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In December 2019, the emergence of SARS-CoV-2 virus in China led to a pandemic. Since both Influenza Like Illness (ILI) and COVID-19 case definitions overlap, we re-investigated the ILI cases using PCR for the presence of SARS-CoV-2 in 739 nasopharyngeal swabs collected from November 2019 to March 2020. SARS-CoV-2 RNA was found in 37 samples (5%) collected mostly during February 2020. It was followed by confirmation of evolutionary and spatial relationships using next generation sequencing (NGS). We observed that the overall incidence of ILI cases during 2019–2020 influenza season was considerably higher than previous years and was gradually replaced with SARS-CoV-2, which indicated a silent transmission among ambulatory patients. Sequencing of representative isolates confirmed independent introductions and silent transmission earlier than previously thought. Evolutionary and spatial analyses revealed clustering in the GH clade, characterized by three amino acid substitutions in spike gene (D614G), RdRp (P323L) and NS3 (Q57H). P323L causes conformational change near nsp8 binding site that might affect virus replication and transcription. In conclusion, assessment of the community transmission among patients with mild COVID-19 illness, particularly those without epidemiological link for acquiring the virus, is of utmost importance to guide policy makers to optimize public health interventions. The detection of SARS-CoV-2 in ILI cases shows the importance of ILI surveillance systems and warrants its further strengthening to mitigate the ongoing transmission of SARS-CoV-2. The effect of NS3 substitutions on oligomerization or membrane channel function (intra- and extracellular) needs functional validation.
Bandar Alosaimi; Asif Naeem; Majed Alghoribi; Lilian Okdah; Maaweya Hamed; Ahmad AlYami; Athari Alotaibi; Mushira Enani. Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients. Viruses 2021, 13, 136 .
AMA StyleBandar Alosaimi, Asif Naeem, Majed Alghoribi, Lilian Okdah, Maaweya Hamed, Ahmad AlYami, Athari Alotaibi, Mushira Enani. Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients. Viruses. 2021; 13 (1):136.
Chicago/Turabian StyleBandar Alosaimi; Asif Naeem; Majed Alghoribi; Lilian Okdah; Maaweya Hamed; Ahmad AlYami; Athari Alotaibi; Mushira Enani. 2021. "Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients." Viruses 13, no. 1: 136.
The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a lethal zoonotic pathogen circulating in the Arabian Peninsula since 2012. There is no vaccine for MERS and anti-viral treatment is generally not applicable. We investigated the evolution of the MERS-CoV spike gene sequences and changes in viral loads over time from patients in Saudi Arabia from 2015–2017. All the MERS-CoV strains belonged to lineage 5, and showed high sequence homology (99.9%) to 2017 strains. Recombination analysis showed a potential recombination event in study strains from patients in Saudi Arabia. The spike gene showed eight amino acid substitutions, especially between the A1 and B5 lineage, and contained positively selected codon 1020. We also determined that the viral loads were significantly (p < 0.001) higher in fatal cases, and virus shedding was prolonged in some fatal cases beyond 21 days. The viral concentration peaked during the first week of illness, and the lower respiratory specimens had higher levels of MERS-CoV RNA. The presence of the diversifying selection and the topologies with the structural mapping of residues under purifying selection suggested that codon 1020 might have a role in the evolution of spike gene during the divergence of different lineages. This study will improve our understanding of the evolution of MERS-CoV, and also highlights the need for enhanced surveillance in humans and dromedaries. The presence of amino acid changes at the N-terminal domain and structural mapping of residues under positive selection at heptad repeat 1 provides better insight into the adaptive evolution of the spike gene and might have a potential role in virus-host tropism and pathogenesis.
Asif Naeem; Maaweya E. Hamed; Majed F. Alghoribi; Waleed Aljabr; Hadel Alsaran; Mushira A. Enani; Bandar Alosaimi. Molecular Evolution and Structural Mapping of N-Terminal Domain in Spike Gene of Middle East Respiratory Syndrome Coronavirus (MERS-CoV). Viruses 2020, 12, 502 .
AMA StyleAsif Naeem, Maaweya E. Hamed, Majed F. Alghoribi, Waleed Aljabr, Hadel Alsaran, Mushira A. Enani, Bandar Alosaimi. Molecular Evolution and Structural Mapping of N-Terminal Domain in Spike Gene of Middle East Respiratory Syndrome Coronavirus (MERS-CoV). Viruses. 2020; 12 (5):502.
