Suspected reinfections of SARS-COV-2 in Khyber Pakhtunkhwa, Pakistan - analysis of province-wide testing database.
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ABSTRACT:
SUBMITTER: Ahmad HA
PROVIDER: S-EPMC8501516 | biostudies-literature | 2022 Feb
REPOSITORIES: biostudies-literature
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Suspected reinfections of SARS-COV-<sub>2</sub> in Khyber Pakhtunkhwa, Pakistan - analysis of province-wide testing database.
Ahmad Habab Ali HA Khan Haleema H Shahzad Muhammad M Haq Zia Ul ZU Harakeh Steve S Yousafzai Yasar Mehmood YM
The Journal of infection 20211009 2
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Project description:Among viral outbreaks, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is one of the deadliest ones, and it has triggered the global COVID-19 pandemic. In Pakistan, until 5th September 2020, a total of 6342 deaths have been reported, of which 1255 were from the Khyber Pakhtunkhwa (KPK) province. To understand the disease progression and control and also to produce vaccines and therapeutic efforts, whole genome sequence analysis is important. In the current investigation, we sequenced a single sample of SARS-CoV-2 genomes (accession no. MT879619) from a male suspect from Peshawar, the KPK capital city, during the first wave of infection. The local SARS-CoV-2 strain shows some unique characteristics compared to neighboring Iranian and Chinese isolates in phylogenetic tree and mutations. The circulating strains of SARS-CoV-2 represent an intermediate evolution from China and Iran. Furthermore, eight complete whole genome sequences, including the current Pakistani isolates which have been submitted to Global Initiative on Sharing All Influenza Data (GSAID), were also investigated for specific mutations and characters. Some novel mutations [NSP2 (D268del), NSP5 (N228K), and NS3 (F105S)] and specific characters have been detected in the coding regions, which may affect viral transmission, epidemiology, and disease severity. The computational modeling revealed that a majority of these mutations may have a stabilizing effect on the viral protein structure. In conclusion, the genome sequencing of local strains is important for better understanding the pathogenicity, immunogenicity, and epidemiology of causative agents.
| S-EPMC7944396 | biostudies-literature
Project description:The number of tuberculosis (TB) cases in Pakistan ranks fifth in the world. The National TB Control Program (NTP) has recently reported more than 462,920 TB patients in Khyber Pakhtunkhwa province, Pakistan from 2002 to 2017. This study aims to identify spatial and space-time clusters of TB cases in Khyber Pakhtunkhwa province Pakistan during 2015-2019 to design effective interventions. The spatial and space-time cluster analyses were conducted at the district-level based on the reported TB cases from January 2015 to April 2019 using space-time scan statistics (SaTScan). The most likely spatial and space-time clusters were detected in the northern rural part of the province. Additionally, two districts in the west were detected as the secondary space-time clusters. The most likely space-time cluster shows a tendency of spread toward the neighboring districts in the central part, and the most likely spatial cluster shows a tendency of spread toward the neighboring districts in the south. Most of the space-time clusters were detected at the start of the study period 2015-2016. The potential TB clusters in the remote rural part might be associated to the dry-cool climate and lack of access to the healthcare centers in the remote areas.
| S-EPMC7068355 | biostudies-literature
Project description:This study primarily aimed to identify the causative species of cutaneous leishmaniasis (CL) in the Khyber Pakhtunkhwa Province of Pakistan and to distinguish any species-specific variation in clinical manifestation of CL. Diagnostic performance of different techniques for identifying CL was assessed. Isolates of Leishmania spp. were detected by in vitro culture, polymerase chain reaction (PCR) on DNA extracted from dried filter papers and microscopic examination of direct lesion smears from patients visiting three major primary care hospitals in Peshawar. A total of 125 CL patients were evaluated. Many acquired the disease from Peshawar and the neighboring tribal area of Khyber Agency. Military personnel acquired CL while deployed in north and south Waziristan. Leishmania tropica was identified as the predominant infecting organism in this study (89.2%) followed by Leishmania major (6.8%) and, unexpectedly, Leishmania infantum (4.1%). These were the first reported cases of CL caused by L. infantum in Pakistan. PCR diagnosis targeting kinetoplast DNA was the most sensitive diagnostic method, identifying 86.5% of all samples found positive by any other method. Other methods were as follows: ribosomal DNA PCR (78.4%), internal transcribed spacer 2 region PCR (70.3%), culture (67.1%), and microscopy (60.5%). Clinical examination reported 14 atypical forms of CL. Atypical lesions were not significantly associated with the infecting Leishmania species, nor with "dry" or "wet" appearance of lesions. Findings from this study provide a platform for species typing of CL patients in Pakistan, utilizing a combination of in vitro culture and molecular diagnostics. Moreover, the clinical diversity described herein can benefit clinicians in devising differential diagnosis of the disease.
