Publications by authors named "Muhammad Masroor Alam"

72 Publications

Importation of SARS-CoV-2 Variant B.1.1.7 in Pakistan.

J Med Virol 2021 Feb 11. Epub 2021 Feb 11.

Department of Virology, National Institute of Health, Islamabad, Pakistan.

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http://dx.doi.org/10.1002/jmv.26869DOI Listing
February 2021

Overlapping clinical manifestations of COVID-19 with endemic infectious diseases in Pakistan: A looming threat of multiple lethal combinations.

Infect Ecol Epidemiol 2021 Jan 20;11(1):1873494. Epub 2021 Jan 20.

Department of Virology, National Institute of Health, Islamabad, Pakistan.

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http://dx.doi.org/10.1080/20008686.2021.1873494DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7832986PMC
January 2021

Clinical and laboratory characteristics of recovered versus deceased COVID-19 patients in Islamabad, Pakistan.

J Infect 2020 Nov 13. Epub 2020 Nov 13.

Department of Virology, National Institute of Health, Park Road, Chak Shehzad, Islamabad 45500, Pakistan.

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http://dx.doi.org/10.1016/j.jinf.2020.11.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7664341PMC
November 2020

Impact of COVID-19 pandemic on Measles surveillance in Pakistan.

J Infect 2020 Oct 8. Epub 2020 Oct 8.

Department of Virology, National Institute of Health, Park Road, Chak Shehzad, Islamabad 45500, Pakistan.

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http://dx.doi.org/10.1016/j.jinf.2020.10.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7543746PMC
October 2020

First trimester miscarriage in a pregnant woman infected with COVID-19 in Pakistan.

J Infect 2021 01 5;82(1):e27-e28. Epub 2020 Sep 5.

Department of Virology, National Institute of Health, Park Road, Chak Shehzad, Islamabad 45500, Pakistan.

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http://dx.doi.org/10.1016/j.jinf.2020.09.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7831960PMC
January 2021

Detection of SARS-CoV-2 in ophthalmic secretions.

J Infect 2021 02 25;82(2):e25-e26. Epub 2020 Aug 25.

National Institute of Health, Islamabad, Pakistan. Electronic address:

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http://dx.doi.org/10.1016/j.jinf.2020.08.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7445145PMC
February 2021

Novel coronavirus outbreak in Pakistan: Beware of dengue.

J Formos Med Assoc 2021 01 22;120(1 Pt 3):765-766. Epub 2020 Jul 22.

National Institute of Health, Islamabad, Pakistan. Electronic address:

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http://dx.doi.org/10.1016/j.jfma.2020.07.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7375274PMC
January 2021

Serotype diversity of dengue virus reveals the predominance of type 2 in Pakistan during 2019.

J Med Virol 2020 Jul 21. Epub 2020 Jul 21.

Department of Virology, National Institute of Health, Islamabad, Pakistan.

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http://dx.doi.org/10.1002/jmv.26324DOI Listing
July 2020

Phyto-fabricated CrO nanoparticle for multifunctional biomedical applications.

Nanomedicine (Lond) 2020 07 16;15(17):1653-1669. Epub 2020 Jul 16.

UNESCO UNISA Africa Chair in Nanosciences & Nanotechnology, College of Graduate Studies, University of South Africa (UNISA), Pretoria, South Africa.

The biosynthesis of chromium oxide nanoparticles (CrO NPs), using as a bioreductant, for assessment of their potential nanomedicinal applications. Biosynthesized CrO NPs were characterized by x-ray diffraction, Fourier-transform infrared spectroscopy, energy dispersive x-ray spectroscopy, scanning and transmission electron microscopy, selected area electron diffraction, UV-Vis spectroscopy and ζ-potential measurement. assays were used to assess the biological properties of CrO NPs. Nanoparticles with size approximately 25-38 nm were obtained with a characteristic Cr-O vibration at 417 cm. A broad spectrum antimicrobial potential and antioxidant nature is reported. Slight inhibition of polio virus and biocompatibility at low doses was observed. We conclude a multifunctional nature of biogenic CrO NPs.
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http://dx.doi.org/10.2217/nnm-2020-0129DOI Listing
July 2020

Rapid and Sensitive Direct Detection and Identification of Poliovirus from Stool and Environmental Surveillance Samples by Use of Nanopore Sequencing.