Chicago/Turabian StyleAsif Naeem; Maaweya E. Hamed; Majed F. Alghoribi; Waleed Aljabr; Hadel Alsaran; Mushira A. Enani; Bandar Alosaimi. 2020. "Molecular Evolution and Structural Mapping of N-Terminal Domain in Spike Gene of Middle East Respiratory Syndrome Coronavirus (MERS-CoV)." Viruses 12, no. 5: 502.
Saffold virus (SAFV), a picornavirus, is occasionally detected in children with acute flaccid paralysis, meningitis, and cerebellitis; however, the neuropathogenicity of SAFV remains undetermined. The virulence of two clinical isolates of SAFV type 3 (SAFV-3) obtained from a patient with aseptic meningitis (AM strain) and acute upper respiratory inflammation (UR strain) was analyzed in neonatal and young mice utilizing virological, pathological, and immunological methods. The polyproteins of the strains differed in eight amino acids. Both clinical isolates were infective, exhibited neurotropism, and were mildly neurovirulent in neonatal ddY mice. Both strains pathologically infected neural progenitor cells and glial cells, but not large neurons, with the UR strain also infecting epithelial cells. UR infection resulted in longer inflammation in the brain and spinal cord because of demyelination, while the AM strain showed more infectivity in the cerebellum in neonatal ddY mice. Additionally, young BALB/c mice seroconverted following mucosal inoculation with the UR, but not the AM, strain. Both SAFV-3 isolates had neurotropism and mild neurovirulence but showed different cell tropisms in both neonatal and young mouse models. This animal model has the potential to recapitulate the potential neuropathogenicity of SAFV-3.
Osamu Kotani; Asif Naeem; Tadaki Suzuki; Naoko Iwata-Yoshikawa; Yuko Sato; Noriko Nakajima; Takushi Hosomi; Hiroyuki Tsukagoshi; Kunihisa Kozawa; Hideki Hasegawa; Fumihiro Taguchi; Hiroyuki Shimizu; Noriyo Nagata. Neuropathogenicity of Two Saffold Virus Type 3 Isolates in Mouse Models. PLOS ONE 2016, 11, e0148184 .
AMA StyleOsamu Kotani, Asif Naeem, Tadaki Suzuki, Naoko Iwata-Yoshikawa, Yuko Sato, Noriko Nakajima, Takushi Hosomi, Hiroyuki Tsukagoshi, Kunihisa Kozawa, Hideki Hasegawa, Fumihiro Taguchi, Hiroyuki Shimizu, Noriyo Nagata. Neuropathogenicity of Two Saffold Virus Type 3 Isolates in Mouse Models. PLOS ONE. 2016; 11 (2):e0148184.
Chicago/Turabian StyleOsamu Kotani; Asif Naeem; Tadaki Suzuki; Naoko Iwata-Yoshikawa; Yuko Sato; Noriko Nakajima; Takushi Hosomi; Hiroyuki Tsukagoshi; Kunihisa Kozawa; Hideki Hasegawa; Fumihiro Taguchi; Hiroyuki Shimizu; Noriyo Nagata. 2016. "Neuropathogenicity of Two Saffold Virus Type 3 Isolates in Mouse Models." PLOS ONE 11, no. 2: e0148184.
Human cardioviruses or Saffold viruses (SAFVs) of the family Picornaviridae are newly emerging viruses whose genetic and phenotypic diversity are poorly understood. We report here the full genome sequence of 11 SAFV genotypes from Pakistan and Afghanistan, along with a re-evaluation of their genetic diversity and recombination. We detected 88 SAFV from stool samples of 943 acute flaccid paralysis cases using reverse transcriptase-PCR targeting the 5′ untranslated region (UTR). Further characterization based on complete VP1 analysis revealed 71 SAFVs belonging to 11 genotypes, including three previously unidentified genotypes. SAFV showed high genetic diversity and recombination based on phylogenetic, pairwise distance distributions and recombination mapping analyses performed herein. Phylogenies based on non-structural and UTRs were highly incongruent indicating frequent recombination events among SAFVs. We improved the SAFV genotyping classification criteria by determining new VP1 thresholds based on the principles used for the classification of enteroviruses. For genotype assignment, we propose a threshold of 23 and 10 % divergence for VP1 nucleotide and amino acid sequences, respectively. Other members of the species Theilovirus, such as Thera virus and Theiler’s murine encephalomyelitis virus, are difficult to classify in the same species as SAFV, because they are genetically distinct from SAFV, with 41–56 % aa pairwise distances. The new genetic information obtained in this study will improve our understanding of the evolution and classification of SAFV.
