Seroprevalence of SARS-CoV-2 infection in the general population of Nepal during the first and second generalized waves of the COVID-19 pandemic-2020-2021.

Few seroprevalence studies have been conducted on coronavirus disease (COVID-19) in Nepal. Here, we aimed to estimate seroprevalence and assess risk factors for infection in the general population of Nepal by conducting two rounds of sampling. The first round was in October 2020, at the peak of the first generalized wave of COVID-19, and the second round in July-August 2021, following the peak of the wave caused by the delta variant of SARS-CoV-2. We used cross-sectional probability-to-size (PPS)-based multistage cluster sampling to estimate the seroprevalence in the general population of Nepal at the national and provincial levels. We tested for anti-SARS-CoV-2 total antibody using the WANTAI SARS-CoV-2 Ab ELISA kit. In Round 1, the overall national seroprevalence was 14.4%, with provincial estimates ranging from 5.3% in Sudurpaschim to 27.3% in Madhesh Province. In Round 2, the estimated national seroprevalence was 70.7%, with the highest in the Madhesh Province (84.8%) and the lowest in the Gandaki Province (62.9%). Seroprevalence was comparable between males and females (Round 1, 15.8% vs. 12.2% and Round 2, 72.3% vs. 68.7%). The seroprevalence in the ecozones-Terai, hills, and mountains-was 76.3%, 65.3%, and 60.5% in Round 2 and 17.7%, 11.7%, and 4.6% in Round 1, respectively. In Nepal, COVID-19 vaccination was introduced in January 2021. At the peak of the first generalized wave of COVID-19, most of the population of Nepal remained unexposed to SARS-CoV-2. Towards the end of the second generalized wave in April 2021, two thirds of the population was exposed.

Operational Gaps in Implementing the COVID-19 Case Investigation and Contact Tracing in Madhesh Province of Nepal, May-July 2021.

In Nepal, case investigation and contact tracing (CICT) was adopted as an important public health measure to reduce COVID-19 transmission. In this study, we assessed the performance of CICT in Madhesh Province of Nepal against national benchmarks, using routine programmatic data reported by district CICT teams. Between May and July 2021, 17,943 COVID-19 cases were declared in the province, among which case investigation was performed for 30% (95% CI: 29.6-31.0%) within 24 h (against 80% benchmark). As a result of case investigations, 6067 contacts were identified (3 contacts per 10 cases), of which 40% were traced and tested for SARS-CoV-2 infection (against 100% benchmark). About 60% of the contacts tested positive. At most 14% (95% CI: 13.1% to 14.9%) of traced contacts underwent a 14-day follow-up assessment (against 100% benchmark). We found the performance of the CICT program in Madhesh Province to be sub-optimal and call for corrective measures to strengthen CICT in the province and the country at large. Similar studies with wider geographical scope and longer time frames are needed to identify and address deficiencies in data recording and reporting systems for COVID-19, in low- and middle-income countries like Nepal and others.

Antibiotic Use and Treatment Outcomes among Children with Community-Acquired Pneumonia Admitted to a Tertiary Care Public Hospital in Nepal.

In the era of growing antimicrobial resistance, there is a concern about the effectiveness of first-line antibiotics such as ampicillin in children hospitalized with community-acquired pneumonia. In this study, we describe antibiotic use and treatment outcomes among under-five children with community-acquired pneumonia admitted to a tertiary care public hospital in Nepal from 2017 to 2019. In this cross-sectional study involving secondary analysis of hospital data, there were 659 patients and 30% of them had a history of prehospital antibiotic use. Irrespective of prehospital antibiotic use, ampicillin monotherapy (70%) was the most common first-line treatment provided during hospitalization followed by ceftriaxone monotherapy (12%). The remaining children (18%) were treated with various other antibiotics alone or in combination as first-line treatment. Broad-spectrum antibiotics such as linezolid, vancomycin, and meropenem were used in less than 1% of patients. Overall, 66 (10%) children were required to switch to second-line treatment and only 7 (1%) children were required to switch to third-line treatment. Almost all (99%) children recovered without any sequelae. This study highlights the effectiveness of ampicillin monotherapy in the treatment of community-acquired pneumonia in hospitalized children in a non-intensive care unit setting.