J Clin Microbiol 2020 Aug 24;58(9). Epub 2020 Aug 24.

Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom.

Global poliovirus surveillance involves virus isolation from stool and environmental samples, intratypic differential (ITD) by PCR, and sequencing of the VP1 region to distinguish vaccine (Sabin), vaccine-derived, and wild-type polioviruses and to ensure an appropriate response. This cell culture algorithm takes 2 to 3 weeks on average between sample receipt and sequencing. Direct detection of viral RNA using PCR allows faster detection but has traditionally faced challenges related to poor sensitivity and difficulties in sequencing common samples containing poliovirus and enterovirus mixtures. We present a nested PCR and nanopore sequencing protocol that allows rapid (<3 days) and sensitive direct detection and sequencing of polioviruses in stool and environmental samples. We developed barcoded primers and a real-time analysis platform that generate accurate VP1 consensus sequences from multiplexed samples. The sensitivity and specificity of our protocol compared with those of cell culture were 90.9% (95% confidence interval, 75.7% to 98.1%) and 99.2% (95.5% to 100.0%) for wild-type 1 poliovirus, 92.5% (79.6% to 98.4%) and 98.7% (95.4% to 99.8%) for vaccine and vaccine-derived serotype 2 poliovirus, and 88.3% (81.2% to 93.5%) and 93.2% (88.6% to 96.3%) for Sabin 1 and 3 poliovirus alone or in mixtures when tested on 155 stool samples in Pakistan. Variant analysis of sequencing reads also allowed the identification of polioviruses and enteroviruses in artificial mixtures and was able to distinguish complex mixtures of polioviruses in environmental samples. The median identity of consensus nanopore sequences with Sanger or Illumina sequences from the same samples was >99.9%. This novel method shows promise as a faster and safer alternative to cell culture for the detection and real-time sequencing of polioviruses in stool and environmental samples.
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http://dx.doi.org/10.1128/JCM.00920-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7448630PMC
August 2020

Genetic diversity and phylogenetic analysis of Crimean-Congo Hemorrhagic Fever viruses circulating in Pakistan during 2019.

PLoS Negl Trop Dis 2020 06 29;14(6):e0008238. Epub 2020 Jun 29.

Department of Virology, National Institute of Health, Islamabad, Pakistan.

Being an endemic country for Crimean Congo hemorrhagic fever (CCHF), this study aimed to explore the genetic diversity of CCHF virus (CCHFV) detected in Pakistan during 2019. Serum samples from patients with clinical signs of hemorrhagic fever attending tertiary care hospitals in Pakistan were tested for CCHFV RNA using real-time PCR at Department of Virology, National Institute of Health. The partial S-gene fragments were directly sequenced to determine the prevailing CCHFV genotypes and their molecular epidemiology in Pakistan. During January-December 2019, 280 samples from suspected CCHF patients were tested and 28 (10%) were found positive on real-time PCR. Positive cases were detected from 14 districts and across all four provinces of Pakistan with majority reported during August-September. The mean age of CCHFV positive patients was 37.25 years (range 5-65 years) with a high frequency in males (92.8%; n = 26) and a case fatality rate of 40.7% was observed. Phylogenetic analysis showed that S- segment of 2019 PAK CCHFV strains (n = 13) belonged to Asia-1 genotype and clustered with regional strains from Iran, Oman, and Afghanistan. We conclude that Asia-1 genotype of CCHF virus remains endemic in Pakistan. Our findings emphasize to establish a laboratory based surveillance program to monitor the disease burden and identify outbreak hotspots for effective control.
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http://dx.doi.org/10.1371/journal.pntd.0008238DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7351229PMC
June 2020

Emergence of Chikungunya Virus, Pakistan, 2016-2017.

