Mortality Associated with Priority Diseases in Flood-Affected Areas Using District Health Information System (DHIS2) During September-December 2022: Pakistan Experience.

OBJECTIVES: To quantify the burden of communicable diseases and characterize the most reported infections during public health emergency of floods in Pakistan. METHODS: The study's design is a descriptive trend analysis. The study utilized the disease data reported to District Health Information System (DHIS2) for the 12 most frequently reported priority diseases under the Integrated Disease Surveillance and Response (IDSR) system in Pakistan. RESULTS: In total, there were 1,532,963 suspected cases during August to December 2022 in flood-affected districts (n = 75) across Pakistan; Sindh Province reported the highest number of cases (n = 692,673) from 23 districts, followed by Khyber Pakhtunkhwa (KP) (n = 568,682) from 17 districts, Balochistan (n = 167,215) from 32 districts, and Punjab (n = 104,393) from 3 districts. High positivity was reported for malaria (79,622/201,901; 39.4%), followed by acute diarrhea (non-cholera) (23/62; 37.1%), hepatitis A and E (47/252; 18.7%), and dengue (603/3245; 18.6%). The crude mortality rate was 11.9 per 10 000 population (1824/1,532,963 [deaths/cases]). CONCLUSION: The study identified acute respiratory infection, acute diarrhea, malaria, and skin diseases as the most prevalent diseases. This suggests that preparedness efforts and interventions targeting these diseases should be prioritized in future flood response plans. The study highlights the importance of strengthening the IDSR as a Disease Early Warning System through the implementation of the DHIS2.

Estimation of seasonal influenza disease burden using sentinel site data in Pakistan 2017-2019: A cross-sectional study.

Background: The influenza A(H1N1)pdm09 pandemic highlighted the need for reliable disease burden estimation from low- and middle-income countries like Pakistan. We designed retrospective age-stratified estimation of influenza-related severe acute respiratory infections (SARIs) incidence in Islamabad Pakistan 2017-2019. Materials and Methods: The catchment area was mapped on SARI data from one designated influenza sentinel site and other healthcare facilities in the Islamabad region. The incidence rate was calculated as per 100,000 for each age group with 95% confidence interval. Results: The catchment population for the sentinel site was 0.7 million against the total denominator of 1.015 million, and incidence rates were adjusted. During January 2017 to December 2019, among 13,905 hospitalizations, 6715 (48%) patients were enrolled; 1208 of these (18%) were positive for influenza. During 2017, influenza A/H3 dominated with 52% detections followed by A(H1N1)pdm09 (35%) and influenza B (13%). Furthermore, elderly 65+ years age group had highest hospitalizations and influenza positive. The incidence rates of all cause respiratory and influenza-related SARI were highest among children >5 years; highest incidence was found in 0 to 11 month/year group with 424/100,000 cases and lowest in 5-15 years 56/100,000. The estimated average annual influenza-associated hospitalization percentage was 29.3% during the study period. Conclusion: Influenza accounts for a significant proportion of respiratory morbidity and hospitalization. These estimates would enable governments for evidence-based decisions and priority allocation of health resources. It is necessary to test for other respiratory pathogens for more clear disease burden estimation.

Breakthrough cases of Omicron and Delta variants of SARS-CoV-2 during the fifth wave in Pakistan.