Asif Naeem; Takushi Hosomi; Yorihiro Nishimura; Muhammad Masroor Alam; Tomoichiro Oka; Syed Sohail Zahoor Zaidi; Hiroyuki Shimizu. Genetic diversity of circulating Saffold viruses in Pakistan and Afghanistan. Journal of General Virology 2014, 95, 1945 -1957.
AMA StyleAsif Naeem, Takushi Hosomi, Yorihiro Nishimura, Muhammad Masroor Alam, Tomoichiro Oka, Syed Sohail Zahoor Zaidi, Hiroyuki Shimizu. Genetic diversity of circulating Saffold viruses in Pakistan and Afghanistan. Journal of General Virology. 2014; 95 (9):1945-1957.
Chicago/Turabian StyleAsif Naeem; Takushi Hosomi; Yorihiro Nishimura; Muhammad Masroor Alam; Tomoichiro Oka; Syed Sohail Zahoor Zaidi; Hiroyuki Shimizu. 2014. "Genetic diversity of circulating Saffold viruses in Pakistan and Afghanistan." Journal of General Virology 95, no. 9: 1945-1957.
Since 2005, a large poliomyelitis outbreak associated with type 2 circulating vaccine-derived poliovirus (cVDPV2) has occurred in northern Nigeria, where immunization coverage with trivalent oral poliovirus vaccine (tOPV) has been low. Phylogenetic analysis of P1/capsid region sequences of isolates from each of the 403 cases reported in 2005 to 2011 resolved the outbreak into 23 independent type 2 vaccine-derived poliovirus (VDPV2) emergences, at least 7 of which established circulating lineage groups. Virus from one emergence (lineage group 2005-8; 361 isolates) was estimated to have circulated for over 6 years. The population of the major cVDPV2 lineage group expanded rapidly in early 2009, fell sharply after two tOPV rounds in mid-2009, and gradually expanded again through 2011. The two major determinants of attenuation of the Sabin 2 oral poliovirus vaccine strain (A481 in the 5′-untranslated region [5′-UTR] and VP1-Ile143) had been replaced in all VDPV2 isolates; most A481 5′-UTR replacements occurred by recombination with other enteroviruses. cVDPV2 isolates representing different lineage groups had biological properties indistinguishable from those of wild polioviruses, including efficient growth in neuron-derived HEK293 cells, the capacity to cause paralytic disease in both humans and PVR-Tg21 transgenic mice, loss of the temperature-sensitive phenotype, and the capacity for sustained person-to-person transmission. We estimate from the poliomyelitis case count and the paralytic case-to-infection ratio for type 2 wild poliovirus infections that ∼700,000 cVDPV2 infections have occurred during the outbreak. The detection of multiple concurrent cVDPV2 outbreaks in northern Nigeria highlights the risks of cVDPV emergence accompanying tOPV use at low rates of coverage in developing countries.
Cara C. Burns; Jing Shaw; Jaume Jorba; David Nadeba Bukbuk; Festus Adu; Nicksy Gumede; Muhammed Ali Pate; Emmanuel Ade Abanida; Alex Gasasira; Jane Iber; Q. Chen; Annelet Vincent; Paul Chenoweth; Elizabeth Henderson; Kathleen Wannemuehler; Asif Naeem; Rifqiyah Nur Umami; Yorihiro Nishimura; Hiroyuki Shimizu; Marycelin Baba; Johnson Adeniji; A. J. Williams; David R. Kilpatrick; M. Steven Oberste; Steven G. Wassilak; Oyewale Tomori; Mark A. Pallansch; Olen Kew. Multiple Independent Emergences of Type 2 Vaccine-Derived Polioviruses during a Large Outbreak in Northern Nigeria. Journal of Virology 2013, 87, 4907 -4922.