Emerg Infect Dis 2020 02;26(2):307-310

During December 2016-May 2017, an outbreak of chikungunya virus infection occurred across Pakistan. The East/Central/South African genotype was predominant. This study provides baseline data on the virus strain and emphasizes the need for active surveillance and implementation of preventive interventions to contain future outbreaks.
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http://dx.doi.org/10.3201/eid2602.171636DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986857PMC
February 2020

Phytosynthesis of BiVO nanorods using Hyphaene thebaica for diverse biomedical applications.

AMB Express 2019 Dec 12;9(1):200. Epub 2019 Dec 12.

UNESCO UNISA Africa Chair in Nanosciences and Nanotechnology, College of Graduate Studies, University of South Africa, Pretoria, South Africa.

Biosynthesis of bismuth vanadate (BiVO) nanorods was performed using dried fruit extracts of Hyphaene thebaica as a cost effective reducing and stabilizing agent. XRD, DRS, FTIR, zeta potential, Raman, HR-SEM, HR-TEM, EDS and SAED were used to study the main physical properties while the biological properties were established by performing diverse assays. The zeta potential is reported as - 5.21 mV. FTIR indicated Bi-O and V-O vibrations at 640 cm and 700 cm/1120 cm. Characteristic Raman modes were observed at 166 cm, 325 cm and 787 cm. High resolution scanning and transmission electron micrographs revealed a rod like morphology of the BiVO. Bacillus subtilis, Klebsiella pneumonia, Fusarium solani indicated highest susceptibility to the different doses of BiVO nanorods. Significant protein kinase inhibition is reported for BiVO nanorods which suggests their potential anticancer properties. The nanorods revealed good DPPH free radical scavenging potential (48%) at 400 µg/mL while total antioxidant capacity of 59.8 µg AAE/mg was revealed at 400 µg/mL. No antiviral activity is reported on sabin like polio virus. Overall excellent biological properties are reported. We have shown that green synthesis can replace well established processes for synthesizing BiVO nanorods.
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http://dx.doi.org/10.1186/s13568-019-0923-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6908540PMC
December 2019

Prevention and control of escalating dengue epidemics in Pakistan.

J Med Virol 2020 08 2;92(8):927-928. Epub 2019 Dec 2.

National Institute of Health, Islamabad, Pakistan.

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http://dx.doi.org/10.1002/jmv.25635DOI Listing
August 2020

Genetic Epidemiology Reveals 3 Chronic Reservoir Areas With Recurrent Population Mobility Challenging Poliovirus Eradication in Pakistan.

Clin Infect Dis 2020 Oct;71(7):e58-e67

Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan.

Background: Pakistan is among 3 countries endemic for wild poliovirus type 1 (WPV1) circulation that are still struggling for eradication of poliomyelitis. Active clinical and environmental surveillance with meticulous laboratory investigations provide insights into poliovirus transmission patterns and genomic diversity to inform decisions for strategic operations required to achieve eradication.

Methods: We analyzed epidemiological and virological data to comprehend the current epidemiological status of WPV1 in Pakistan during 2015-2017. Stool specimens of patients with acute flaccid paralysis (AFP) and sewage samples collected from 60 environmental sites were tested. Viral culturing, intratypic differentiation by real-time polymerase chain reaction, and nucleic acid sequencing of the VP1 region of the poliovirus genome to determine genetic relatedness among WPV1 strains were applied.

Results: Poliovirus isolates were grouped into 11 distinct clusters, which had ≥95% nucleotide homology in the VP1 coding region. Most of the poliovirus burden was shared by 3 major reservoirs: Karachi, Peshawar, and Quetta block (64.2% in 2015, 75.4% in 2016, and 76.7% in 2017).

Conclusions: Environmental surveillance reveals importations and pockets of unimmunized children that dictate intensive target mop-up campaigns to contain poliovirus transmission. A decrease in the number of orphan isolates reflects effective combination of AFP and environmental surveillance in Pakistan. The genetic data reflect sustained transmission within reservoir areas, further expanded by periodic importations to areas of high immunity reflected by immediate termination of imported viruses. Improved immunization coverage with high-quality surveillance is vital for global certification of polio eradication.
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http://dx.doi.org/10.1093/cid/ciz1037DOI Listing
October 2020

Epidemiological trend of chikungunya outbreak in Pakistan: 2016-2018.

