Shift in SARS-CoV-2 variants of concern from Delta to Omicron was associated with reduced hospitalizations, increased risk of breakthrough infections but lesser disease severity.

Background: COVID-19 epidemiology changed with the emergence of SARS-CoV-2 variants of concern (VOC). Pakistan administered mostly inactivated vaccines. We investigated the association between VOC and breakthrough infections in a mixed-vaccination-status population of Karachi.

Exploring the relationship between SARS-CoV-2 variants, illness severity at presentation, in-hospital mortality and COVID-19 vaccination in a low middle-income country: A retrospective cross-sectional study.

Background And Aims: COVID-19 morbidity and mortality varied globally through the pandemic We studied the relationship of SARS-CoV-2 variants of concern (VOC) with COVID-19 severity and mortality among hospitalized patients in Pakistan.

Methods: A retrospective review of clinical, laboratory, and vaccination data of 197 COVID-19 adult patients at the Aga Khan University Hospital, Karachi between April 2021, and February 2022 was performed. SARS-CoV-2 VOC identified in respiratory samples were analyzed.

Sequential viral introductions and spread of BA.1 across Pakistan provinces during the Omicron wave.

Background: COVID-19 waves caused by specific SARS-CoV-2 variants have occurred globally at different times. We focused on Omicron variants to understand the genomic diversity and phylogenetic relatedness of SARS-CoV-2 strains in various regions of Pakistan.

Methods: We studied 276,525 COVID-19 cases and 1,031 genomes sequenced from December 2021 to August 2022.

Tracking SARS-CoV-2 variants through pandemic waves using RT-PCR testing in low-resource settings.

COVID-19 resulted in extensive morbidity and mortality worldwide. SARS-CoV-2 evolved rapidly, with increasing transmission due to Variants of Concern (VOC). Identifying VOC became important but genome submissions from low-middle income countries (LMIC) remained low leading to gaps in genomic epidemiology.

A Mentorship Program to Develop Biorisk Manuals for Laboratories in Pakistan.

Introduction: Institutions implementing a biorisk management system need to establish comprehensive guidance to support the implementation of biosafety and biosecurity practices. A biorisk manual describes how a biorisk management system will be implemented in an organization and includes topics such as facility-specific policies and procedures to safely and securely handle, store, and dispose of biological agents and toxins in adherence with international guidance.

Methods: To promote the adoption of biosafety and biosecurity in Pakistan, the Pakistan Biological Safety Association and Health Security Partners developed a biorisk manual writing project in 2019 in partnership with experts from the BioRisk Association of the Philippines 2015, Inc.

Evolutionary history and introduction of SARS-CoV-2 Alpha VOC/B.1.1.7 in Pakistan through international travelers.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to emerge, and their identification is important for the public health response to coronavirus disease 2019 (COVID-19). Genomic sequencing provides robust information but may not always be accessible, and therefore, mutation-based polymerase chain reaction (PCR) approaches can be used for rapid identification of known variants. International travelers arriving in Karachi between December 2020 and February 2021 were tested for SARS-CoV-2 by PCR.

Molecular detection and genetic characterization of human metapneumovirus strains circulating in Islamabad, Pakistan.

Lower respiratory illness is one of the leading causes of death among children in low- and high-income countries. Human metapneumovirus (hMPV) is a key contributor to respiratory illnesses commonly reported among children and causes serious clinical complications ranging from mild respiratory infections to severe lower respiratory tract anomalies mainly in the form of bronchiolitis and pneumonia. However, due to the lack of a national surveillance system, the clinical significance of hMPV remains obscure in the Pakistani population.

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.

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.

Phylogenetic analysis of open reading frame of 11 gene segments of novel human-bovine reassortant RVA G6P[1] strain in Pakistan.

Multiple Rotavirus A (RVA) strains are linked with gastrointestinal infections in children that fall in age bracket of 0 to 60 months. However, the problem is augmented with emergence of unique strains that reassort with RVA strains of animal origin. The study describes the sequence analysis of a rare G6P[1] rotavirus strain isolated from a less than 1 year old child, during rotavirus surveillance in Rawalpindi district, Pakistan in 2010.

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.

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.

Epidemiological and molecular investigation of a measles outbreak in Punjab, Pakistan, 2013-2015.

Despite the availability of an effective vaccine, the measles virus continues to cause significant morbidity and mortality in children worldwide. Molecular characterization of wild-type measles strains is an invaluable component of epidemiological studies or surveillance systems that provides important information pertinent to outbreak linkages and transmission pathways. Serum samples and throat swabs were collected from suspected measles cases from the Punjab province of Pakistan (2013-2015) and further tested for measles immunoglobulin M (IgM) through enzyme-linked immunosorbent assay and reverse-transcriptase polymerase chain reaction for molecular characterization.

Global respiratory syncytial virus-associated mortality in young children (RSV GOLD): a retrospective case series.

Background: Respiratory syncytial virus (RSV) infection is an important cause of pneumonia mortality in young children. However, clinical data for fatal RSV infection are scarce. We aimed to identify clinical and socioeconomic characteristics of children aged younger than 5 years with RSV-related mortality using individual patient data.

A measles outbreak in Sindh, Pakistan caused by a genotype B3 virus.

Measles continues to be a major public health issue causing substantial outbreaks worldwide, mostly affecting young children. Molecular analysis of measles viruses provides important information on outbreak linkages and transmission pathways that can be helpful towards implementation of appropriate control programs. In Pakistan, the control of measles is still tenuous, and progress towards elimination has been irregular and challenging.

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.

"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.

Dengue Virus Serotypes Circulating in Khyber Pakhtunkhwa Province, Pakistan, 2013-2015.

From 2013 to 2015, the National Institute of Health, Pakistan, received 1,270 blood samples of suspected dengue cases reported from inpatient and outpatient departments of various hospitals in Khyber Pakhtunkhwa (KPK) province. In this study, we determined the circulating dengue virus (DENV) serotypes using real-time reverse transcriptase (RT)-PCR to understand the serotype-based epidemiology of DENV. All four serotypes (DENV-1 [6%], DENV-2 [33%], DENV-3 [47%], and DENV-4 [0.

NS1 antigen: A new beam of light in the early diagnosis of dengue infection.

Objective: To evaluate NS1 antigen detection ELISA for the early laboratory diagnosis of dengue virus infection.

Methods: The present study was conducted to evaluate the overall positivity of NS1 antigen detection ELISA and its comparison with viral RNA detection via real time PCR and IgM antibodies detection by ELISA.

Results: A total of 1270 serum samples were tested 86% (1097/1270) were detected positive by one or more than one diagnostic test.

Distribution of Cytomegalovirus Genotypes among Neonates Born to Infected Mothers in Islamabad, Pakistan.

Background: Congenital cytomegalovirus (cCMV) infection contributes to considerable long-term sequelae in neonates and children all over the world. The association between viral genotypes and severity of clinical cytomegalovirus (CMV) infection is yet to be defined. The objective of this study was to find the impact of active CMV infection during pregnancy and the clinical significance of genotypes in neonates with congenital cytomegalovirus infections in Pakistan.

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.

CCHF virus variants in Pakistan and Afghanistan: Emerging diversity and epidemiology.

Background: Crimean Congo hemorrhagic fever (CCHF) has been reported from more than 30 countries in Africa, Asia, Eastern Europe and Middle East. The disease is considered endemic in Pakistan and neighboring countries like Iran and Afghanistan.

Objectives: This study aimed to explore the genetic diversity of CCHF virus (CCHFV) detected in Pakistan and Afghanistan based on analysis of partial S-segment sequences.

'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.