AMA StyleCara C. Burns, Jing Shaw, Jaume Jorba, David Nadeba Bukbuk, Festus Adu, Nicksy Gumede, Muhammed Ali Pate, Emmanuel Ade Abanida, Alex Gasasira, Jane Iber, Q. Chen, Annelet Vincent, Paul Chenoweth, Elizabeth Henderson, Kathleen Wannemuehler, Asif Naeem, Rifqiyah Nur Umami, Yorihiro Nishimura, Hiroyuki Shimizu, Marycelin Baba, Johnson Adeniji, A. J. Williams, David R. Kilpatrick, M. Steven Oberste, Steven G. Wassilak, Oyewale Tomori, Mark A. Pallansch, Olen Kew. Multiple Independent Emergences of Type 2 Vaccine-Derived Polioviruses during a Large Outbreak in Northern Nigeria. Journal of Virology. 2013; 87 (9):4907-4922.
Chicago/Turabian StyleCara C. Burns; Jing Shaw; Jaume Jorba; David Nadeba Bukbuk; Festus Adu; Nicksy Gumede; Muhammed Ali Pate; Emmanuel Ade Abanida; Alex Gasasira; Jane Iber; Q. Chen; Annelet Vincent; Paul Chenoweth; Elizabeth Henderson; Kathleen Wannemuehler; Asif Naeem; Rifqiyah Nur Umami; Yorihiro Nishimura; Hiroyuki Shimizu; Marycelin Baba; Johnson Adeniji; A. J. Williams; David R. Kilpatrick; M. Steven Oberste; Steven G. Wassilak; Oyewale Tomori; Mark A. Pallansch; Olen Kew. 2013. "Multiple Independent Emergences of Type 2 Vaccine-Derived Polioviruses during a Large Outbreak in Northern Nigeria." Journal of Virology 87, no. 9: 4907-4922.
Rotaviruses are among the major causes of gastroenteritis and diarrhea among children in developed as well as the developing countries. The rapidly evolving strain prevalence and circulation have resulted in the emergence of novel strains over the period worldwide. The introduction of G12 prototype in 1987 from Philippines and subsequently re-emergence among most of the Asian countries along with USA and Europe has provoked new research horizons to address the global distribution of rotavirus serotypes. These newly emerging subtypes and their sustenance among the population have posed tremendous challenge to the development of an effectual vaccine with heterotypic protective efficacy. In Pakistan, no data is available regarding the prevalent rotavirus serotypes; therefore, this is the first study to report the prevalence of G12 strain in Pakistan in hospitalized children with diarrhea addressing a dire need of further large-scale epidemiological surveys to resolve the underlying rotavirus isolates in both the hospitalized and the community neonatal and child population before formulating the vaccine introduction policies in the country's routine immunization program.
Muhammad Masroor Alam; Salman Akbar Malik; Shahzad Shaukat; Asif Naeem; Salmaan Sharif; Mehar Angez; Muhammad Suleman Rana; Adnan Khurshid; Sohail Zahoor Zaidi. Genetic characterization of rotavirus subtypes in Pakistan-first report of G12 genotype from Pakistan under WHO-Eastern Mediterranean region. Virus Research 2009, 144, 280 -284.
AMA StyleMuhammad Masroor Alam, Salman Akbar Malik, Shahzad Shaukat, Asif Naeem, Salmaan Sharif, Mehar Angez, Muhammad Suleman Rana, Adnan Khurshid, Sohail Zahoor Zaidi. Genetic characterization of rotavirus subtypes in Pakistan-first report of G12 genotype from Pakistan under WHO-Eastern Mediterranean region. Virus Research. 2009; 144 (1-2):280-284.
Chicago/Turabian StyleMuhammad Masroor Alam; Salman Akbar Malik; Shahzad Shaukat; Asif Naeem; Salmaan Sharif; Mehar Angez; Muhammad Suleman Rana; Adnan Khurshid; Sohail Zahoor Zaidi. 2009. "Genetic characterization of rotavirus subtypes in Pakistan-first report of G12 genotype from Pakistan under WHO-Eastern Mediterranean region." Virus Research 144, no. 1-2: 280-284.