PLoS Negl Trop Dis 2019 04 18;13(4):e0007118. Epub 2019 Apr 18.

Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan.

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http://dx.doi.org/10.1371/journal.pntd.0007118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6472721PMC
April 2019

Assessing the sensitivity of the polio environmental surveillance system.

PLoS One 2018 28;13(12):e0208336. Epub 2018 Dec 28.

Institute for Disease Modeling, Bellevue, WA, United States of America.

Background: The polio environmental surveillance (ES) system has been an incredible tool for advancing polio eradication efforts because of its ability to highlight the spatial and temporal extent of poliovirus circulation. While ES often outperforms, or is more sensitive than AFP surveillance, the sensitivity of the ES system has not been well characterized. Fundamental uncertainty of ES site sensitivity makes it difficult to interpret results from ES, particularly negative results.

Methods And Findings: To study ES sensitivity, we used data from Afghanistan and Pakistan to examine the probability that each ES site detected the Sabin 1, 2, or 3 components of the oral polio vaccine (OPV) as a function of virus prevalence within the same district (estimated from AFP data). Accounting for virus prevalence is essential for estimating site sensitivity because Sabin detection rates should vary with prevalence-high immediately after supplemental immunization activities (SIAs), but low in subsequent months. We found that most ES sites in Pakistan and Afghanistan are highly sensitive for detecting poliovirus relative to AFP surveillance in the same districts. For example, even when Sabin poliovirus is at low prevalence of ~0.5-3% in AFP surveillance, most ES sites have ~34-50% probability of detecting Sabin. However, there was considerable variation in ES site sensitivity and we flagged several sites for re-evaluation based on low sensitivity rankings and low wild polio virus detection rates. In these areas, adding new sites or modifying collection methods in current sites could improve sensitivity of environmental surveillance.

Conclusions: Relating ES detections to virus prevalence significantly improved our ability to evaluate site sensitivity compared to evaluations based solely on ES detection rates. To extend our approach to new sites and regions, we provide a preliminary framework for relating ES and AFP detection rates, and descriptions of how detection rates might relate to SIAs and natural seasonality.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0208336PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6310268PMC
May 2019

Environmental Surveillance Reveals Complex Enterovirus Circulation Patterns in Human Populations.

Open Forum Infect Dis 2018 Oct 1;5(10):ofy250. Epub 2018 Oct 1.

Division of Virology, National Institute for Biological Standards and Control (NIBSC), South Mimms, Potters Bar, Herts, United Kingdom.

Background: Enteroviruses are common human pathogens occasionally associated with severe disease, notoriously paralytic poliomyelitis caused by poliovirus. Other enterovirus serotypes such as enterovirus A71 and D68 have been linked to severe neurological syndromes. New enterovirus serotypes continue to emerge, some believed to be derived from nonhuman primates. However, little is known about the circulation patterns of many enterovirus serotypes and, in particular, the detailed enterovirus composition of sewage samples.

Methods: We used a next-generation sequencing approach analyzing reverse transcriptase polymerase chain reaction products synthesized directly from sewage concentrates.

Results: We determined whole-capsid genome sequences of multiple enterovirus strains from all 4 A to D species present in environmental samples from the United Kingdom, Senegal, and Pakistan.

Conclusions: Our results indicate complex enterovirus circulation patterns in human populations with differences in serotype composition between samples and evidence of sustained and widespread circulation of many enterovirus serotypes. Our analyses revealed known and divergent enterovirus strains, some of public health relevance and genetically linked to clinical isolates. Enteroviruses identified in sewage included vaccine-derived poliovirus and enterovirus D-68 stains, new enterovirus A71 and coxsackievirus A16 genogroups indigenous to Pakistan, and many strains from rarely reported serotypes. We show how this approach can be used for the early detection of emerging pathogens and to improve our understanding of enterovirus circulation in humans.
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http://dx.doi.org/10.1093/ofid/ofy250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6201154PMC
October 2018

High prevalence of G3 rotavirus in hospitalized children in Rawalpindi, Pakistan during 2014.