Detection and characterization of ESBL-producing Enterobacteriaceae from the gut of subsistence farmers, their livestock, and the surrounding environment in rural Nepal.

The increasing trend of gut colonization by extended-spectrum ß-lactamase (ESBL) producing Enterobacterales has been observed in conventional farm animals and their owners. Still, such colonization among domesticated organically fed livestock has not been well studied. This study aimed to determine the gut colonization rate of ESBL-producing Enterobacteriaceae and carbapenemase-producing Enterobacteriaceae (CPE) among rural subsistence farming communities of the Kaski district in Nepal. Rectal swabs collected by systematic random sampling from 128 households of subsistence farming communities were screened for ESBL-producing Enterobacteriaceae and CPE by phenotypic and molecular methods. A total of 357 (57%) ESBL-producing Enterobacteriaceae isolates were obtained from 626 specimens, which included 97 ESBL-producing Enterobacteriaceae (75.8%) from 128 adult humans, 101 (79.5%) from 127 of their children, 51 (47.7%) from 107 cattle, 26 (51%) from 51 goats, 30 (34.9%) from 86 poultry and 52 (42%) from 127 environmental samples. No CPE was isolated from any of the samples. blaCTX-M-15 was the most predominant gene found in animal (86.8%) and human (80.5%) isolates. Out of 308 Escherichia coli isolates, 16 human and two poultry isolates were positive for ST131 and were of clade C. Among non-cephalosporin antibiotics, the resistance rates were observed slightly higher in tetracycline and ciprofloxacin among all study subjects. This is the first one-health study in Nepal, demonstrating the high rate of CTX-M-15 type ESBL-producing Enterobacteriaceae among gut flora of subsistence-based farming communities. Gut colonization by E. coli ST131 clade C among healthy farmers and poultry birds is a consequential public health concern.

A rare coexistence of papillary carcinoma and anaplastic carcinoma of thyroid in multinodular goitre: Case report and literature review.

INTRODUCTION: Multinodular goiter is defined as multiple discrete nodules in the thyroid gland. The incidence of Papillary carcinoma thyroid was found to be highest out of total Multinodular Goiter cases while that of Anaplastic carcinoma was the least. We report a rare coexistence of Papillary carcinoma and Anaplastic carcinoma in adult patient with a long-standing Multinodular Goiter. CASE PRESENTATION: Here we present a case of 54 years male with huge anterior neck swelling for 20 years with a gradual increase in size. Computerized tomography of neck revealed solidocystic mass lesion without any significant lymphadenopathy, features suggesting Multinodular goiter with differential diagnosis of Carcinoma Thyroid. Cytological examination showed Papillary thyroid Carcinoma. He underwent total thyroidectomy with central neck dissection. Postoperative period was uneventful. Histopathological report revealed features suggestive of mixed tumor of Papillary thyroid Carcinoma and Anaplastic Carcinoma thyroid TNM Staging T3 N0 M0, Stage IVA. After the final reports patient was sent for adjuvant therapy three weeks later where he received megavoltage external beam radiation and he was followed up till 12th week. He was assessed radiologically which showed no signs of physical progression of the disease. However, he was lost to follow up after that visit. DISCUSSION: Long-standing benign conditions of thyroid can transform into malignant forms in the undefined duration of time. CONCLUSION: Regular follow up and early management of multinodular goiter at the right time can save a patient from undue stress and complication like the conversion into malignancy.

Rare giant maxillay mucocele: A rare case report and literature review.

