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Genomic epidemiology of SARS-CoV-2 in Pakistan [article]

Shuhui Song, Cuiping Li, Lu Kang, Dongmei Tian, Nazish Badar, Wentai Ma, Shilei Zhao, Xuan Jiang, Chun Wang, Yongqiao Sun, Wenjie Li, Meng Lei (+14 others)
2021 medRxiv   pre-print
To investigate the initial introductions and transmissions of the SARS-CoV-2 in the country, we performed the largest genomic epidemiology study of COVID-19 in Pakistan and generated 150 complete SARS-CoV  ...  This study has inferred the introductions and transmissions of SARS-CoV-2 in Pakistan, which could provide a guidance for an effective strategy for disease control.  ...  DISCUSSION This is the largest genomic epidemiology study of COVID-19 in Pakistan, with 150 high quality complete SARS-CoV-2 genomes obtained and analyzed.  ... 
doi:10.1101/2021.06.24.21255875 fatcat:odsnwbs6ojc6zcddswhpv6cjaq

Genomic Epidemiology of SARS-CoV-2 Divulge B.1, B.1.36, and B.1.1.7 as the Most Dominant Lineages in First, Second, and Third Wave of SARS-CoV-2 Infections in Pakistan

Atia Basheer, Imran Zahoor
2021 Microorganisms  
The present study aims to investigate the genomic variability and epidemiology of SARS-CoV-2 in Pakistan along with its role in the spread and severity of infection during the three waves of COVID-19.  ...  A total of 453 genomic sequences of Pakistani SARS-CoV-2 were retrieved from GISAID and subjected to MAFFT-based alignment and QC check which resulted in removal of 53 samples.  ...  Conflicts of Interest: The authors declare that they have no conflict of interest. This study had no role in the patient consent under the current frame of research.  ... 
doi:10.3390/microorganisms9122609 pmid:34946210 pmcid:PMC8708969 fatcat:bwqwydu4nbchjl42gexxtntfue

Molecular epidemiology of SARS-CoV-2 in Faisalabad, Pakistan: A real-world clinical experience

Hassan Raza, Braira Wahid, Ghazala Rubi, Adil Gulzar
2020 Infection, Genetics and Evolution  
This retrospective study is the first report of epidemiological trends of COVID-19 in Faisalabad, Pakistan.  ...  As of May 17th, 2020, SARS-CoV-2 has infected 4.6 million people and caused 310,000 deaths, worldwide.  ...  Conflict of interest: None Funding: None  ... 
doi:10.1016/j.meegid.2020.104374 pmid:32450246 pmcid:PMC7242943 fatcat:t4tl6f53sfgzniv5xou6zcoowm

Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan

Massab Umair, Aamer Ikram, Muhammad Salman, Adnan Khurshid, Masroor Alam, Nazish Badar, Rana Suleman, Faheem Tahir, Salmaan Sharif, Joel Montgomery, Shannon Whitmer, John Klena (+1 others)
2021 PLoS ONE  
Although an unprecedented number of SARS-CoV-2 full genomes have been submitted in GISAID and NCBI, data from Pakistan is scarce.  ...  We report the sequencing, genomic characterization, and phylogenetic analysis of five SARS-CoV-2 strains isolated from patients in Pakistan.  ...  Acknowledgments The authors thank all the researchers who deposited SARS-CoV-2 genomes in GISAID contributing to the genomic diversity and phylogenetic relationship of virus.  ... 
doi:10.1371/journal.pone.0248371 pmid:33755704 fatcat:3vjaettvb5h5fcjfoyhphqslci

Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan

Najia Karim Ghanchi, Asghar Nasir, Kiran Iqbal Masood, Syed Hani Abidi, Syed Faisal Mahmood, Akbar Kanji, Safina Razzak, Waqasuddin Khan, Saba Shahid, Maliha Yameen, Ali Raza, Javaria Ashraf (+6 others)
2021 PLoS ONE  
We investigated the genome diversity of SARS-CoV-2 associated with the early COVID-19 period to investigate evolution of the virus in Pakistan.  ...  Whole genome sequences from our laboratory and available genomes were used to investigate phylogeny, genetic variantion and mutation rates of SARS-CoV-2 strains in Pakistan.  ...  Roger Hewson and Barry Atkinson, Public Health England, UK for their assistance in establishing SARS-CoV-2 diagnostics at AKU.  ... 
doi:10.1371/journal.pone.0256451 pmid:34464419 fatcat:vbctkfx4nvgtpcmcn57s2lbyi4

Sequencing of SARS-CoV-2 in local transmission cases through Oxford Nanopore MinION platform from Karachi Pakistan

