Risk of infection with arboviruses in a healthy population in Pakistan based on seroprevalence.

Infectious diseases caused by arboviruses are a public health concern in Pakistan. However, the studies on data prevalence and threats posed by arboviruses are limited. This study investigated the seroprevalence of arboviruses in a healthy population in Pakistan, including severe fever with thrombocytopenia syndrome virus (SFTSV), Crimean-Congo hemorrhagic fever virus (CCHFV), Tamdy virus (TAMV), and Karshi virus (KSIV) based on a newly established luciferase immunoprecipitation system (LIPS) assays, and Zika virus (ZIKV) by enzyme-linked immunosorbent assays (ELISA). Neutralizing activities against these arboviruses were further examined from the antibody positive samples. The results showed that the seroprevalence of SFTSV, CCHFV, TAMV, KSIV, and ZIKV was 17.37%, 7.58%, 4.41%, 1.10%, and 6.48%, respectively, and neutralizing to SFTSV (1.79%), CCHFV (2.62%), and ZIKV (0.69%) were identified, as well as to the SFTSV-related Guertu virus (GTV, 0.83%). Risk factors associated with the incidence of exposure and levels of antibody response were analyzed. Moreover, co-exposure to different arboviruses was demonstrated, as thirty-seven individuals were having antibodies against multiple viruses and thirteen showed neutralizing activity. Males, individuals aged ≤40 years, and outdoor workers had high risk of exposure to arboviruses. All these results reveal the substantial risks of infection with arboviruses in Pakistan, and indicate the threat from co-exposure to multiple arboviruses. The findings raise the need for further epidemiologic investigation in expanded regions and populations and the necessity to improve health surveillance in Pakistan.

Herpes Simplex Virus Encephalitis: An Unexpected Outcome in a Polytrauma Patient.

An 84-year male was brought in the emergency after a road traffic accident leading to polytrauma with deteriorating consciousness. Prolonged unexplained unconsciousness led to cerebrospinal fluid examination. The polymerase chain reaction (PCR) of cerebrospinal fluid (CSF) was found to be positive for HSV-1 DNA. The patient was started on intravenous acyclovir and the consciousness level of the patient improved gradually. In this case, encephalitis was not suspected initially, because of the multiple traumatic injuries that needed management. Moreover, no features suggestive of encephalitis were present at the time of presentation, except for the non-specific symptom of drowsiness at the time of the accident. The patient was also diabetic and had chronic kidney disease as predisposing factors. It was primarily encephalitis which led to impaired consciousness that resulted in the road traffic accident in a very unlikely situation, i.e., hit by an ambulance inside the hospital. The reasons to suspect herpes simplex virus encephalitis (HSE) in this case were unexplained worsening level of consciousness, CSF findings suggestive of viral encephalitis along with highly deranged alanine aminotransferase (ALT) levels. This case highlights the importance of keeping a high index of suspicion for viral encephalitis in patients with risk factors, even in such a scenario of polytrauma. Key Words: Herpes simplex virus, Polytrauma, Viral encephalitis, Polymerase chain reaction.

BK virus associated haemorrhagic cystitis in related donor haematopoietic stem cell transplant recipients: A developing country experience.

A retrospective cross sectional study was conducted at the Virology Department, Armed Forces Institute of Pathology (AFIP) and Armed Forces Bone Marrow Transplant Centre (AFBMTC), Rawalpindi, from January 2016 to July 2018. Medical records of 193 patients were examined to determine the number of patients developing Haemorrhagic Cystitis associated with BK virus (BKV). BKV PCR testing was done on the patients' urine samples. Cytomegalovirus reactivation was also assessed weekly from day 30 to day 100, by CMV quantitative PCR testing on blood samples. Out of 193 patients, 11 (5.6%) developed haemorrhagic cystitis and all these patients were positive for BKV on urine samples. The maximum number of positive cases, i.e. 5 (2.6%) was in the age group three months to 10 years. Primary disease in seven out of 11 cases was Beta-Thalassemia Major.

Coding-Complete Genome Sequence of a SARS-CoV-2 Strain Isolated in Gilgit, Pakistan.

Here, we report the coding-complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolate obtained from a nasopharyngeal swab from the first patient with COVID-19 in Gilgit, Pakistan.

Phylogenetic and sequencing analysis of Chikungunya virus strains from local Pakistani population.

OBJECTIVE: To outline the genotype of Chikungunya virus strains and to form their phylogenetic tree. METHODS: The cross-sectional study was conducted at the Armed Forces Institute of Pathology, Rawalpindi, Pakistan, from August 2016 to September 2017, and comprised suspected Chikungunya samples. The viral ribonucleic acid was extracted and amplified. The purified product was sequenced using Sanger dideoxy method. Phylogenetic tree was constructed. Sequences generated were checked for alignment with sequences reported globally. Structural prediction and analysis was performed using Phyre2 and the models were visualised in PyMol2.2. RESULTS: In the 11 suspected samples, 7(63.6%) were found to be positive for Chikungunya. Of them, 5(71.4%) sequences generated were found to be aligned with other full structural polyprotein sequences, having 99% similarity with amino acid sequences. CONCLUSIONS: The Chikungunya strains in the study belonged to the East/Central/South African genotype.