INTRODUCTION: Mucocele is a slow growing, benign but locally aggressive cystic structure lined by true epithelium. It often results due to obstructed sinus outflow or obstruction of gland-like mucous retention cyst. It can cause bony destruction and might result in orbital symptoms like diplopia, orbital displacement, visual disturbances. Other clinical features are facial numbness, dental problems, etc. Radiological evaluation is the preferred diagnostic modality. Surgical removal is the treatment of choice both endoscopic and open (could well luc) approach or combined approach are preferred. Here we report a very typical case of maxillary mucocele who presented with subtle symptoms of nasal obstruction. The study was done in compliance with SCARE guidelines.[1]. CASE PRESENTATION: We present a very unique case of 24 years man with complaints of nasal obstruction and swelling over the right cheek for 2 years. He had a history of facial trauma two years back. Diagnosis was made on the basis of radiological examination CT (Computed Tomography) scan. He underwent enucleation via Cold well Luc's approach with good postoperative results. CONCLUSION: Maxillary mucoceles are slow growing benign lesions. However, they are locally aggressive and cause bony destruction resulting into orbital and dental symptoms. Thus early recognistion with regular folllowr up and planning for surgical intervention can help avoid complications.

Localization of the kinase Ataxia Telangiectasia Mutated to Adenovirus E4 mutant DNA replication centers is important for its inhibitory effect on viral DNA accumulation.

Adenovirus (Ad) type 5 (Ad5) E4 deletion mutants including H5dl1007 (E4-) induce a DNA damage response (DDR) that activates the kinase ataxia-telangiectasia mutated (ATM), which can interfere with efficient viral DNA replication. We find that localization of active phosphorylated ATM (pATM) to E4- viral replication centers (VRCs) is important for its inhibitory effect. ATM is necessary for localization of RNF8 and 53BP1 to E4 mutant VRCs, while recruitment of DDR factors Mre11, Mdc1 and γH2AX is ATM-independent, raising the possibility that ATM may affect viral chromatin at VRCs. We assessed E4- and Ad5 chromatin organization by micrococcal nuclease (MN) digestion. A significant fraction of Ad5 DNA is somewhat resistant to MN digestion, whereas E4- DNA is more susceptible. ATM inhibition increases the fraction of E4- DNA that is resistant to MN digestion. Our results address possible mechanisms through which ATM inhibits E4- DNA replication.

Excision of rare carotid body tumour without preembolisation: Case report and literature review.

INTRODUCTION: Carotid body tumors also known as parganglioma or chemodactomas are one of the rare tumors of head and neck which present as slow growing masses in the neck region. We present a case of 40 years female with painless slow growing mass over left side of her neck for 6 months. Diagnosis was made on basis of clinical history, examination and radiological findings. Tumor was graded as Shamblin grade II. She was managed with excision of the tumor without preoperative embolisation. Intraoperative and postoperative periods were uneventful. CASE PRESENTATION: A forty years female presented with left sided painless neck swelling∼5 × 4 cm2 over left anterior triangle for 6 months with no history of dysphagia, odynophagia, change in voice, shortness of breath, palpitations, tremors or syncopal attacks. She underwent USG neck and CT angiogram. Based upon the radiological and clinical findings, she was diagnosed asCarotid body tumor. She was managed with excision of the tumor without preembolisation. Her diagnosis was confirmed with histopathology. CONCLUSION: Carotid body tumours are rare entities of head and neck region. They are mostly benign in nature. Though mostly bening, increasing size might result in grave complications. Thus, the recommended treatment for carotid body tumors is early excision with or without pre-embolisation. In our case preembolisation was not performed. Though some studies have suggested the use of preoperative embolisation in large sized tumors, more studies are yet required to justify the choice of preembolisation despite the dreaded complications.

SETD2-dependent H3K36me3 plays a critical role in epigenetic regulation of the HPV31 life cycle.

