STRENGTH OF ASSOCIATION BETWEEN GENERALIZED/NONSPECIFIC COVID-19 SIGNS & SYMPTOMS WITH SARS-COV 2 SPECIFIC ORF, N, E GENES IDENTIFIED THROUGH REAL TIME PCR. (preprint)

BACKGROUND Constant mutation in the SARS-COV2 virus genetic material is resulting in the appearance of new variants frequently hence the overall virulence, treatment resistance, replication modalities, transmissions rates and COVID-19 signs & symptoms are all changing regularly. METHODOLOGY: From 1 January 2021 to 30 August 2022, the clinical lab at Fatima Jinnah General & Chest Hospital Quetta, Balochistan, determined a total of 3375 individuals to be COVID-19 positive because RT-PCR detected ORF, N, and E genes or their various Bi & Tri combinations in their samples. A questionnaire-based interview was conducted with each participant during sample collection. Body temperature more than 370c was recorded as Fever/Chill. Age, Comorbidities, A-symptomatic individuals & Vaccination status were all neglected during this study. Frequency tables were generated using MS-excel 2016, while Odds ratios were calculated using Chi-square test of association whereby 2x2 contingency tables between Mono, Bi & Tri combinations for ORF, N & E genes were cross associated with various generalized nonspecific COVID -19 signs and symptoms using Epi-info software. Absence of Genetic sequencing was the major limitation. RESULTS: The study showed that individually the presence of ORF gene was found to be strongly associated Shortness of Breath/Difficulty in Breathing, Diarrhea, Head ache & Vomitting. While the presence of N-gene was found to be strongly associated with Loss of smell & taste, Head ache,Presistant Chest Pain & Bluish lips/Face. Where as the presence of E-gene was found to be strongly associated with Cough, Shortness of breath/ Difficulty in breathing, Sore throat, Diarrhea, Head ache & Laziness. In addition, the study also found that different Bi & Tri combinations of ORF, N & E genes in a COVID-19 positive patient expressed generalized non-specific COVID-19 signs & symptoms differently. DISCUSSION & CONCLUSION: The presence of various SARS-COV2 genetic markers significantly alters the clinical presentation of COVID-19.

Prevalence of SARS-CoV-2: An age-stratified, population-based, sero-epidemiological survey in Islamabad, Pakistan (preprint)

Introduction Serological surveys are valuable tools to evaluate the extent of disease transmission, measuring preventive effectiveness and proportion of asymptomatic individuals. This age-stratified, serological survey was aimed to measure the COVID-19 distribution and determinants in district Islamabad of Pakistan. Methodology Three-stage cluster sampling, using population proportionate to size technique, starting with a random number was used. A structured, pretested questionnaire was used after taking informed written consent, to gather demographic, risk factor information. Results Seroprevalence was found 16.5% (AR: 16.5%/100,000). The mean age was 35 (±16 Years). The majority were male (64%), self-employed (29%), and had primary level education (33%). The highest seroprevalence was found in the 21-30 years age group (24.8%) while the 41-50 years age group showed the highest attack rate (112.9/100,000 population). The proportion of the population tested that were asymptomatic was 69% (n=711) while the most frequently reported sign/symptom was cough (99%) followed by fever (20%). No known co-morbidity was reported in 86% (n=884) of respondents while hypertension remained the most reported condition (8%). High seroprevalence was observed in urban areas (12.3%) compared to rural union councils (6.4%). Visiting a house where COVID-19 case was isolated (OR 2, CI 1.38-2.84, P < 0.001), history of contact with a known case of COVID-19 (OR 1.42, CI 1.11-1.82, P =0.005), and attending a mass gathering (OR 1.21, CI: 1.02-1.42, p=0.02) were significant risk factors associated with contracting an infection. A Chi-Square test of independence showed significant protection while using regular hand hygiene practices (6.5; p<0.05) and regular usage of face masks (8.6; p<0.05). Conclusion Seroprevalence gives a direct estimation of population groups exposed to the virus. A remarkable difference in prevalence is found in urban and rural areas, extreme age groups, and socioeconomic statuses, suggesting targeted public health interventions. Sero-studies are affordable counterparts of molecular testing where quick estimation, prevention effectiveness, and data-driven public health policies are priorities.