Rising HIV seroconversion rates & associated risks among employees of organization 'X': A case control study, Pakistan, 2017.

BACKGROUND AND OBJECTIVES: In 2004 Pakistan escalated from 'low-prevalence' to 'concentrated' phase of HIV epidemic. Despite global decline in HIV incidence since 1997, rate of HIV infections in Pakistan is persistently rising since 1990. Available literature focusses on key populations or localized outbreaks limited by short study duration and regional applicability of results. We studied HIV seroconversion trends over a period of 8 years in a geographically diverse population and evaluated associated risk factors. METHODS: A desk review of HIV surveillance data from 2010 to 2017 was carried out at Armed Forces Institute of Pathology. A case was defined as any adult employed in organization 'X', initially screened for HIV but later seroconverted on ELISA and western blot. Case-control study was conducted on cases diagnosed in 2017. Age and sex matched controls were identified from same population sub-group. Structured telephonic interviews were conducted and statistical analysis done at 5% margin of error. RESULTS: The annual HIV diagnosis rate remained relatively stable till 2015 (< 40 /100,000/yr) after which it rose sharply to 60/100,000/yr in 2016 .Upward trend continued in 2017 to reach 125/100,000/yr (>200% increase from baseline). Acquisition of HIV was significantly associated with commercial sex activities (OR=9; 95% CI: 1.25-395). CONCLUSION: HIV seroconversion rates among employees of organization X have increased significantly in the past two years. Unlike HIV outbreaks previously reported from Pakistan, sexual route seems to be the predominant mode of transmission. Focus is mandated on prevention of sexual transmission of HIV at national level as well for all vulnerable populations.

JC Virus Infection: A Clinical Conundrum.

John Cunningham virus (JCV), a member of polyomaviridae family, has been described as a cause of the progressive multifocal leukoencephalopathy (PML). It is a potentially fatal, disabling demyelinating infection of the brain occurring mostly in the setting of immunosuppression. A few cases of JCV-associated meningitis and encephalitis have been described in literature. We report a case presenting with laboured breathing and reduced conscious level, who after thorough investigations was diagnosed to be a case of PML.

Detection of West Nile virus lineage 1 sequences in blood donors, Punjab Province, Pakistan.

OBJECTIVES: This study was performed to determine the presence of West Nile virus (WNV) in mosquito specimens and human blood donors in Pakistan. METHODS: A total of 4150 mosquito specimens were collected using CO2-baited traps from five selected districts of Punjab Province, Pakistan. The mosquitoes were taxonomically identified using standard morphological keys, resulting in 166 pools. In addition, 1070 serum samples were collected from human blood donors. RNA was extracted from mosquito and human samples and screened for WNV using a reverse transcriptase PCR (RT-PCR). RESULTS: None of the mosquito pools tested positive for WNV, whereas three samples from asymptomatic humans tested positive. To determine the WNV strains, partial sequences were compared against a global representation of 23 WNV sequences. The study strains were determined to come from WNV lineage 1. CONCLUSIONS: This study is novel in reporting the circulation of lineage 1 WNV in Pakistan. Given its ability to transmit from human to human via blood transfusion, this highlights the urgent need for nationwide surveillance to assess the distribution and impact of WNV in Pakistan. Determining the source of human infection will require more extensive mosquito sampling.

A Case of Multiple Myeloma with Triple Herpes Virus Infections.

Multiple myeloma is rare B cell malignancy that affects elderly. Therapeutic regimens consist of high dose chemotherapy followed by haematopoietic stem cell transplantation (HSCT). Both humoral and cell mediated immunities are compromised in these patients, leading to increased susceptibility to infections. Here, we report a case of 62-year male with multiple myeloma who developed infection with three viruses from herpes family during the first cycle of chemotherapy.

Nucleic Acid Amplification Test For Detection Of West Nile Virus Infection In Pakistani Blood Donors.

BACKGROUND: The study was planned to determine the presence of West Nile Virus (WNV) infection in Pakistani blood donors, using Nucleic Acid Amplification Test (NAT). METHODS: The blood donors for study were selected on the basis of the standard questionnaire and routine screening results. Six donors were pooled using an automated pipettor and NAT for WNV was performed on Roche Cobas s 201 NAT system. The reactive pools were resolved in Individual Donation-NAT (ID-NAT) format and a sample from FFP bags of reactive donations was retrieved. NAT was again performed on retrieved plasma bag (RPB) sample to confirm the reactive donations. The donors were also recalled and interviewed about history of illness related to recent WNV infection. RESULTS: After serological screening of 1929 donors during the study period, 1860 donors were selected for NAT test for WNV detection. The mean age of the donors was 28±8.77 (range: 18-57 years). 1847 (99.3%) donors were male and 13 (0.7%) were female. NAT for WNV identified six initially reactive pools (0.32%). On follow-up testing with RPB samples, 4 donors (0.21%) were found confirmed reactive for WNV RNA (NAT yield of 1 in 465 blood donors). CONCLUSIONS: WNV is a threat to safety of blood products in Pakistan. A screening strategy can be implemented after a large-scale study and financial considerations. One of the reduced cost screening strategies is seasonal screening of blood donors for WNV, with pooling of samples.