The life cycle of HPV is tied to the differentiation status of its host cell, with productive replication, late gene expression and virion production restricted to the uppermost layers of the stratified epithelium. HPV DNA is histone-associated, exhibiting a chromatin structure similar to that of the host chromosome. Although HPV chromatin is subject to histone post-translational modifications, how the viral life cycle is epigenetically regulated is not well understood. SETD2 is a histone methyltransferase that places the trimethyl mark on H3K36 (H3K36me3), a mark of active transcription. Here, we define a role for SETD2 and H3K36me3 in the viral life cycle. We have found that HPV positive cells exhibit increased levels of SETD2, with SETD2 depletion leading to defects in productive viral replication and splicing of late viral RNAs. Reducing H3K36me3 by overexpression of KDM4A, an H3K36me3 demethylase, or an H3.3K36M transgene also blocks productive viral replication, indicating a significant role for this histone modification in facilitating viral processes. H3K36me3 is enriched on the 3' end of the early region of the high-risk HPV31 genome in a SETD2-dependent manner, suggesting that SETD2 may regulate the viral life cycle through the recruitment of H3K36me3 readers to viral DNA. Intriguingly, we have found that activation of the ATM DNA damage kinase, which is required for productive viral replication, is necessary for the maintenance of H3K36me3 on viral chromatin and for processing of late viral RNAs. Additionally, we have found that the HPV31 E7 protein maintains the increased SETD2 levels in infected cells through an extension of protein half-life. Collectively, our findings highlight the importance of epigenetic modifications in driving the viral life cycle and identify a novel role for E7 as well as the DNA damage response in the regulation of viral processes through epigenetic modifications.

Chromatin Remodeling Protein SMAR1 Is a Critical Regulator of T Helper Cell Differentiation and Inflammatory Diseases.

T cell differentiation from naïve T cells to specialized effector subsets of mature cells is determined by the iterative action of transcription factors. At each stage of specific T cell lineage differentiation, transcription factor interacts not only with nuclear proteins such as histone and histone modifiers but also with other factors that are bound to the chromatin and play a critical role in gene expression. In this review, we focus on one of such nuclear protein known as tumor suppressor and scaffold matrix attachment region-binding protein 1 (SMAR1) in CD4+ T cell differentiation. SMAR1 facilitates Th1 differentiation by negatively regulating T-bet expression via recruiting HDAC1-SMRT complex to its gene promoter. In contrast, regulatory T (Treg) cell functions are dependent on inhibition of Th17-specific genes mainly IL-17 and STAT3 by SMAR1. Here, we discussed a critical role of chromatin remodeling protein SMAR1 in maintaining a fine-tuned balance between effector CD4+ T cells and Treg cells by influencing the transcription factors during allergic and autoimmune inflammatory diseases.

Homologous Recombination Repair Factors Rad51 and BRCA1 Are Necessary for Productive Replication of Human Papillomavirus 31.

UNLABELLED: High-risk human papillomavirus 31 (HPV31)-positive cells exhibit constitutive activation of the ATM-dependent DNA damage response (DDR), which is necessary for productive viral replication. In response to DNA double-strand breaks (DSBs), ATM activation leads to DNA repair through homologous recombination (HR), which requires the principal recombinase protein Rad51, as well as BRCA1. Previous studies from our lab demonstrated that Rad51 and BRCA1 are expressed at high levels in HPV31-positive cells and localize to sites of viral replication. These results suggest that HPV may utilize ATM activity to increase HR activity as a means to facilitate viral replication. In this study, we demonstrate that high-risk HPV E7 expression alone is sufficient for the increase in Rad51 and BRCA1 protein levels. We have found that this increase occurs, at least in part, at the level of transcription. Studies analyzing protein stability indicate that HPV may also protect Rad51 and BRCA1 from turnover, contributing to the overall increase in cellular levels. We also demonstrate that Rad51 is bound to HPV31 genomes, with binding increasing per viral genome upon productive replication. We have found that depletion of Rad51 and BRCA1, as well as inhibition of Rad51's recombinase activity, abrogates productive viral replication upon differentiation. Overall, these results indicate that Rad51 and BRCA1 are required for the process of HPV31 genome amplification and suggest that productive replication occurs in a manner dependent upon recombination. IMPORTANCE: Productive replication of HPV31 requires activation of an ATM-dependent DNA damage response, though how ATM activity contributes to replication is unclear. Rad51 and BRCA1 play essential roles in repair of double-strand breaks, as well as the restart of stalled replication forks through homologous recombination (HR). Given that ATM activity is required to initiate HR repair, coupled with the requirement of Rad51 and BRCA1 for productive viral replication, our findings suggest that HPV may utilize ATM activity to ensure localization of recombination factors to productively replicating viral genomes. The finding that E7 increases the levels of Rad51 and BRCA1 suggests that E7 contributes to productive replication by providing DNA repair factors required for viral DNA synthesis. Our studies not only imply a role for recombination in the regulation of productive HPV replication but provide further insight into how HPV manipulates the DDR to facilitate the productive phase of the viral life cycle.

