Evaluation of RT-PCR pooling test for the detection of SARS-CoV-2 in low-resource setting

BackgroundSpecimen pooling is an efficient method when there is limited accessibility or scarcity of test kits and reagents for nucleic acid extraction and molecular detection. We evaluated the ability of the standard real-time reverse transcriptase-polymerase chain reaction (RT-PCR) test for detecting a single positive sample of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within a pool of negative samples and to find out the maximum pool dilution limit up to which a single positive sample can be detected. MethodsRNA extracts from nasopharyngeal and oropharyngeal samples were pooled for the detection of the SARS-CoV-2 virus by RT-PCR. Positive samples were serially diluted in negative samples pools with dilutions ranging from 1/2 to 1/64 to estimate the optimal pool size. The viral transport medium (VTM) of three positive samples was also evaluated for optimal pool size determination. ResultsA single positive sample with a Cycle threshold (Ct) value range from 16-23 (high viral load) can be detected in dilution pools upto1/64 for both genes. In pooling before RNA extraction, a positive sample with a low Ct value (13) and intermediate Ct value (25) was detected till 1/32 dilution pool but a positive sample with a high Ct value (32) was not detected further 1/4 dilution. Besides, two positive VTM samples were detected in pools of sizes 5, 8, and 10. ConclusionsThis study concluded that sample testing by pooling is reliable if done properly and can help increase testing capacity in a low-resource setting.

Characteristics and outcomes of hospitalized adults with COVID-19 in Nepal: a multicenter, prospective cohort study

IntroductionThere is limited data on clinical course and outcomes of hospitalized adults with COVID-19 in Nepal. Thus, it is imperative to characterize the features of this disease in the domestic context. MethodologyWe identified all adult patients with laboratory-confirmed COVID-19 admitted to five different hospitals in Nepal from June 15 to July 15, 2020. We collected epidemiological, socio-cultural and clinicopathologic data, and stratified the patients based on their symptom status. ResultsThe study included 220 patients with an overall median age of 31.5 (25-37) years, and 181 (82.3%) were males. 159 (72.3%) were asymptomatic, and 163 (74.1%) were imported cases. Of 217 patients with the available data, 110 (50.7%) reported their annual household income less than 2000 US dollars, and 122 (56.2%) practiced Pranayama (yogic rhythmic breathing techniques) regularly. Eight patients (3.6%) required supplemental oxygen and two patients (0.9%) died. None of the patients who practiced Pranayama regularly required supplemental oxygen. Compared to asymptomatic patients, symptomatic patients had greater proportion of females (31.1% vs. 12.6%, p=0.001), imported cases (85.2% vs. 69.8%, p=0.02), illiterates (26.8% vs. 12.1%, p=0.01), alcohol users (43.3% vs. 24.5%, p=0.01), patients feeling stigmatized by society (45.8% vs. 22.6%, p=0.001), and had higher platelet count (253x 109/L vs. 185x109/L, p=0.02). ConclusionsMost cases were imported, asymptomatic young males, with very few deaths. Pranayama practice was associated with protection against severe COVID-19, but more data is needed to substantiate this. The association of platelets count with symptom status in the Nepalese population needs further exploration.

Burden of cervical neoplasia in mid-western rural Nepal: a population-based study / 부인종양

OBJECTIVE: To assess the burden of cervical neoplasia in mid-western rural, Nepal using cytology, visual inspection with acetic acid (VIA) and visual inspection with Lugol's iodine (VILI). METHOD: A cross-sectional, population-based study was conducted. Total of 2,279 married, non-pregnant women aged 20–65 years participated in a screening clinic from May 2016 to January 2017. All eligible women completed self-report of socio-demographic and reproductive health data followed by screening tests. Biopsies were obtained from areas on the cervix assessed by VIA and or VILI to be abnormal. Final disease was confirmed by biopsy report. RESULTS: A total of 96.09% (n=2,190) women were eligible for this study with mean age 32.78±9.33 years. The overall rate of positive cytology, VIA, and VILI were 3.69%, 12.45%, and 16.89%, respectively. Sixty-two cases were biopsy proven cervical neoplasia. Altogether 78 (3.69%) cases were cytologically abnormal: 25 (1.18%) were atypical squamous cells of undetermined significance, 33 (1.56%) were low-grade squamous intraepithelial lesion, 11 (0.52%) were high-grade squamous intraepithelial lesion, and 9 (0.42%) were squamous cell carcinoma. Illiterate women appeared to be at higher risk for cervical neoplasia (p < 0.001). Similarly, age ≥ 46 years (p < 0.013), participant's multiple marriages or sexual partners (p < 0.005), and positive human immunodeficiency virus status (p < 0.001) were significantly associated with abnormal cytology. CONCLUSION: Based on cytology report, there is 3.69% prevalence of cervical neoplasia among women in a rural region of mid-western, Nepal. A “screen and treat” approach would be more attractive in low resource settings.

Knowledge, attitude, practice and barriers of cervical cancer screening among women living in mid-western rural, Nepal / 부인종양

OBJECTIVE: To find out the knowledge, attitude, practice, and barriers of cervical cancer screening in mid-western rural, Nepal. METHODS: A hospital-based cross-sectional study was conducted. Women aged 20 or more were interviewed using a structured questionnaire regarding the socio-demographic information, knowledge, attitude, practice, and barriers to the cervical cancer screening. RESULTS: Total of 360 participants were recruited for this study, mean age was 30.13±10.4 years. More than 87% of participants had inadequate knowledge, but around 72% had a favorable attitude towards cervical cancer screening. There was a significant portion of women (86.4%) had never done any cervical cancer screening test. Despite being higher literacy rate of Brahmin and Chhetri ethnic group, they were less likely to attend the cervical cancer screening than Dalit and Janajati (p < 0.001); and those who had a positive family history of cancer were more likely to attend the cervical cancer screening (p < 0.001). Similarly, married women, who had adequate knowledge and or favorable attitude, were more likely to practice cervical cancer screening, though statistically not significant. Factors such as “No symptoms,”“Lack of awareness,”“Embarrassment,” etc. were the most common barriers for the cervical cancer screening. CONCLUSION: The adequate knowledge and practice of cervical cancer screening were meager among rural Nepalese women, but most of them had a favorable attitude. There is an imperative need for related awareness programs to promote the uptake of cervical cancer screening tests.