key: cord-0950176-iz8e6cf1
authors: Badar, N.; Ikram, A.; Mirza, H. A.; Ahad, A.; Alam, M. M.; Arshad, Y.; Umair, M.; Sharif, S.; Amir, A.; Salman, M.
title: Laboratory based surveillance of SARS-CoV-2 in Pakistan
date: 2020-06-12
journal: nan
DOI: 10.1101/2020.06.10.20126847
sha: 0b60550ac0d3a6b782b1d5e1128c6ee08c9d7b0e
doc_id: 950176
cord_uid: iz8e6cf1

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. The genomic surveillance of SARS-CoV-2 strains isolated locally has been conducted based on partial ORF1b. The sequences were classified to show the phylogenetic correlation and showed 100% homology with those detected in neighboring countries India and China. The rapid increase in cases has led to development of robust strategies to enhance the laboratory testing capacity. We are currently meeting the country requirement to diagnose the virus in the community. Nonetheless, factors like recent ease in lockdown measures has led to massive rise in number of cases in few weeks time.

with those detected in neighboring countries India and China. The rapid increase in cases has led to development of robust strategies to enhance the laboratory testing capacity. We are currently meeting the country requirement to diagnose the virus in the community. Nonetheless, factors like recent ease in lockdown measures has led to massive rise in number of cases in few weeks time.

The world is currently going through one of the major public health challenges of twenty first century: SARS-CoV-2 pandemic that emerged from Wuhan, China during December 2019.

Pakistan has joined the growing number of Asian countries reporting cases of novel coronavirus disease (COVID-19), starting with two confirmed patients on 25 th Feb 2020 and since then, the situation is propagating atrociously. As of May 21 2020, 50694 laboratory confirmed cases and 1067 deaths (2.14% case fatality rate) have been reported in Pakistan ( Figure 1B and 1C ).

Since February 2020, Pakistan has initiated hospital-based surveillance system for SARS-CoV-2 infections, mainly targeting tertiary care and teaching hospitals across Pakistan. These hospitals serve as the filter clinic for initial screening of patients based on their clinical signs and symptoms and act as STAT labs to collect and refer specimen to designated laboratories. The diagnostic capacity in Pakistan has been timely strengthened by engaging laboratories from both public and private sector and currently expanded to 70 facilities. The vertical program already functional in the country including (but not limited to) polio, measles, rotavirus, influenza and tuberculosis supported the government by transforming their infrastructure and allocating human resource for COVID-19 laboratory diagnostics services. All rights reserved. No reuse allowed without permission.

(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted June 12, 2020. 

Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

World Health Organization. Coronavirus disease (COVID-19) technical guidance: Surveillance and case definitions

Closed environments facilitate secondary transmission of coronavirus disease 2019 (COVID-19)

All rights reserved. No reuse allowed without permission.(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint this version posted June 12, 2020. . https://doi.org/10.1101/2020.06.10.20126847 doi: medRxiv preprint All rights reserved. No reuse allowed without permission.(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint this version posted June 12, 2020. . https://doi.org/10.1101/2020.06.10.20126847 doi: medRxiv preprint

None declared by any co-author (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint this version posted June 12, 2020. . https://doi.org/10.1101/2020.06.10.20126847 doi: medRxiv preprint All rights reserved. No reuse allowed without permission.(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint this version posted June 12, 2020. . https://doi.org/10.1101/2020.06.10.20126847 doi: medRxiv preprint