COVID-19 pandemic has severely affected Pakistan with 1,557,134 cases as of August 4, 2022. However, the data regarding breakthrough infections in Pakistan is scant. Hence, the objective was to analyze SARS-CoV-2 breakthrough infections with respect to vaccines and variants during the fifth wave in Pakistan. Therefore, the Department of Virology (NIH, Pakistan) genotyped 2,467 randomly selected individuals between November 2021 and February 2022 using the SNPsig® SARS-CoV-2 (EscapePLEX) kit (PrimerDesign, UK). P681R and K417N mutations were used to distinguish delta and omicron. Data on the patient's age, gender, date of collection, variant, and vaccination status were analyzed using Statistical Package for Social Sciences (SPSS) software. Among 2,467 genotyped samples, Omicron was detected in 58.6% (n = 1445), Delta in 40.4% (n = 998) and undetermined/wildtype variant in 24 samples. The vaccination status of omicron-positive patients showed (49.7%; n = 718/1445) and Delta-positive patients (39.67%; n = 396/998) to be fully vaccinated. Of note, a high percentage 85% of breakthrough cases (n = 947) were identified among fully vaccinated individuals (n = 1114). Among them, 85.9% (n = 617/718) belonged to omicron and 83.3% (n = 330/396) to delta. Moreover, 76.7% (n = 855) of vaccinated individuals (n = 1114) received Sinopharm (n = 432) and Sinovac (n = 423) vaccines. The majority of breakthrough subjects who contracted Omicron were vaccinated with Sinopharm (93.0%, n = 256) and delta with Cansino (100%, n = 44). Individuals vaccinated with Sinovac showed the most frequent breakthrough cases for both Omicron and Delta variant between the 4th and 6th months (n = 278) after primary vaccination as compared to the 7th to 9th months (n = 24) category. While in case of Sinopharm, maximum breakthrough cases occurred between 7th to 9th months (n = 234) as compared to the 4th to 6th months (n = 120) after primary vaccination. Omicron and Delta breakthrough cases in men (n = 364 and 193) are more frequently seen than women (n = 253 and 138) respectively and breakthrough majority cases (n = 392) occurred in individuals aged 18-33 years. Breakthrough cases limiting monitoring in Pakistan impose a substantial constraint on policymakers' ability to take timely effective decisions. Since the current study consists of only a 2,467-genotyped sample, comprehensive data should be analyzed.

Geographic accessibility to childhood tuberculosis care in Pakistan.

BACKGROUND: Tuberculosis (TB) in children is difficult to detect and often needs specialists to diagnose; the health system is supposed to refer to higher level of health care when diagnosis is not settled in a sick child. In Pakistan, the primary health care level can usually not diagnose childhood TB and will refer to a paediatricians working at a secondary or tertiary care hospital. We aimed to determine the health services access to child TB services in Pakistan. OBJECTIVE: We aimed to determine the geographical access to child TB services in Pakistan. METHOD: We used geospatial analysis to calculate the distance from the nearest public health facility to settlements, using qGIS, as well as population living within the World Health Organization's (WHO) recommended 5-km distance. RESULT: At primary health care level, 14.1% of facilities report child TB cases to national tuberculosis program and 74% of the population had geographical access to general primary health care within 5-km radius. To secondary- and tertiary-level health care, 33.5% of the population had geographical access within 5-km radius. The average distance from a facility for diagnosis of childhood TB was 26.3 km from all settlement to the nearest child TB sites. The population of one province (Balochistan) had longer distances to health care services. CONCLUSION: With fairly good coverage of primary health care but lower coverage of specialist care for childhood TB, the health system depends heavily on a good referral system from the communities.

Diagnosis of childhood tuberculosis in Pakistan: Are national guidelines used by private healthcare providers?

BACKGROUND: The National Tuberculosis Control Program (NTP) in Pakistan developed, with the Pakistan Paediatric Association, a pediatric scoring chart to aid diagnosis of childhood tuberculosis (TB). Our study compared the diagnostic practice of private healthcare providers in Pakistan with the NTP guidelines. METHODS: A cross-sectional study comparing diagnosis of TB in children <15 years by Non-NTP private providers with the NTP's pediatric scoring chart. A generalized linear model was used to determine the difference in adherence by Non-NTP private providers to the NTP guidelines for childhood TB diagnosis by associated factors. RESULTS: A total of 5193 (79.7% of presumptive childhood TB cases identified in the selected districts during the study) children were diagnosed with TB by Non-NTP private providers. A strong clinical suspicion of TB was present in 17.3%, and chest x-ray was suggestive of TB in 34.3%. The Kappa score between Non-NTP private providers and the NTP guidelines for diagnosing TB was 0.152. Only 47.8% of cases were diagnosed in line with the NTP guidelines. Children <5 years old with a history of TB contact had a higher chance of being diagnosed according to the NTP guidelines. CONCLUSION: This study indicates a low adherence of NTP guidelines for diagnosing childhood TB by private providers in Pakistan.

Epidemiology of Influenza among patients with influenza-like illness and severe acute respiratory illness in Pakistan: A 10-year surveillance study 2008-17.