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Project description:BackgroundThis study aimed to assess the extent of knowledge and understanding of rabies disease in rural and urban communities of Pakistan. It also identified malpractices after suspected dog bite that might pose a risk for humans contracting rabies.MethodsA cross-sectional study was conducted (n = 1466) on people having different age groups and educational levels in four different geographic regions of Punjab and Khyber Pakhtunkhwa provinces in Pakistan. Knowledge, attitude, and practices of people were assessed using a structured questionnaire. We used a bivariate and multivariate analysis to study the association between rabies related mortalities in near or extended family members and different risk behaviors.ResultsOur results demonstrate that the majority of the juvenile population (less than 18 years of age) were not aware of the clinical signs of rabies in animals. 75% of the total respondents were not vaccinated against rabies, 60% did not seek a doctor's advice after a suspected animal bite, and 55% had inadequate health care facilities for rabies patients in local hospitals. Respondents that had pets at home had not vaccinated (38%; p < 0.05; odds ratio 1.58) themselves against rabies due to lack of knowledge and awareness of pre-exposure prophylaxis for rabies (51%; p < 0.05; odds ratio 1.25). They also tend to not visit doctor after suspected bite (52%; p < 0.05; odds ratio 1.97), which may had resulted in more deaths (65%; p < 0.05; odds ratio 1.73) of someone in their near or extended family due to rabies.ConclusionsLack of knowledge about the nature of rabies disease and prophylaxis has contributed to increase of rabies related deaths. Inadequate health care facilities and poor attitude of not seeking medical attention after suspected dog bite are the major reasons of rabies related deaths. These findings could help in devising a targeted management strategy and awareness program to control and reduce the incidence of human rabies related deaths in Pakistan.
| S-EPMC7448460 | biostudies-literature
Project description:AbstractSwat, a lush green valley of 1.3 million persons, remained under militant insurgency from 2007 to 2009, which damaged the health infrastructure. An outbreak of dengue fever (DF) was declared in the valley in 2013. To investigate this outbreak, we established active surveillance of national hospitals and private clinics, reviewed available clinical and laboratory records, and conducted entomological survey. From August to November 2013, 16,000 suspected patients with acute febrile illness were presented to health facilities. Among those, 9,036 were confirmed positive for DF by clinical manifestation and presence of nonstructural protein 1-soluble antigen. Of 9,036 patients, majority were men and aged 21-40. The epidemic peaked in September 2013 (N = 6,487). The attack rate was 7.18/1,000 populations. Among the confirmed case-patients, 36 deaths were reported, and proportion of mortality was 0.4%. Each year, increase in age was significantly associated with risk of complication due to DF leading to death (P < 0.001).
| S-EPMC5392639 | biostudies-literature
Project description:Cutaneous leishmaniasis (CL) is a zoonotic infection caused by obligate intracellular protozoa of the genus Leishmania. This study aimed to investigate CL in Khyber Pakhtunkhwa, Pakistan and to estimate the risk of epidemics. Clinico-epidemiological data of 3188 CL patients were collected from health facilities in 2021. Risk factors were analyzed using the chi-square test. ArcGIS V.10.7.1 was applied for spatial analysis. The association between CL occurrence and climatic variables was examined by Bayesian geostatistical analysis. The clinical data revealed males or individuals younger than 20 years old were more affected. Most patients presented with a single lesion, and the face was the most attacked body part. CL was prevalent in the southern region in winter. A proportional symbol map, a choropleth map, and a digital elevation model map were built to show the distribution of CL. Focal transmission was predicted by inverse distance weighting interpolation. Cluster and outlier analysis identified clusters in Bannu, Dir Lower, and Mardan, and hotspot analysis suggested Bannu as a high-risk foci. Bayesian geostatistical analysis indicated that increasing precipitation and temperature as well as low altitudes were associated with CL infection. The study has provided important information for public health sectors to develop intervention strategies for future CL epidemics.