Productive replication of human papillomavirus 31 requires DNA repair factor Nbs1.

UNLABELLED: Activation of the ATM (ataxia telangiectasia-mutated kinase)-dependent DNA damage response (DDR) is necessary for productive replication of human papillomavirus 31 (HPV31). We previously found that DNA repair and homologous recombination (HR) factors localize to sites of HPV replication, suggesting that ATM activity is required to recruit factors to viral genomes that can productively replicate viral DNA in a recombination-dependent manner. The Mre11-Rad50-Nbs1 (MRN) complex is an essential component of the DDR that is necessary for ATM-mediated HR repair and localizes to HPV DNA foci. In this study, we demonstrate that the HPV E7 protein is sufficient to increase levels of the MRN complex and also interacts with MRN components. We have found that Nbs1 depletion blocks productive viral replication and results in decreased localization of Mre11, Rad50, and the principal HR factor Rad51 to HPV DNA foci upon differentiation. Nbs1 contributes to the DDR by acting as an upstream activator of ATM in response to double-strand DNA breaks (DSBs) and as a downstream effector of ATM activity in the intra-S-phase checkpoint. We have found that phosphorylation of ATM and its downstream target Chk2, as well as SMC1 (structural maintenance of chromosome 1), is maintained upon Nbs1 knockdown in differentiating cells. Given that ATM and Chk2 are required for productive replication, our results suggest that Nbs1 contributes to viral replication outside its role as an ATM activator, potentially through ensuring localization of DNA repair factors to viral genomes that are necessary for efficient productive replication. IMPORTANCE: The mechanisms that regulate human papillomavirus (HPV) replication during the viral life cycle are not well understood. Our finding that Nbs1 is necessary for productive replication even in the presence of ATM (ataxia telangiectasia-mutated kinase) and Chk2 phosphorylation offers evidence that Nbs1 contributes to viral replication downstream of facilitating ATM activation. Nbs1 is required for the recruitment of Mre11 and Rad50 to viral genomes, suggesting that the MRN complex plays a direct role in facilitating productive viral replication, potentially through the processing of substrates that are recognized by the key homologous recombination (HR) factor Rad51. The discovery that E7 increases levels of MRN components, and MRN complex formation, identifies a novel role for E7 in facilitating productive replication. Our study not only identifies DNA repair factors necessary for HPV replication but also provides a deeper understanding of how HPV utilizes the DNA damage response to regulate viral replication.

The kinase activity of ataxia-telangiectasia mutated interferes with adenovirus E4 mutant DNA replication.

Adenovirus (Ad) mutants that lack early region 4 (E4) are unable to produce the early regulatory proteins that normally inactivate the Mre11/Rad50/Nbs1 (MRN) sensor complex, which is a critical component for the ability of cells to respond to DNA damage. E4 mutant infection therefore activates a DNA damage response, which in turn interferes with a productive viral infection. MRN complex proteins localize to viral DNA replication centers in E4 mutant-infected cells, and this complex is critical for activating the kinases ataxia-telangiectasia mutated (ATM) and ATM and Rad3-related (ATR), which phosphorylate numerous substrates important for DNA repair, cell cycle checkpoint activation, and apoptosis. E4 mutant growth defects are substantially rescued in cells lacking an intact MRN complex. We have assessed the role of the downstream ATM and ATR kinases in several MRN-dependent E4 mutant phenotypes. We did not identify a role for either ATM or ATR in "repair" of E4 mutant genomes to form concatemers. ATR was also not observed to contribute to E4 mutant defects in late protein production. In contrast, the kinase activity of ATM was important for preventing efficient E4 mutant DNA replication and late gene expression. Our results suggest that the MRN complex interferes with E4 mutant DNA replication at least in part through its ability to activate ATM.