COVID-19 Rapid Diagnostic test results and their associations with certain factors among the residents of Balochistan. (preprint)

BackgroundThis paper analyses any possible association of various factors like gender, last COVID-19 PCR test results, BCG Vaccination, Seasonal Flu vaccination, Occupation and confirmed case contact history with COVID-19 RDT results of the participants. COVID-19 will soon become endemic in Pakistan, the government should adopt COVID-19 RDT kits for trace, test and quarantine activities. MethodologyConsidering the availability of COVI-19 rapid diagnostic kits, 596 individuals all previously COVID-19 PCR tested were made part of this cross sectional study. Simple random sampling was used for the selection of study participants. The whole study was conducted during September and October 2020. ResultsThe major findings of this study is clearly showing that the Positive Likely hood ratio of the COVID-19 RDT Kits (LR+) is well above 1; similarly the Negative Likely hood ratio is approaching 0.On the other hand the Sensitivity and Specificity 80% and 74% respectively. Similarly study found statistically significant association was between RDT out comes and Last PCR Test status, Occupation and Contact with COVID-19 positive individuals. While other variables like Gender, BCG Vaccination and history of seasonal flu vaccinations were found to have no significant associations with COVID-19 RDT Kit out comes. ConclusionBeing the first study of its kind in Pakistan the major findings of this study are almost in line with the set hypothesis and objectives of this study and based on study findings it will be of high value to use COVID-19 RDT kits during mass screening especially during Test, Trace and Quarantine activities.

Mortality Analysis of COVID-19 Confirmed cases in Pakistan (preprint)

Introduction: COVID-19, a novel disease, appeared in December 2019 in China and rapidly spread across the world. Till the second week of April 2020, high incidence (2.9/100,000) and cases fatality rates (1.7%) were observed in Pakistan. This study was conducted to determine the temporal and spatial distribution of the first 100 deaths attributed to COVID-19 in Pakistan and their associated demographic factors. Method: We conducted a descriptive epidemiological analysis of the first 100 deaths reported among RT-PCR confirmed COVID-19 cases. Demographic, epidemiological, and risk factors information was obtained associated comorbidities and clinical signs and symptoms were recorded and frequencies were determined. Results: A total of 100 mortalities with overall Case Fatality Rate 1.67% (CFR) were analysed. Median age of patients was 64.5 years (IQR: 54-70) with 75% (n=75) Males. Among all deaths reported, 71 (71%) cases had one or more documented comorbidities at the time of diagnosis. Most frequently reported co-morbidities were; hypertension (67 %), followed by Diabetes Mellitus 945%) and Ischemic Heart Diseases (27%). First death was reported on 18 March 2020 and the most frequent presenting symptoms were shortness of breath (87%) and fever (79%). Median duration of illness was eight days (IQR: 4-11 days), the median delay reaching hospital to seek health care was three days (IQR: 0-6 days) while median duration of hospital stay was also three days (IQR: 1-7 days). Among all reported deaths, 62% were attributed to local transmission as these cases had no history of international travel. The most affected age group was 60-69 years while no death reported in age group below 20 years. Conclusion: High CFR among old age group and its association with co-morbidities (chronic disease) suggests targeted interventions such as social distancing and strict quarantine measure for elderly and morbid people. Comparative studies among deaths and recovered patients are recommended to explore further disease dynamics. Key words: COVID-19, Cases Fatality Rates, Co-morbidities, Epidemiology, Pakistan, Co-morbidities

Detection of SARS-Coronavirus-2 in wastewater, using the existing environmental surveillance network: An epidemiological gateway to an early warning for COVID-19 in communities. (preprint)

The ongoing COVID-19 pandemic caused by SARs-CoV-2 was considered to be transmitted person to person via droplet infections and fecal-oral transmission. To determine this, we used the existing polio environment surveillance network in Pakistan to investigate presence of SARs-CoV-2 using three commercially available kits and E-Gene detection published assay for surety and confirmatory of positivity. A Two-phase separation method is used for sample clarification and concentration. Before proceeding directly for RNA extraction, an additional high-speed centrifugation (14000Xg for 30 min) step was introduced to increase viral RNA yield resulting decrease in Cq value. A total of 78 wastewater samples collected from 38 districts across Pakistan, 74 wastewater samples from existing polio environment surveillance sites, 3 from drains of COVID-19 infected areas and 1 from COVID 19 quarantine center drainage, were tested for presence of SARs-CoV-2. 21 wastewater samples (27%) from 13 districts turned to be positive on RT-qPCR. SARs-COV-2 RNA positive samples from areas with COVID patients and COVID 19 patient quarantine center drainage strengthen the findings and use of wastewater surveillance in future. Furthermore, sequence data of partial ORF 1a generated from COVID 19 patient quarantine center drainage sample also reinforce our findings that SARs-CoV-2 can be detected in wastewater. This study finding indicates that SARs-CoV-2 detection through wastewater surveillance has an epidemiologic potential that can be used as early warning system to monitor viral tracking and circulation in cities with lower COVID-19 disease burden or heavily populated areas where door-to-door tracing may not be possible. However, attention needed on virus concentration and detection assay to increase the sensitivity. Development of highly sensitive assay will be an indicator for virus monitoring and to provide early warning signs.