PLoS One 2018 30;13(4):e0195947. Epub 2018 Apr 30.

Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan.

Rotavirus A species (RVA) is the leading cause of severe diarrhea among children in both developed and developing countries. Among different RVA G types, humans are most commonly infected with G1, G2, G3, G4 and G9. During 2003-2004, G3 rotavirus termed as "new variant G3" emerged in Japan that later disseminated to multiple countries across the world. Although G3 rotaviruses are now commonly detected globally, they have been rarely reported from Pakistan. We investigated the genetic diversity of G3 strains responsible RVA gastroenteritis in children hospitalized in Rawalpindi, Pakistan during 2014. G3P[8] (18.3%; n = 24) was detected as the most common genotype causing majority of infections in children less than 06 months. Phylogenetic analysis of Pakistani G3 strains showed high amino acid similarity to "new variant G3" and G3 strains reported from China, Russia, USA, Japan, Belgium and Hungary during 2007-2012. Pakistani G3 strains belonged to lineage 3 within sub-lineage 3d, containing an extra N-linked glycosylation site compared to the G3 strain of RotaTeqTM. To our knowledge, this is the first report on the molecular epidemiology of G3 rotavirus strains from Pakistan and calls for immediate response measures to introduce RV vaccine in the routine immunization program of the country on priority.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0195947PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5927433PMC
July 2018

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

J Med Virol 2018 08 25;90(8):1297-1303. Epub 2018 May 25.

Department of Virology, National Institute of Health, Chak Shahzad, Pakistan.

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. Among the total of 5415 blood samples, 59% tested positive for measles IgM. Males had a higher infection rate (55%) than females (45%), and the highest frequency of positive cases (63%) was found in the age group of 0 to 5 years. Partial sequencing of the nucleoprotein gene showed that 27 strains belonged to the B3 genotype, whereas 2 viruses were identified as D4. On phylogenetic analysis, Pakistani B3 strains were found to be closely related to previously reported indigenous strains and those from neighboring countries of Iran and Qatar. This is the first report on the detection of the measles B3 genotype from Punjab, Pakistan. The current study shows a high burden of measles infections in Punjab province owing to poor routine immunization coverage in major cities. It is imperative that national health authorities adopt strategic steps on an urgent basis for improvement of routine immunization coverage. Molecular epidemiology of the measles viruses circulating in different parts of the country can provide useful data to manage future outbreaks.
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http://dx.doi.org/10.1002/jmv.25206DOI Listing
August 2018

Rotavirus surveillance in Pakistan during 2015-2016 reveals high prevalence of G12P[6].

J Med Virol 2018 07 12;90(7):1272-1276. Epub 2018 Apr 12.

Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan.

The G12 rotavirus genotype has emerged globally since their first detection in 1987 from the Philippines; however it remains a rare cause of gastroenteritis in Pakistan. Rotavirus surveillance conducted during 2015-2016, assessed 3446 children <5 years hospitalized for gastroenteritis and found 802 (23.2%) positive on ELISA. Genotyping of a subset of positive samples (n = 319) revealed G12P[6] (11.28%) as the third most common G/P combination following G3P[8] (28.5%) and G1P[8] (12.5%); G2P[4] (10.65%) and G3P[6] (8.15%) were other frequently detected strains. Phylogenetic analysis of G12 strains from Pakistan revealed high genetic similarity to G12 strains from Italy, Thailand, Korea, and Great Britain as well as local strains within G12 lineage III. In conclusion, G12P[6] was a major contributor of RVA gastroenteritis in Pakistani children. Robust surveillance after the introduction of rotavirus vaccines will help determine the evolution of G12 and other circulating genotypes in the country.
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http://dx.doi.org/10.1002/jmv.25075DOI Listing
July 2018

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

Arch Virol 2017 Dec 12;162(12):3603-3610. Epub 2017 Aug 12.