Samina Naz Mukry, Shariq Ahmed, Ali Raza Bukhari, Aneeta Shahni, Gul Sufaida, Arshi Naz, Tahir Sultan Shamsi
2021 Journal of Infection in Developing Countries  
In this study, the epidemiology of SARS-CoV-2 was studied and locally transmitted SARS-CoV-2 isolates from Karachi were sequenced to compared and identify any possible variants.  ...  The first case of severe acute respiratory syndrome 2 (SARS-CoV-2) was imported to Pakistan in February 2020, since then 8,260 deaths have been witnessed.  ...  Acknowledgements The authors are thankful to Scientechnic for providing the MinION MK1B instrument and timely supply of all ordered consumable for this project during the pandemic.  ... 
doi:10.3855/jidc.14900 pmid:34780358 fatcat:t2e365vrmzd37ec5qdpu6ljgpi

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

Massab Umair, Aamer Ikram, Muhammad Salman, Muhammad Masroor Alam, Nazish Badar, Zaira Rehman, Sana Tamim, Adnan Khurshid, Abdul Ahad, Hamza Ahmad, Samee Ullah
2021 Journal of Medical Virology  
On December 14 2020, a variant of SARS-CoV-2 characterized as VOC-202012/01 (lineage B.1.1.7) emerged in the United Kingdom [1] with rapid expansion to over 64 countries as of January 27, 2021.  ...  The national authorities should proactively focus on expanding genomic surveillance of SARS-CoV-2 to fortify global containment efforts in identifying epidemiologically and clinically significant variants  ...  For phylogenetic analysis, Wuhan reference SARS-CoV-2 (EPI_ISL_529213) sequence and whole genome sequences of B.1.1.7 SARS-CoV-2 strain deposited on GISAID till January 8, 2021 were downloaded followed  ... 
doi:10.1002/jmv.26869 pmid:33570181 pmcid:PMC8013196 fatcat:parb6dk3bfekdipujckxrf6rji

COMPARISON OF SARS-COV2 GENOME SEQUENCES FROM PAKISTAN WITH GENOME SEQUENCES FROM OTHER COUNTRIES

Muhammad Tariq, Fatima Jehan, Nooria Ali Liaqat, , Mehnaz, Umar Farooq
2021 Khyber Medical University Journal  
OBJECTIVE: To analyze SARS-CoV-2 whole genome reported of Pakistan and compare them with other viral strains collected from other world region to better understand the origin and genetic characterization  ...  METHODS: All the available genomic information of SARS-CoV-2 including Pakistani strains were collected from various online sources.  ...  of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.  ... 
doi:10.35845/kmuj.2021.20999 fatcat:7xq2l63k6za6diyiqgmthpqc6y

Laboratory based surveillance of SARS-CoV-2 in Pakistan [article]

Nazish Badar, Aamer Ikram, Hamza Ahmad Mirza, Abdul Ahad, Muhammad Masroor Alam, Yasir Arshad, Massab Umair, Salman Sharif, Afreenish Amir, Muhammad Salman
2020 medRxiv   pre-print
The genomic surveillance of SARS-CoV-2 strains isolated locally has been conducted based on partial ORF1b.  ...  COVID-19 cases are alarmingly increasing in Pakistan since May 2020. Laboratory based surveillance system has been in place since the start of the pandemic.  ...  In addition to diagnostic services, the NIH Pakistan is supporting the national authorities to monitor the extent of community transmission in the country by genomic surveillance of SARS-CoV-2 strains  ... 
doi:10.1101/2020.06.10.20126847 fatcat:bagvtegdznagpld2nykmrnbjxq

SARS-CoV-2 Variants of Concern (VOC) Alpha, Beta, Gamma, Delta, and Omicron coincident with consecutive pandemic waves in Pakistan [article]

Asghar Nasir, Uzma Bashir Aamir, Akbar Kanji, Azra Samreen, Zeeshan Ansar, Najia K. Ghanchi, Ali Raza Bukhari, Kiran Iqbal Masood, Nazneen Islam, Samina Ghani, M. Asif Syed, Mansoor Wassan (+2 others)
2022 medRxiv   pre-print
AbstractIdentification and monitoring of SARS-CoV-2 Variants of Concern/Interest (VOC/VOIs) is essential to guide public health measures.  ...  Of the SARS-CoV-2 PCR positive samples, 81.7% had VOC/VOI, while 18.3% were undetermined. Alpha variants were predominant at 82.5% and 40.3% of the cases in April and May 2021.  ...  Thanks also to the COVID-19 testing staff at the Section of Molecular Pathology, AKUH.  ... 
doi:10.1101/2022.05.19.22275149 fatcat:3f5xn4o56jfi7lyy6xptb5b23e