| S-EPMC9962270 | biostudies-literature
Project description:Tuberculosis (TB), caused by Mycobacterium tuberculosis, is endemic in Pakistan. Resistance to both firstline rifampicin and isoniazid drugs (multidrug-resistant TB; MDR-TB) is hampering disease control. Rifampicin resistance is attributed to rpoB gene mutations, but rpoA and rpoC loci may also be involved. To characterise underlying rifampicin resistance mutations in the TB endemic province of Khyber Pakhtunkhwa, we sequenced 51 M. tuberculosis isolates collected between 2016 and 2019; predominantly, MDR-TB (n = 44; 86.3%) and lineage 3 (n = 30, 58.8%) strains. We found that known mutations in rpoB (e.g. S405L), katG (e.g. S315T), or inhA promoter loci explain the MDR-TB. There were 24 unique mutations in rpoA, rpoB, and rpoC genes, including four previously unreported. Five instances of within-host resistance diversity were observed, where two were a mixture of MDR-TB strains containing mutations in rpoB, katG, and the inhA promoter region, as well as compensatory mutations in rpoC. Heteroresistance was observed in two isolates with a single lineage. Such complexity may reflect the high transmission nature of the Khyber Pakhtunkhwa setting. Our study reinforces the need to apply sequencing approaches to capture the full-extent of MDR-TB genetic diversity, to understand transmission, and to inform TB control activities in the highly endemic setting of Pakistan.
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Project description:In Pakistan, the degradation of drinking water quality is exacerbated by the increasing population size and rapid industrialization. Contaminated water serves as the predominant source of numerous diseases, including diarrhea, gastroenteritis, and typhoid. This article explores the evolution of waterborne diseases across 21 districts of the Khyber Pakhtunkhwa province in Pakistan by monitoring changes in the clustering solutions. The data employed in this study were sourced from 21 districts of KP by the Director-General Health Services. Cluster analysis was utilized to uncover patterns in waterborne disease incidence, while principal component analysis was employed to reveal underlying patterns and reduce dimensionality. Additionally, the MONItoring Clusters (MONIC) framework was applied for change detection, facilitating the identification of significant shifts in disease patterns over time and aiding in the understanding of temporal dynamics. Our analysis indicates that two clusters survived consistently over time, while other clusters exhibited inconsistency. Profiling of the surviving clusters (C12 → C24 → C32 → C43) suggests a gradual increase in cases of bloody diarrhea in the Swat Valley, Hangu, Karak, and Lakki Marwat regions. Similarly, profiling of the surviving clusters (⊙→ C22 → C34 → C44) suggests an increase in the acute watery diarrhea (non-cholera) and typhoid fever in the regions of Peshawar, Nowshera, and Swabi. The findings of this study hold significant importance as they pinpoint the most vulnerable regions for various waterborne diseases. These insights offer valuable guidance to policymakers and health officials, empowering them to implement effective measures for controlling waterborne diseases in the respective regions of Khyber Pakhtunkhwa, Pakistan.