In Pakistan, the burden of influenza was largely unknown, as no formal surveillance system was in place. In 2008, an influenza surveillance system was set up in eight sentinel sites. This study describes the epidemiology of influenza virus using a 10-year surveillance data from 2008 to 2017. Nasopharyngeal/throat swabs were collected from patients with influenza-like illness (ILI) and severe acute respiratory illness (SARI) along with relevant epidemiological information. The samples were tested using real-time reverse transcriptase-polymerase chain reaction for the detection and characterization of influenza viruses. A total of 17 209 samples were tested for influenza, out of which 3552 (20.6%) were positive; 2151/11 239 (19.1%) were patients with ILI, whereas 1401/5970 (23.5%) were patients with SARI. Influenza A/H1N1pdm09 was the predominant strain with 40.6% (n = 1442) followed by influenza B (936, 26.4%). Influenza A/H1N1pdm09 was predominant among the children (5-14 years) and adults (15-64 years). Influenza B strain was predominantly found in the elderly age group (≥ 65 years) accounting for 48% of cases followed by children (2-4 years) accounting for 37% of cases. This 10-year surveillance data provides evidence of influenza activity in the country throughout the year with seasonal winter peaks. The results could be used to strengthen the epidemic preparedness and response plan.

Evolutionary analysis of influenza A(H1N1)pdm09 during the pandemic and post-pandemic period in Pakistan.

BACKGROUND: The first case of influenza A(H1N1)pdm09 was detected in Pakistan in June 2009. Since then, it has continued to circulate causing considerable morbidity and mortality. The purpose of this study was to evaluate the evolutionary changes in influenza A(H1N1)pdm09 viruses from 2009 to 2016 and their relevance to the current vaccine viruses. METHODS: Respiratory specimens (throat or nasopharyngeal swabs) were collected from patients with influenza-like illness and severe acute respiratory illness. Samples were processed following the protocol of the US Centers for Disease Control and Prevention. Sequencing and phylogenetic analysis of Haemagglutinin and neuraminidase genes were carried out on representative isolates of Pakistan viruses. RESULTS: Between January 2009 and February 2016, out of 16,024 samples analysed, 1950 (12%) were positive for influenza A. During the pandemic period (2009-2010), influenza A(H1N1)pdm09 was the dominant strain with 366 out of 808 (45%) total influenza positive cases. In the post-pandemic period (2011-2016), a total of 1078 out of 1911 (56%) cases were positive for influenza A(H1N1)pdm09 with co-circulation of different influenza A subtypes. The Pakistan A(H1N1)pdm09 viruses belonged to two genetic clades: clade 7 in the pandemic period, and clade 7 (2011) and clade 6B (2015) in the post-pandemic period. Sequence analysis of genes coding for surface glycoprotein's of Haemagglutinin and neuraminidase had a high degree of sequence similarity with corresponding genes of regional viruses circulating in South-East Asia. CONCLUSION: Influenza A(H1N1)pdm09 viruses from Pakistan clustered into two genetic clades, with co-circulation of some variants. Key substitutions in the receptor binding site and a few changes indicative of virulence were also detected in the post-pandemic strains. Continued monitoring of the viruses is essential for early identification of potential variants of high virulence and their relevance to current vaccine strains.

Molecular characterization of circulating respiratory syncytial virus genotypes in Pakistani children, 2010-2013.