Department of Virology, National Institute of Health, Park Road, Chak Shahzad, Islamabad, 45500, Pakistan.

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. In the 2013 measles outbreak we received 4,682 sera collected from suspected patients in 23 districts across Sindh. A total of 3,283 samples were confirmed measles positive using IgM ELISA with the highest infection rate in children aged 1-12 months. Males were more affected than females and a visible peak was observed from January to April. Among the 3,283 cases, 59.1% were unvaccinated, 29.6% had received 1 dose and 10.3% had received 2 doses of measles vaccine while 0.85% had an unknown vaccination status. For genotype detection and phylogenetic analysis, 60 throat swab samples were collected from suspected patients below 15 years of age in eight districts of Sindh province. Forty four (73%; 44/60) throat swab samples were successfully genotyped using RT-PCR. Phylogenetic analyses based on partial sequences of the nucleocapsid protein gene revealed that all Pakistani measles virus strains belonged to genotype B3 and were closely related to those isolated from neighboring countries such as Iran, Afghanistan (99.1-100%) and India with 98.6 - 99.6% nucleotide homology. This is the first report on the phylogenetic analysis of measles B3 genotype strains from Pakistan and highlights the need for strengthening the surveillance systems and improving immunization coverage across the country.
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http://dx.doi.org/10.1007/s00705-017-3524-9DOI Listing
December 2017

Surveillance of Crimean-Congo haemorrhagic fever in Pakistan.

Lancet Infect Dis 2017 08;17(8):806

Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan.

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http://dx.doi.org/10.1016/S1473-3099(17)30403-6DOI Listing
August 2017

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

Infect Genet Evol 2017 09 17;53:160-166. Epub 2017 May 17.

Department of Virology, National Institute of Health, Park Road, Chak Shahzad, Islamabad, Pakistan. Electronic address:

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.
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http://dx.doi.org/10.1016/j.meegid.2017.05.009DOI Listing
September 2017

Outbreaks of chikungunya in Pakistan.

Lancet Infect Dis 2017 05;17(5):483

Department of Virology, National Institute of Health, Chak Shahzad, 44000 Islamabad, Pakistan. Electronic address:

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http://dx.doi.org/10.1016/S1473-3099(17)30191-3DOI Listing
May 2017

Demographic characteristics of dengue virus outbreaks in Khyber Pakhtunkhwa province, Pakistan during 2003-2015.

J Formos Med Assoc 2017 09 11;116(9):727-729. Epub 2017 Mar 11.

Department of Virology, National Institute of Health, Park Road, Chak Shahzad, Islamabad, Pakistan. Electronic address:

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http://dx.doi.org/10.1016/j.jfma.2017.02.004DOI Listing
September 2017

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

Infect Dis Poverty 2017 Mar 9;6(1):48. Epub 2017 Mar 9.

Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan.

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.
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http://dx.doi.org/10.1186/s40249-017-0258-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5343310PMC
March 2017

Outbreak of dengue virus type-3 in Malakand, Pakistan 2015; A laboratory perspective.

Acta Trop 2017 May 17;169:202-206. Epub 2017 Feb 17.

Department of Virology, National Institute of Health,Park Road, Chak Shahzad, Islamabad, Pakistan. Electronic address:

An outbreak of dengue fever was reported in Malakand district, Khyber Pakhtunkhwa (KP) province of Pakistan during 2015. Detection of viral RNA by real-time PCR confirmed dengue virus serotype-3 (DENV-3) to be the causative agent causing the outbreak. Phylogenetic analysis based on partial E-NS1 gene sequences showed that the DENV-3 viruses belonged to genotype III with maximum homology with the dengue-3 strains previously reported from Pakistan and India. Our current report provides updated information on molecular epidemiology and phylogenetic analysis of dengue virus serotypes responsible for 2015 outbreak in KP.
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http://dx.doi.org/10.1016/j.actatropica.2017.02.011DOI Listing
May 2017