.948; p = 0.022). However, PD-1.3/A genotypes and platelets count were significantly related to response in univariate analysis only (OR = 1.973; p = 0.023; OR = 1.007; p = 0.009 respectively). CONCLUSION: IL28B SNP, AFP level, and CTLA-4 SNP could be used in conjunction to predict treatment response in HCV genotype 4 infected Egyptian patients.