BACKGROUND: Data on the viral etiology of acute lower respiratory infections are scarce in Pakistan. Human respiratory syncytial virus (RSV) is an important cause of morbidity in children but no effective vaccine or antiviral therapy is currently available. As vaccines are expected to become available in the future, it is important to understand the epidemiology of locally prevalent RSV subtypes. This study aimed to define the molecular epidemiology of RSV (A and B) genotypes in Pakistani children under 5 years. METHODS: World Health Organization case definitions for influenza-like illness (ILI) and severe acute respiratory illness (SARI) were used for case selection. Children under 5 years who presented with ILI or SARI at tertiary care hospitals from all provinces/regions, including the eight influenza sentinel sites, during October-April each year between 2010 and 2013 were enrolled. Demographic and clinical data of the children were recorded and nasopharyngeal/throat swabs taken for analysis. All samples were tested for RSV A and B using real-time polymerase chain reaction for non-influenza respiratory viruses. Specific oligonucleotide primers for RSV A and B were used for subtyping and sequencing of the G protein, followed by phylogenetic analysis. RESULTS: A total of 1941 samples were included. RSV was detected in 472 (24%) children, with RSV A detected in 367 (78%) and RSV B in 105 (22%). The G protein of all RSV A strains clustered in the NA1/GA2 genotype while RSV B strains carried the signature 60 nucleotide duplication and were assigned to three BA genotypes: BA-9, BA-10 and the new BA-13 genotype. CONCLUSIONS: This study highlights the importance of RSV as a viral etiologic agent of acute respiratory infections in children in Pakistan, and the diversity of RSV viruses. Continued molecular surveillance for early detection of prevalent and newly emerging genotypes is needed to understand the epidemiology of RSV infections in Pakistan.

Seasonality of influenza and its association with meteorological parameters in two cities of Pakistan: A time series analysis.

BACKGROUND: Influenza is known to have a specific pattern of seasonality the reasons for which are yet to be fully ascertained. Temperate zones show influenza epidemic during the winter months. The tropical and subtropical regions show more diverse influenza outbreak patterns. This study explores the seasonality of influenza activity and predicts influenza peak based on historical surveillance time series data in Islamabad and Multan, Pakistan. METHODS: This is a descriptive study of routinely collected monthly influenza sentinel surveillance data and meteorological data from 2012-16 in two sentinel sites of Pakistan: Islamabad (North) and Multan (Central). RESULTS: Mean number of cases of influenza and levels of precipitation were higher in Islamabad compared to Multan. Mean temperature and humidity levels were similar in both the cities. The number of influenza cases rose with decrease in precipitation and temperature in Islamabad during 2012-16, although the same cannot be said about humidity. The relationship between meteorological parameters and influenza incidence was not pronounced in case of Multan. The forecasted values in both the cities showed a significant peak during the month of January. CONCLUSION: The influenza surveillance system gave a better understanding of the disease trend and could accurately forecast influenza activity in Pakistan.

Molecular analysis of group A rotaviruses detected in hospitalized children from Rawalpindi, Pakistan during 2014.

As a part of strategy to control diarrheal diseases, World Health Organization (WHO) recommends to include rotavirus vaccines in national immunization programs. Sentinel surveillance networks have been established to monitor rotavirus disease burden and genotype distribution in both pre and post vaccine era in many countries. Unfortunately, due to lack of proper surveillance programs, data on rotavirus disease burden and genotype distribution from Pakistan is scarce. We investigated 502 stool samples from children (<5years) hospitalized due to gastroenteritis in Rawalpindi, Pakistan during 2014 for the presence of group A rotavirus (RVA) and its genotypic diversity. Among 147 ELISA positive samples, 131 were successfully genotyped for RVA. Common G types detected were G1 (23.6%), followed by G3 (22.9%), G12 (19.8%), G2 (19.08%) and G9 (9.9%). The most common P-type was P[8] (41.2%), followed by P[6] (29%) and P[4] (28.24%). G3P[8] (17.55%) was the most prevalent genotype combination followed by G12P[6] (16.7%), G2P[4] (15.2%) and G1P[8] (14.5%). Mixed infection of rotavirus G-P types was also observed in 6% of samples. Phylogenetic analysis of VP7 and VP4 genes of Pakistani strains showed that G1, G2, G9 and P[4], P[6], P[8] were closely related to strains circulating worldwide as well as previously reported strains from Pakistan. Pakistani G12P[8] strains NIH-BBH-3981 and NIH-BBH-4003 belonged to lineage 3 cluster 3a along with strains from USA and Italy whereas G12P[6] strains NIH-BBH-3978, NIH-BBH-4052 and NIH-BBH-4444 were closely related to strains from Italy, Thailand, United Kingdom and with previously reported G12 strains from Pakistan within lineage 3 cluster 3b. This pre-vaccination data supports the need for RVA vaccine inclusion at our national level and will be helpful in assessing the effect of vaccination on RVA genotype diversity due to vaccine selection pressure once post-vaccination data becomes available.