THE DEVELOPING EPIDEMIOLOGICAL AND THERAPEUTIC CHARACTERISTICS OF 2019 CORONAVIRUS PNEUMONIA NOVEL INCLUDES UNIQUE CHECKS

Muhammad Haris Khan Malik Azaz Haider
2020 Zenodo  
Authors sum up most recent literary works on hereditary, epidemiological, and clinical highlights of COVID-19 in contrast with SARS and MERS as well as underscore unique measures on examination and expected  ...  Constrained epidemiological and medical information propose that sickness range of COVID-19 may contrast from SARS or MERS.  ...  extreme intense respiratory complaint coronavirus also renamed this as SARS-CoV-2 [2] .  ... 
doi:10.5281/zenodo.4025974 fatcat:nrjkru4l2jgzpex2vzqjraduke

A longitudinal survey for genome-based identification of SARS-CoV-2 in sewage water in selected lockdown areas of Lahore city, Pakistan; a potential approach for future smart lockdown strategy [article]

Tahir Yaqub, Muhammad Nawaz, Muhammad Zubair Shabbir, Muhammad Asad Ali, Imran Altaf, Sohail Raza, Muhammad Abu Bakr Shabbir, Muhammad Adnan Ashraf, Syed Zahid Aziz, Sohail Qadir Cheema, Muhammad Bilal Shah, Sohail Hassan (+17 others)
2020 medRxiv   pre-print
With the excretion of SARS-CoV-2 in the stool of symptomatic and asymptomatic COVID-19 patients, its genome detection in the sewage water can be used as a powerful epidemiological tool to predict the number  ...  This study was conducted to detect SARS-CoV-2 genome in sewage water during the lockdown.  ...  ACKNOWLEDGMENTS We thank Government of Punjab for financial support to this project and the WASA directorate Lahore region in facilitation of sampling across the district.  ... 
doi:10.1101/2020.07.31.20165126 fatcat:bcmnrxbb3zfc7nbgo3znl4zgsi

SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021 [article]

Muhammad Bilal Sarwar, Muhammad Yasir, Nabil-Fareed Alikhan, Nadeem Afzal, Leonardo de Oliveria Martins, Thanh Le Viet, Alexander J Trotter, Sophie J Prosolek, Gemma L Kay, Ebenezer Foster-Nyarko, Steven Rudder, David J Baker (+8 others)
2021 medRxiv   pre-print
Currently very few SARS-CoV-2 genomes collected in Pakistan are available, with just 12 covering the third wave, 9 of which are from Islamabad.  ...  Pakistan has one of the worlds largest populations, of over 200 million people and is experiencing a severe third wave of infections caused by SARS-CoV-2 beginning in March 2021.  ...  This report shows the critical importance of whole-genome sequencing of SARS-CoV-2 to determine the prevalence and changing epidemiology of different variants of the virus.  ... 
doi:10.1101/2021.06.04.21258352 fatcat:gad6fxmsbza6bfr2hgzr6ow6zi

THE DEVELOPING EPIDEMIOLOGICAL AND THERAPEUTIC CHARACTERISTICS OF 2019 CORONAVIRS PNEUMONIA NOVEL INCLUDES UNIQUE CHECKS

Dr Zuha Afrinish, Dr. Waqas Ahmad, Dr. Muhammad Tayyab Abbas
2020 Zenodo  
Authors sum up most recent literary works on hereditary, epidemiological, and clinical highlights of COVID‐19 in contrast with SARS and MERS what's more, underscore unique measures on examination and expected  ...  Constrained epidemiological and medical information propose that sickness range of COVID‐19 may contrast from SARS or MERS.  ...  extreme intense respiratory complaint coronavirus also renamed this as SARS-CoV-2 [2] .  ... 
doi:10.5281/zenodo.4009535 fatcat:6ci555jd6rbldbjvznatrwqu3q

THE DEVELOPING EPIDEMIOLOGICAL AND THERAPEUTIC CHARACTERISTICS OF 2019 CORONAVIRS PNEUMONIA NOVEL INCLUDES UNIQUE CHECKS

Muhammad Haris Khan Malik Azaz Haider
2020 Zenodo  
Authors sum up most recent literary works on hereditary, epidemiological, and clinical highlights of COVID‐19 in contrast with SARS and MERS what's more, underscore unique measures on examination and expected  ...  Constrained epidemiological and medical information propose that sickness range of COVID‐19 may contrast from SARS or MERS.  ...  extreme intense respiratory complaint coronavirus also renamed this as SARS-CoV-2 [2] .  ... 
doi:10.5281/zenodo.4016101 fatcat:oqfamgnwwjhhffcx4uff3yfyc4
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