| S-EPMC11292715 | biostudies-literature
Project description:BackgroundAccess of all people to the healthcare they need, without financial hardship is the goal of Universal Health Coverage (UHC). As UHC initiatives expand, assessing the needs of vulnerable populations can reveal gaps in the system which may be covered by relevant policies. In this study we (i) identify the met and unmet primary healthcare needs of the poorest population of Khyber Pakhtunkhwa province (KP), Pakistan, and (ii) explore why the gaps exist.MethodsWe used Leveque's Framework of Patient-centred Access to Healthcare to examine unmet primary healthcare (PHC) needs and their underlying causes for the poorest population in four districts of Khyber Pakhtunkhwa province, Pakistan. Using a triangulation mixed methods design, we analysed data from a quantitative household survey of744 households, 17 focus group discussions with household members and, 11 interviews with healthcare providers.ResultsOur results show that indicate that despite service utilization, PHC needs were not met, primarily due to prohibitively high costs at each stage of access. Furthermore, gaps in outreach and information (approachability), and varying availability of medicines and diagnostics at facilities (appropriateness) the supply side as well as difficulties in navigating the system (inability to perceive) and adhering to prescriptions (inability to engage) on the demand side, also led to unmet PHC needs. Going beyond utilization, our findings highlight that engagement with care is an important determinant of met needs for vulnerable populations.ConclusionSocial health protection policies can contribute to advancing UHC for primary care. However, in our setting, enhancing communication and outreach, addressing gender and age disparities, and improving quality of care and health infrastructure are necessary to fully meet the needs of the poorest populations.
| S-EPMC11421121 | biostudies-literature
Project description:Ticks and tick-borne diseases are considered a major challenge for human and animal health in tropical, sub-tropical, and temperate regions of the world. However, only scarce information is available on the characterization of tick species infesting dogs in Pakistan. In this study, we present a comprehensive report on the epidemiological and phylogenetic aspects of ticks infesting dogs in Pakistan using the mitochondrial markers i.e. Cytochrome c oxidase subunit 1 (cox1) and 16S ribosomal RNA (16S rRNA) nucleotide sequences. A total of 300 dogs were examined and 1150 ixodid ticks were collected across central Khyber Pakhtunkhwa, Pakistan. The morpho-molecular characterization of hard ticks revealed the presence of two ixodid tick genera on dogs, i.e., Hyalomma and Rhipicephalus, including six tick species viz. Hyalomma dromedarii (15.9%), Hyalomma excavatum (3%), Rhipicephalus sanguineus s.l. (41.3%), Rhipicephalus turanicus s.s. (28.7%), Rhipicephalus haemaphysaloides (10.2%), and Rhipicephalus microplus (2%). The total prevalence of tick infestation in dogs was 61%. The district with the highest tick prevalence rate in dogs was Mardan (14.7%), followed by Peshawar (13%), Swabi (12%), Charsadda (11%), and Malakand (10.3%), respectively. Risk factors analysis indicated that some demographic and host management-associated factors such as host age, breed, exposure to acaricides treatment, and previous tick infestation history were associated with a higher risk of tick infestation on dogs. This is the first molecular report confirming the infestation of Hyalomma and Rhipicephalus tick species in the dog population from the study area. The present study also reported a new tick-host association between Hy. excavatum, Hy. dromedarii, and dogs. Phylogenetic analysis revealed that cox1 partial nucleotide sequences of Hy. excavatum in our dataset were 100% identical to similar tick specimens identified in Turkey, and those of Hy. dromedarii were identical to tick specimens from Iran. Whereas, Rh. haemaphysaloides and Rh. microplus'&nbsp;cox1 partial nucleotide sequences were identical to sequences previously published from Pakistan. Rhipicephalus turanicus s.s. 's cox1 isolates from the present study were 99.8-100% identical to Pakistani-reported isolates, and those of Rh. sanguineus s.l. were 100% identical to Chinese specimens. Results on the genetic characterization of ticks were further confirmed by 16S rRNA partial nucleotide sequences analysis, which revealed 100% identity between the tick isolates of this study and those of Hy. excavatum reported from Turkey; Hy. dromedarii specimens reported from Senegal; Rh. haemaphysaloides, Rh. microplus, and Rh. turanicus s.s., previously published from Pakistan, and Rh. sanguineus&nbsp;s.l., published from China. Furthermore, phylogenetic analysis showed that the Rh. sanguineus s.l. isolates of this study clustered with specimens of the tropical lineage with 7.7-10% nucleotide divergence from the specimens of the temperate lineage. Further molecular works need to be performed throughout Pakistan to present a more detailed map of tick distribution with information about dog host associations, biological characteristics, and pathogen competence.
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