"Preliminary Seroepidemiological survey of dengue infections in Pakistan, 2009-2014".

BACKGROUND: Dengue virus is the causative agent of dengue fever, a vector borne infection which causes self-limiting to life threatening disease in humans. A sero-epidemiological study was conducted to understand the current epidemiology of dengue virus in Pakistan which is now known as a dengue endemic country after its first reported outbreak in 1994. METHODS: To investigate the prevalence of dengue virus in Pakistan during 2009-2014, a total of 9,493 blood samples were screened for the detection of anti-dengue IgM antibodies using ELISA. Clinical and demographic features available with hospital records were reviewed to ascertain mortalities related to dengue hemorrhagic shock syndrome. RESULTS: Out of 9,493 samples tested, 37% (3,504) were found positive for anti-dengue IgM antibodies. Of the seropositive cases, 73.6% (2,578/3,504) were male and 26.4% (926/3,504) were female. The highest number (382/929; 41.1%) of sero-positive cases was observed among the individuals of age group 31-40 years. The highest number of symptomatic cases was reported in October (46%; 4,400/9,493), and the highest number of sero-positive cases among symptomatic cases was observed in November (45.7%; 806/1,764). Mean annual patient incidence (MAPI) during 2009-2014 in Pakistan remained 0.30 with the highest annual patient incidence (11.03) found in Islamabad. According to the available medical case record, 472 dengue related deaths were reported during 2009-2014. CONCLUSION: The data from earlier reports in Pakistan described the dengue virus incidence from limited areas of the country. Our findings are important considering the testing of clinical samples at a larger scale covering patients of vast geographical regions and warrants timely implementation of dengue vector surveillance and control programs. TRIAL REGISTRATION NUMBER: It is an epidemiological research study, so trial registration is not required.

Molecular detection and characterization of respiratory syncytial virus B genotypes circulating in Pakistani children.

Respiratory syncytial virus (RSV) is the major cause of acute lower respiratory tract infections in young children, but very little is known about its epidemiology and circulating genotypes in Pakistan. This study analyzed the epidemiological and molecular characteristics of RSV B genotypes in Pakistani children below 5years with acute respiratory tract infections (ARIs) during three consecutive winter seasons from 2010 to 2013. A total of 1941 samples were analyzed for RSV infection by real time PCR and 24% (472/1941) samples were found positive out of which 22.3% (105/472) were sub-typed as RSV-B. The frequency of outpatient cases was higher (62.5%; 295/472) as compared to hospitalized patients (37.5%; 177/472). Patient ages ranged from 2month to 5years with a mean age of 1.48±1.2 (years) and a median age of 1year. Children below one year made up the highest percentage of enrolled subjects and male to female ratio of RSVB positive cases was nearly equivalent (1:1.1). The most common clinical symptoms were cough (96%), fever (80%) and sore throat (50%). All Pak RSVB strains ascribed to the BA genotype showing 91.9-97.1% and 86.2-95.3% homology at the nucleotide and amino acid levels respectively in comparison to BA prototype strain. On phylogenetic analysis, three genotypes of Pakistan RSV B viruses were observed; BA-9 and BA-10 which have been reported previously from other regions, and a third novel genotype assigned as BA-13 which formed a distinct cluster with protein length of 319 AA and showed 9-11 unique AA substitutions. All the RSV B isolates had two potential N-glycosylation sites in HVR2 of G protein and with heavy O-glycosylation of serine and threonine residues (G scores of 0.5-0.7). This study highlights the diversity of RSVB viruses and the significance of RSV as a dominant viral etiologic agent of pediatric ARI. It also emphasizes the need for continued molecular surveillance for early detection of prevalent and newly emerging genotypes to understand epidemiology of RSV infections in various regions of Pakistan.

Respiratory syncytial virus and influenza are the key viral pathogens in children <2 years hospitalized with bronchiolitis and pneumonia in Islamabad Pakistan.