We analyzed viral nucleic acids in stool samples collected from 35 South Asian children with nonpolio acute flaccid paralysis (AFP). Sequence-independent reverse transcription and PCR amplification of capsid-protected, nuclease-resistant viral nucleic acids were followed by DNA sequencing and sequence similarity searches. Limited Sanger sequencing (35 to 240 subclones per sample) identified an average of 1.4 distinct eukaryotic viruses per sample, while pyrosequencing yielded 2.6 viruses per sample. In addition to bacteriophage and plant viruses, we detected known enteric viruses, including rotavirus, adenovirus, picobirnavirus, and human enterovirus species A (HEV-A) to HEV-C, as well as numerous other members of the Picornaviridae family, including parechovirus, Aichi virus, rhinovirus, and human cardiovirus. The viruses with the most divergent sequences relative to those of previously reported viruses included members of a novel Picornaviridae genus and four new viral species (members of the Dicistroviridae , Nodaviridae , and Circoviridae families and the Bocavirus genus). Samples from six healthy contacts of AFP patients were similarly analyzed and also contained numerous viruses, particularly HEV-C, including a potentially novel Enterovirus genotype. Determining the prevalences and pathogenicities of the novel genotypes, species, genera, and potential new viral families identified in this study in different demographic groups will require further studies with different demographic and patient groups, now facilitated by knowledge of these viral genomes.
Joseph G. Victoria; Amit Kapoor; Linlin Li; Olga Blinkova; Beth Slikas; Chunlin Wang; Asif Naeem; Sohail Zaidi; Eric Delwart. Metagenomic Analyses of Viruses in Stool Samples from Children with Acute Flaccid Paralysis. Journal of Virology 2009, 83, 4642 -4651.
AMA StyleJoseph G. Victoria, Amit Kapoor, Linlin Li, Olga Blinkova, Beth Slikas, Chunlin Wang, Asif Naeem, Sohail Zaidi, Eric Delwart. Metagenomic Analyses of Viruses in Stool Samples from Children with Acute Flaccid Paralysis. Journal of Virology. 2009; 83 (9):4642-4651.
Chicago/Turabian StyleJoseph G. Victoria; Amit Kapoor; Linlin Li; Olga Blinkova; Beth Slikas; Chunlin Wang; Asif Naeem; Sohail Zaidi; Eric Delwart. 2009. "Metagenomic Analyses of Viruses in Stool Samples from Children with Acute Flaccid Paralysis." Journal of Virology 83, no. 9: 4642-4651.
Cardioviruses cause enteric infections in mice and rats which when disseminated have been associated with myocarditis, type 1 diabetes, encephalitis, and multiple sclerosis-like symptoms. Cardioviruses have also been detected at lower frequencies in other mammals. The Cardiovirus genus within the Picornaviridae family is currently made up of two viral species, Theilovirus and Encephalomyocarditis virus . Until recently, only a single strain of cardioviruses (Vilyuisk virus within the Theilovirus species) associated with a geographically restricted and prevalent encephalitis-like condition had been reported to occur in humans. A second theilovirus-related cardiovirus ( Saffold virus [SAFV]) was reported in 2007 and subsequently found in respiratory secretions from children with respiratory problems and in stools of both healthy and diarrheic children. Using viral metagenomics, we identified RNA fragments related to SAFV in the stools of Pakistani and Afghani children with nonpolio acute flaccid paralysis (AFP). We sequenced three near-full-length genomes, showing the presence of divergent strains of SAFV and preliminary evidence of a distant recombination event between the ancestors of the Theiler-like viruses of rats and those of human SAFV. Further VP1 sequencing showed the presence of five new SAFV genotypes, doubling the reported genetic diversity of human and animal theiloviruses combined. Both AFP patients and healthy children in Pakistan were found to be excreting SAFV at high frequencies of 9 and 12%, respectively. Further studies are needed to examine the roles of these highly common and diverse SAFV genotypes in nonpolio AFP and other human diseases.
Olga Blinkova; Amit Kapoor; Joseph Victoria; Morris Jones; Nathan Wolfe; Asif Naeem; Shahzad Shaukat; Salmaan Sharif; Muhammad Masroor Alam; Mehar Angez; Sohail Zaidi; Eric L. Delwart. Cardioviruses Are Genetically Diverse and Cause Common Enteric Infections in South Asian Children. Journal of Virology 2009, 83, 4631 -4641.
AMA StyleOlga Blinkova, Amit Kapoor, Joseph Victoria, Morris Jones, Nathan Wolfe, Asif Naeem, Shahzad Shaukat, Salmaan Sharif, Muhammad Masroor Alam, Mehar Angez, Sohail Zaidi, Eric L. Delwart. Cardioviruses Are Genetically Diverse and Cause Common Enteric Infections in South Asian Children. Journal of Virology. 2009; 83 (9):4631-4641.