Seroprevalence of Human T-Cell Lymphotropic Virus-1/2 in Blood Donors in Northern Pakistan: Implications for Blood Donor Screening.

OBJECTIVE: To determine the seroprevalence of Human T-cell Lymphotropic Virus-1/2 (HTLV-1/2) in blood donors in Northern Pakistan. STUDY DESIGN: Descriptive study. PLACE AND DURATION OF STUDY: Armed Forces Institute of Transfusion, Rawalpindi, from July to August 2013. METHODOLOGY: A total of 2100 blood donors were screened for anti-HTLV-1/2 antibodies during the study period, in a pool of six, on a highly sensitive, Chemiluminiscent Microparticle Immunoassay (CMIA) based system. The screening test-reactive donors were recalled, counseled and interviewed, and a fresh sample was obtained for confirmatory testing. Confirmation was performed using additional immunoassays including Line Immunoassay (LIA); with additional testing for HTLV-1 pvDNAPCR. Frequency and percentages were determined. RESULTS: Four donors (0.19%) were repeatedly screening test-reactive and were subsequently confirmed to be HTLV-1 infected by line immunoassay and HTLV-1 pvDNAPCR. All four donors were male with mean age of 27 ± 6.27 years. Two (50%) of the positive donors gave history of Multiple Sexual Partners (MSP). CONCLUSION: HTLV-1 seroprevalence in Northern Pakistan blood donors was determined to be 0.19%. Large scale studies, including the cost effectiveness of screening blood donations for anti-HTLV-1/2 in Pakistan, are recommended.

Impact of nucleic acid amplification test on screening of blood donors in Northern Pakistan.

BACKGROUND: The Armed Forces Institute of Transfusion located in Rawalpindi, Northern Pakistan, acts as a regional blood center with more than 50,000 donations collected annually. Nucleic acid amplification testing (NAT) was introduced in our institution in September 2012 for screening all seronegative blood donors. STUDY DESIGN AND METHODS: The study was conducted from September 21, 2012, to September 20, 2013. Samples from the seronegative donors were run on cobas s 201 platform (Roche) in pools of six. Reactive donors were followed up for further confirmatory testing to rule out false-positive results. Viral load estimation was done for all NAT-reactive donors. RESULTS: After serologic screening of 56,772 blood donors, 2334 were found to be reactive; 719 (1.27%) were reactive for hepatitis B surface antigen, 1046 (1.84%) for antibody to hepatitis C virus (anti-HCV), 12 (0.02%) for antibody to human immunodeficiency virus, and 557 (0.98%) for syphilis antibodies. A total of 27 NAT-reactive donors were confirmed after testing 54,438 seronegative donors, with an overall NAT yield of one in 2016 donors: 23 for hepatitis B virus (HBV) DNA (HBV NAT yield, 1:2367) and four for HCV RNA (HCV NAT yield, 1:13,609). The residual risk after NAT implementation, calculated for the first-time blood donors, was 62.5 and 4.4 per million donors for HBV and HCV, respectively. CONCLUSIONS: NAT has improved the safety of blood products at our transfusion institution. Confirmation of NAT results must always be done either on follow-up samples or on samples from the retrieved frozen plasma bag.

Status of hospital infection control measures at seven major tertiary care hospitals of northern punjab.

OBJECTIVE: To determine the availability and implementation of various hospital infection control measures at tertiary care hospitals. STUDY DESIGN: Survery. PLACE AND DURATION OF STUDY: National Institute of Science and Technology, Islamabad, from June through August 2008. METHODOLOGY: Seven tertiary care very busy hospitals were selected; one from Islamabad, 5 from Rawalpindi, and one from Lahore. A detailed proforma was designed addressing all the issues pertaining to hospital infection control measures. Air sampling was done and growth yielded was identified by standard methods. RESULTS: Analyses revealed that all of the hospitals had an Infection Control Committee. Microbiological diagnostic facilities were adequate at all the hospitals and overall microorganism yield was very high. Antibiotic policy was claimed by most, not available on ground. Majority of the operation theatres were without proper air flow system and autoclaves were not being regularly monitored. There was no proper disposal for sharps and needles. Incineration was not the usual mode for infectious waste. CONCLUSION: The results of the present study imply availability of proper hospital infection control policies with need of strict implementation of such measures.