Pneumonia remains a leading cause of morbidity and mortality in developing countries. Comprehensive surveillance data are needed to review the prevention and control strategies. We conducted active surveillance of acute lower respiratory infections among children aged <2 years hospitalized at two hospitals of Islamabad, Pakistan. Viral etiology was determined using real-time PCR on respiratory specimens collected during March 2011-April 2012. The overall mean age was 7.83 ± 5.25 months while no statistical difference between age or sex distribution of patients with positive and negative viral etiology (p > 0.05). The average weight of the study group was 6.1 ± 2.25 kg. ≥1 viral pathogens were detected in 75% cases. Major respiratory viruses included RSV-A: 44%, RSV-B: 23%, Influenza-A: 24.5%, Influenza-B: 7%, Adenovirus: 8.4% and HmPV: 5.2%. A single, dual or multiple viral pathogens were detected in 43%, 27% and 5.2% patients respectively. Common symptoms were cough (95%), apnoea (84%), fever (78%), wheeze (64.5%), nasal congestion (55%) and rhinorrhea (48%). Among the RSV positive cases, 2-6 months age group had highest detection rate for RSV-A (30%, n = 21/69) and RSV-B (20%, n = 14/69) while patients infected with Influenza-A were in 2.1-6 months age group (61%, 23/38). Statistically significant difference was observed between RSV-positive and negative cases for nutrition status (p = 0.001), cigarette/wood smoke exposure (p = 0.001) and concomitant clinical findings. Most patients had successful outcome on combination therapy with bronchodilators, inhaled steroids and antibiotics. Our findings underscore high burden of ALRI in Pakistan. Interventions targeting viral pathogens coupled with improved diagnostic approaches are critical for better prevention and control.

Dengue outbreak in Swat and Mansehra, Pakistan 2013: An epidemiological and diagnostic perspective.

OBJECTIVE: To high light some epidemiological, clinical and diagnostic features of dengue fever during an outbreak and the role of different diagnostic techniques to achieve the highest level of accuracy in results. METHODS: Blood samples (n = 323) were collected along with epidemiological and clinical data from suspected dengue patients who visited different hospitals in Swat and Mansehra district of Pakistan between May-November 2013 during a dengue outbreak. Samples were tested for the detection of viral nucleic acid by real-time PCR, non structural protein-1 (NS1) antigen and IgM antibodies by ELISA. RESULTS: Out of 323 cases with clinical dengue infection, 304 were positive by one or more diagnostic parameter; 201 samples were positive by real-time PCR, 209 were positive by NS1 ELISA and 190 were positive by IgM antibodies. Sensitivities of real-time PCR and NS1 ELISA were comparable for early diagnosis of dengue virus infection, IgM antibody detection assay was found useful for the diagnosis in the samples collected later than day 5 of onset. CONCLUSIONS: The use of real-time PCR or detection of non structural protein NS1 by ELISA followed by IgM antibodies detection can be recommended for early diagnosis of dengue virus infection with a high level of accuracy.

'Human bocavirus in Pakistani children with gastroenteritis'.

Human Bocaviruses (HBoV) have been detected in human respiratory and gastrointestinal infections worldwide. Four genotypes of HBoV (HBoV1-4) have been described; HBoV-1 is associated with respiratory tract infections while HBoV-2, -3, and -4 genotypes are considered as entero-pathogenic although the exact role largely remains unclear. The global prevalence of HBoV has been reported, but the epidemiological data from Pakistan is largely unavailable to date. This study was conducted to understand the genetic diversity and disease prevalence of HBoV in hospitalized Pakistani children with acute diarrhea. During 2009, a total of 365 stool samples were collected from children hospitalized with gastrointestinal symptoms (as per WHO case definitions) at Rawalpindi General Hospital, Pakistan. Demographic and clinical data were recorded using a standardized questionnaire. The samples were tested for HBoV and rotavirus using real-time RT-PCR and ELISA, respectively. There were 47 (13%) samples positive for HBoV with 98% (n = 46) showing co-infection with rotavirus. HBoV-1 was the most frequently detected and was found in 94% samples followed by HBoV-2 and HBoV-3 genotypes. The mean age of infected children was 7.57 ± 5.4 months while detection was more frequent in males (n = 32, 68%). All cases recovered after 2.43 ± 1.0 mean days of treatment. On phylogenetic analysis, HBoV strains from Pakistan clustered closely with viruses from neighboring Bangladesh and China. These findings represent the first known epidemiological study in Pakistan to investigate the role of HBoV in acute gastroenteritis. The clinical data demonstrates that HBoV is not significantly associated with gastroenteritis alone and predominantly co-infections with rotavirus are found.