Chicago/Turabian StyleOlga Blinkova; Amit Kapoor; Joseph Victoria; Morris Jones; Nathan Wolfe; Asif Naeem; Shahzad Shaukat; Salmaan Sharif; Muhammad Masroor Alam; Mehar Angez; Sohail Zaidi; Eric L. Delwart. 2009. "Cardioviruses Are Genetically Diverse and Cause Common Enteric Infections in South Asian Children." Journal of Virology 83, no. 9: 4631-4641.
Using a simple metagenomic approach, we identified a divergent human parechovirus (HPeV) in the stool of a child in Pakistan. Genomic characterization showed this virus was distinct enough from reported HPeV types to qualify as candidate prototype for the seventh HPeV type.
Linlin Li; Joseph Victoria; Amit Kapoor; Asif Naeem; Shahzad Shaukat; Salmaan Sharif; Muhammad Masroor Alam; Mehar Angez; Sohail Zahoor Zaidi; Eric Delwart. Genomic Characterization of Novel Human Parechovirus Type. Emerging Infectious Diseases 2009, 15, 288 -291.
AMA StyleLinlin Li, Joseph Victoria, Amit Kapoor, Asif Naeem, Shahzad Shaukat, Salmaan Sharif, Muhammad Masroor Alam, Mehar Angez, Sohail Zahoor Zaidi, Eric Delwart. Genomic Characterization of Novel Human Parechovirus Type. Emerging Infectious Diseases. 2009; 15 (2):288-291.
Chicago/Turabian StyleLinlin Li; Joseph Victoria; Amit Kapoor; Asif Naeem; Shahzad Shaukat; Salmaan Sharif; Muhammad Masroor Alam; Mehar Angez; Sohail Zahoor Zaidi; Eric Delwart. 2009. "Genomic Characterization of Novel Human Parechovirus Type." Emerging Infectious Diseases 15, no. 2: 288-291.
Using viral metagenomics we identified a novel parvovirus species in human stool whose closest phylogenetic relative is the human bocavirus (HBoV). HBoV2 has an identical genomic organization to HBoV but share only 78%, 67%, and 80% identity to its NS1, NP1 and VP1/VP2 proteins. Using PCR we detected HBoV2 sequences in 5/98 Pakistani children stool samples and 3/699 stool samples from the UK. Near full genome sequencing showed the presence of three divergent genotypes and evidence of recombination. Further studies are required to determine sites of replication of HBoV2 and potential associations with clinical symptoms or disease.
Amit Kapoor; Elizabeth Slikas; Peter Simmonds; Thaweesak Chieochansin; Asif Naeem; Shahzad Shaukat; Muhammad Masroor Alam; Salmaan Sharif; Mehar Angez; Sohail Zahoor Zaidi; Eric Delwart. A Newly Identified Bocavirus Species in Human Stool. Journal of Infectious Diseases 2009, 199, 196 -200.
AMA StyleAmit Kapoor, Elizabeth Slikas, Peter Simmonds, Thaweesak Chieochansin, Asif Naeem, Shahzad Shaukat, Muhammad Masroor Alam, Salmaan Sharif, Mehar Angez, Sohail Zahoor Zaidi, Eric Delwart. A Newly Identified Bocavirus Species in Human Stool. Journal of Infectious Diseases. 2009; 199 (2):196-200.
Chicago/Turabian StyleAmit Kapoor; Elizabeth Slikas; Peter Simmonds; Thaweesak Chieochansin; Asif Naeem; Shahzad Shaukat; Muhammad Masroor Alam; Salmaan Sharif; Mehar Angez; Sohail Zahoor Zaidi; Eric Delwart. 2009. "A Newly Identified Bocavirus Species in Human Stool." Journal of Infectious Diseases 199, no. 2: 196-200.
Viral metagenomics focused on particle-protected nucleic acids was used on the stools of South Asian children with nonpolio acute flaccid paralysis (AFP). We identified sequences distantly related to Seneca Valley virus and cardioviruses that were then used as genetic footholds to characterize multiple viral species within a previously unreported genus of the Picornaviridae family. The picornaviruses were detected in the stools of >40% of AFP and healthy Pakistani children. A genetically diverse and highly prevalent enteric viral infection, characteristics similar to the Enterovirus genus, was therefore identified substantially expanding the genetic diversity of the RNA viral flora commonly found in children.