Viral etiologies of acute dehydrating gastroenteritis in pakistani children: confounding role of parechoviruses.

Despite substantial interventions in the understanding and case management of acute gastroenteritis, diarrheal diseases are still responsible for a notable amount of childhood deaths. Although the rotavirus is known to cause a considerable burden of pediatric diarrheal cases, the roles of other viruses remain undefined for the Pakistani population. This study was based on tertiary care hospital surveillance, from January 2009 to December 2010, including the detection of rotavirus, norovirus, astrovirus, and human parechovirus in children under the age of five using serological or molecular assays. Rotavirus, human parechovirus, norovirus, and astrovirus were detected in 66%, 21%, 19.5%, and 8.5% subjects, respectively. Human parechovirus genotypes, determined through analysis of VP1 gene sequences, showed a great diversity among co-circulating strains. Eighty percent of hospitalized children had dual or multiple viral infections, while 98% parechovirus positive cases were co-infected with rotavirus. The remarkable diversity of viruses associated with the childhood diarrhea in Pakistan calls for large-scale epidemiological surveys, coupled with case control studies, to ascertain their role in clinical manifestations. In addition, these findings also highlight the need for the implementation of up-to-date health interventions, such as the inclusion of a rotavirus vaccine in routine immunization programs for the improvement of quality in child health care.

Prediction of clinical factors associated with pandemic influenza A (H1N1) 2009 in Pakistan.

BACKGROUND: Influenza is a viral infection that can lead to serious complications and death(s) in vulnerable groups if not diagnosed and managed in a timely manner. This study was conducted to improve the accuracy of predicting influenza through various clinical and statistical models. METHODOLOGY: A retrospective cross sectional analysis was done on demographic and epidemiological data collected from March 2009 to March 2010. Patients were classified as ILI or SARI using WHO case definitions. Respiratory specimens were tested by RT-PCR. Clinical symptoms and co-morbid conditions were analyzed using binary logistic regression models. RESULTS: In the first approach, analysis compared children (≤12) and adults (>12). Of 1,243 cases, 262 (21%) tested positive for A(H1N1)pdm09 and the proportion of children (≤12) and adults (>12) were 27% and 73% respectively. Four symptoms predicted influenza in children: fever (OR 2.849, 95% CI 1.931-8.722), cough (OR 1.99, 95% CI 1.512-3.643), diarrhea (OR 2.100, 95% CI 2.040-3.25) and respiratory disease (OR 3.269, 95% CI 2.128-12.624). In adults, the strongest clinical predictor was fever (OR 2.80, 95% CI 1.025-3.135) followed by cough (OR 1.431, 95% CI 1.032-2.815). In the second instance, patients were separated into two groups: SARI 326 (26%) and ILI 917 (74%) cases. Male to female ratio was 1.41∶1.12 for SARI and 2∶1.5 for ILI cases. Chi-square test showed that fever, cough and sore throat were significant factors for A(H1N1)pdm09 infections (p = 0.008). CONCLUSION: Studies in a primary care setting should be encouraged focused on patients with influenza-like illness to develop sensitive clinical case definition that will help to improve accuracy of detecting influenza infections. Formulation of a standard "one size fits all" case definition that best correlates with influenza infections can help guide decisions for additional diagnostic testing and also discourage unjustified antibiotic prescription and usage in clinical practice.

Influenza virus surveillance in Pakistan during 2008-2011.