A. Kapoor; J. Victoria; Peter Simmonds; E. Slikas; T. Chieochansin; Asif Naeem; S. Shaukat; S. Sharif; M. M. Alam; M. Angez; C. Wang; R. W. Shafer; S. Zaidi; E. Delwart. A highly prevalent and genetically diversified Picornaviridae genus in South Asian children. Proceedings of the National Academy of Sciences 2008, 105, 20482 -20487.
AMA StyleA. Kapoor, J. Victoria, Peter Simmonds, E. Slikas, T. Chieochansin, Asif Naeem, S. Shaukat, S. Sharif, M. M. Alam, M. Angez, C. Wang, R. W. Shafer, S. Zaidi, E. Delwart. A highly prevalent and genetically diversified Picornaviridae genus in South Asian children. Proceedings of the National Academy of Sciences. 2008; 105 (51):20482-20487.
Chicago/Turabian StyleA. Kapoor; J. Victoria; Peter Simmonds; E. Slikas; T. Chieochansin; Asif Naeem; S. Shaukat; S. Sharif; M. M. Alam; M. Angez; C. Wang; R. W. Shafer; S. Zaidi; E. Delwart. 2008. "A highly prevalent and genetically diversified Picornaviridae genus in South Asian children." Proceedings of the National Academy of Sciences 105, no. 51: 20482-20487.
Eight genotypes of Hepatitis B virus designated A-H, have been known but in Pakistan, no such data is available on the prevalent HBV genotypes. Therefore, the subject study was conducted to determine HBV genotypes in the indigenous Pakistani population.
Muhammad Masroor Alam; Sohail Zahoor Zaidi; Salman Akbar Malik; Shahzad Shaukat; Asif Naeem; Salmaan Sharif; Mehar Angez; Javed Aslam Butt. Molecular epidemiology of Hepatitis B virus genotypes in Pakistan. BMC Infectious Diseases 2007, 7, 115 -115.
AMA StyleMuhammad Masroor Alam, Sohail Zahoor Zaidi, Salman Akbar Malik, Shahzad Shaukat, Asif Naeem, Salmaan Sharif, Mehar Angez, Javed Aslam Butt. Molecular epidemiology of Hepatitis B virus genotypes in Pakistan. BMC Infectious Diseases. 2007; 7 (1):115-115.
Chicago/Turabian StyleMuhammad Masroor Alam; Sohail Zahoor Zaidi; Salman Akbar Malik; Shahzad Shaukat; Asif Naeem; Salmaan Sharif; Mehar Angez; Javed Aslam Butt. 2007. "Molecular epidemiology of Hepatitis B virus genotypes in Pakistan." BMC Infectious Diseases 7, no. 1: 115-115.
The infection rate of hepatitis B virus is continuously increasing in Pakistan. Therefore, a comprehensive study of epidemiological data is the need of time.
Muhammad Masroor Alam; Soahil Zahoor Zaidi; Salman Akbar Malik; Asif Naeem; Shahzad Shaukat; Salmaan Sharif; Mehar Angez; Anis Khan; Javed Aslam Butt. Serology based disease status of Pakistani population infected with Hepatitis B virus. BMC Infectious Diseases 2007, 7, 64 -64.
AMA StyleMuhammad Masroor Alam, Soahil Zahoor Zaidi, Salman Akbar Malik, Asif Naeem, Shahzad Shaukat, Salmaan Sharif, Mehar Angez, Anis Khan, Javed Aslam Butt. Serology based disease status of Pakistani population infected with Hepatitis B virus. BMC Infectious Diseases. 2007; 7 (1):64-64.
Chicago/Turabian StyleMuhammad Masroor Alam; Soahil Zahoor Zaidi; Salman Akbar Malik; Asif Naeem; Shahzad Shaukat; Salmaan Sharif; Mehar Angez; Anis Khan; Javed Aslam Butt. 2007. "Serology based disease status of Pakistani population infected with Hepatitis B virus." BMC Infectious Diseases 7, no. 1: 64-64.