BACKGROUND: There is little information about influenza among the Pakistani population. In order to assess the trends of Influenza-like-Illness (ILI) and to monitor the predominant circulating strains of influenza viruses, a country-wide lab-based surveillance system for ILI and Severe Acute Respiratory Illness (SARI) with weekly sampling and reporting was established in 2008. This system was necessary for early detection of emerging novel influenza subtypes and timely response for influenza prevention and control. METHODS: Five sentinel sites at tertiary care hospitals across Pakistan collected epidemiological data and respiratory samples from Influenza-like illness (ILI) and severe acute respiratory illness (SARI) cases from January 2008 to December 2011. Samples were typed and sub-typed by Real-Time RT-PCR assay. RESULTS: A total of 6258 specimens were analyzed; influenza virus was detected in 1489 (24%) samples, including 1066 (72%) Influenza type A and 423 (28%) influenza type B viruses. Amongst influenza A viruses, 25 (2%) were seasonal A/H1N1, 169 (16%) were A/H3N2 and 872 (82 %) were A(H1N1)pdm09. Influenza B virus circulation was detected throughout the year along with few cases of seasonal A/H1N1 virus during late winter and spring. Influenza A/H3N2 virus circulation was mainly observed during summer months (August-October). CONCLUSIONS: The findings of this study emphasize the need for continuous and comprehensive influenza surveillance. Prospective data from multiple years is needed to predict seasonal trends for vaccine development and to further fortify pandemic preparedness.

Human parechovirus genotypes -10, -13 and -15 in Pakistani children with acute dehydrating gastroenteritis.

Human parechoviruses are known to cause asymptomatic to severe clinical illness predominantly respiratory and gastroenetric infections. Despite their global prevalence, epidemiological studies have not been performed in Pakistan. In this study, we retrospectively analyzed 110 fecal specimen and found 26 (24%) positive for viral RNA with HPeV-10 (n = 3, 23%), HPeV-13 (n = 4, 31%) and HPeV-15 (n = 6, 46%) genotypes. Clinical features of patients with different HPeV genotypes were compared. All HPeV positive children were aged ≤4 years (mean 13.92 months). The male-to-female ratio was 1: 1.17 (46.2 vs 53.8%) with significant association (p = .031) to HPeV infectivity. HPeV-10 and -13 were found during summer while HPeV-15 was only detected during late winter season. Disease symptoms were more severe in children infected with HPeV-10 and -13 as compared to HPeV-15. Fever and vomiting were observed in 100% cases of HPeV-10 and -13 while only 17% patients of HPeV-15 had these complaints. Phylogenetic analyses showed that HPeV-10, -13 and -15 strains found in this study have 9-13%, 16.8% and 21.8% nucleotide divergence respectively from the prototype strains and were clustered to distinct genetic lineages. This is the first report of HPeV-15 infection in humans although first identified in rhesus macaques. The arginine-glycine-aspartic acid (RGD) motif present at the C-terminal of VP1 responsible for the viral attachment to cellular integrins was not found in all of these strains. In conclusion, these findings enhance our knowledge related to the epidemiology and genetic diversity of the HPeV in Pakistan and support the need for continued laboratory based surveillance programs especially in infants and neonatal clinical settings. Further, the parechovirus pathogenesis, cross-species transmission and disease reservoirs must be ascertained to adopt better prevention measures.

Molecular epidemiology of influenza A(H1N1)pdm09 viruses from Pakistan in 2009-2010.

BACKGROUND: In early 2009, a novel influenza A(H1N1) virus that emerged in Mexico and United States rapidly disseminated worldwide. The spread of this virus caused considerable morbidity with over 18000 recorded deaths. The new virus was found to be a reassortant containing gene segments from human, avian and swine influenza viruses. METHODS/RESULTS: The first case of human infection with A(H1N1)pdm09 in Pakistan was detected on 18(th) June 2009. Since then, 262 laboratory-confirmed cases have been detected during various outbreaks with 29 deaths (as of 31(st) August 2010). The peak of the epidemic was observed in December with over 51% of total respiratory cases positive for influenza. Representative isolates from Pakistan viruses were sequenced and analyzed antigenically. Sequence analysis of genes coding for surface glycoproteins HA and NA showed high degree of high levels of sequence identity with corresponding genes of regional viruses circulating South East Asia. All tested viruses were sensitive to Oseltamivir in the Neuraminidase Inhibition assays. CONCLUSIONS: Influenza A(H1N1)pdm09 viruses from Pakistan form a homogenous group of viruses. Their HA genes belong to clade 7 and show antigenic profile similar to the vaccine strain A/California/07/2009. These isolates do not show any amino acid changes indicative of high pathogenicity and virulence. It is imperative to continue monitoring of these viruses for identification of potential variants of high virulence or drug resistance.