Enteroviruses are among the most common viruses infecting humans worldwide and they are associated with diverse clinical syndromes. Acute flaccid paralysis (AFP) is a clinical manifestation of enteroviral neuropathy, transverse myelitis, Guillian-Barre Syndrome, Traumatic neuritis and many other nervous system disorders. The objective of this study was to understand the role of Non-Polio Enteroviruses (NPEV) towards this crippling disorder. Stool specimens of 1775 children, aged less than 15 years, suffering from acute flaccid paralysis were collected after informed consent within 14 days of onset of symptoms during January 2003 to September 2003. The specimens were inoculated on RD and L20B cells using conventional tube cell culture while micro-neutralization test was used to identify the non-polio enterovirus (NPEV) serotypes. Detailed clinical information and 60-days follow-up reports were analyzed for NPEV-associated AFP cases. NPEV were isolated from 474 samples. The male to female ratio was 1.4:1. The isolation of NPEV decreased significantly with the increase in age. Cases associated with fever at the onset of NPEV-associated AFP were found to be 62%. The paralysis was found asymmetrical in 67% cases, the progression of paralysis to peak within 4 days was found in 72% cases and residual paralysis after 60 days of paralysis onset was observed in 39% cases associated with NPEV. A clinical diagnosis of Guillian-Barre syndrome was made in 32% cases. On Microneutralization assay, echo-6 (13%) and coxsackievirus B (13%) were the most commonly isolated serotypes of NPEV along with E-7, E-13, E-11, E-4 and E-30. The isolates (n = 181) found untypable by the antiserum pools were confirmed as NPEV by PCR using Pan-Enterovirus primers. The present study suggests that NPEV are a dominant cause of AFP and different serotypes of NPEV are randomly distributed in Pakistan. The untypable isolates need further characterization and analysis in order to determine their association with clinical presentation of a case.
Mohsan Saeed; Sohail Z Zaidi; Asif Naeem; Muhammad Masroor; Salmaan Sharif; Shahzad Shaukat; Mehar Angez; Anis Khan. Epidemiology and clinical findings associated with enteroviral acute flaccid paralysis in Pakistan. BMC Infectious Diseases 2007, 7, 6 -6.
AMA StyleMohsan Saeed, Sohail Z Zaidi, Asif Naeem, Muhammad Masroor, Salmaan Sharif, Shahzad Shaukat, Mehar Angez, Anis Khan. Epidemiology and clinical findings associated with enteroviral acute flaccid paralysis in Pakistan. BMC Infectious Diseases. 2007; 7 (1):6-6.
Chicago/Turabian StyleMohsan Saeed; Sohail Z Zaidi; Asif Naeem; Muhammad Masroor; Salmaan Sharif; Shahzad Shaukat; Mehar Angez; Anis Khan. 2007. "Epidemiology and clinical findings associated with enteroviral acute flaccid paralysis in Pakistan." BMC Infectious Diseases 7, no. 1: 6-6.
The epidemiological significance of Hepatitis B virus genotypes has been well established and becoming an essential concern day by day however, much little is known about the mixed infection with more than one Hepatitis B virus genotypes and their clinical relevance.
Muhammad Masroor Alam; Sohail Zahoor Zaidi; Shehzad Shaukat; Salmaan Sharif; Mehar Angez; Asif Naeem; Shamim Saleha; Javed Aslam Butt; Salman Akbar Malik. Common Genotypes of Hepatitis B virus prevalent in Injecting drug abusers (addicts) of North West Frontier Province of Pakistan. Virology Journal 2007, 4, 63 -63.
AMA StyleMuhammad Masroor Alam, Sohail Zahoor Zaidi, Shehzad Shaukat, Salmaan Sharif, Mehar Angez, Asif Naeem, Shamim Saleha, Javed Aslam Butt, Salman Akbar Malik. Common Genotypes of Hepatitis B virus prevalent in Injecting drug abusers (addicts) of North West Frontier Province of Pakistan. Virology Journal. 2007; 4 (1):63-63.
Chicago/Turabian StyleMuhammad Masroor Alam; Sohail Zahoor Zaidi; Shehzad Shaukat; Salmaan Sharif; Mehar Angez; Asif Naeem; Shamim Saleha; Javed Aslam Butt; Salman Akbar Malik. 2007. "Common Genotypes of Hepatitis B virus prevalent in Injecting drug abusers (addicts) of North West Frontier Province of Pakistan." Virology Journal 4, no. 1: 63-63.