Respiratory viruses in rural Zambia during the second year of the COVID-19 pandemic.

Objectives: Limited data on respiratory infections are available from sub-Saharan Africa during the COVID-19 pandemic. The objective of this study was to evaluate the burden of respiratory viruses in rural Zambia from 2019-2021. Methods: Surveillance was initiated at Macha Hospital in Zambia in December 2018. Each week, patients with respiratory symptoms were enrolled from the outpatient clinic. Nasopharyngeal samples were collected and tested for respiratory pathogens. The prevalence of respiratory symptoms and viruses in 2021 was compared to results from 2019 and 2020. Results: After seeing few cases of influenza virus and respiratory syncytial virus in 2020, a return to prepandemic levels was observed in 2021. Rhinovirus/enterovirus, parainfluenza virus 1-4, and adenovirus circulated from 2019 to 2021, while human metapneumovirus and human coronaviruses (HKU1, 229E, OC43, and NL63 subtypes) were observed sporadically. SARS-CoV-2 was observed consistently in 2021 after being first identified in December 2020. The proportion of participants with co-infections in 2021 (11.6%) was significantly higher than in 2019 (6.9%) or 2020 (7.7%). Conclusion: Declines in influenza virus and respiratory syncytial virus were reversed once public health measures were lifted. Respiratory viruses contributed to a significant burden of respiratory infections in 2021. This study provides important information about respiratory viruses in this changing context and underrepresented region.

Diversity of Anal HPV and Non-HPV Sexually Transmitted Infections and Concordance with Genital Infections in HIV-Infected and HIV-Uninfected Women in the Tapajós Region, Amazon, Brazil.

The aim of this study was to classify the diversity of anal HPV and non-HPV sexually transmitted infections (STIs) and compare the concordance between anal and genital infections in HIV-infected and uninfected women living in the Tapajós region, Amazon, Brazil. A cross-sectional study was performed with 112 HIV-uninfected and 41 HIV-infected nonindigenous women. Anal and cervical scrapings were collected and analyzed for HPV, Chlamydia trachomatis (CT), Neisseria gonorrheae (NG), Trichomonas vaginalis (TV), Mycoplasma genitalium (MG), and Human alphaherpesvirus 2 (HSV-2). The Kappa test evaluated the concordance between anal and genital infections. The overall prevalence of anal HPV infection was 31.3% in HIV-uninfected and 97.6% in HIV-infected women. The most frequent anal high-risk HPV (hrHPV) types were HPV18 and HPV16 in HIV-uninfected women and HPV51, HPV59, HPV31, and HPV58 in HIV-infected women. Anal HPV75 Betapapillomavirus was also identified. Anal non-HPV STIs were identified in 13.0% of all participants. The concordance analysis was fair for CT, MG, and HSV-2, almost perfect agreement for NG, moderate for HPV, and variable for the most frequent anal hrHPV types. Thus, a high prevalence of anal HPV infection with moderate and fair concordance between anal and genital HPV and non-HPV STIs was observed in our study.

Sexually transmitted infections among HIV-infected and HIV-uninfected women in the Tapajós region, Amazon, Brazil: Self-collected vs. clinician-collected samples.

The anogenital prevalence of sexually transmitted infections (STIs) and the use of cervico-vaginal self-collected vs. clinician-collected samples were evaluated for the diagnosis of human immunodeficiency virus (HIV)-infected and HIV-uninfected women in the Tapajós region, Amazon, Brazil. We recruited 153 women for a cross-sectional study (112 HIV-uninfected and 41 HIV-infected) who sought health services. Anal and cervical scrapings and cervico-vaginal self-collection samples were collected. Real-time polymerase chain reaction methods were used for Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis and Mycoplasma genitalium. A syphilis test was also performed. Risk factors for STIs were identified by multivariate analysis. The overall prevalence of STIs was 30.4% (34/112) in HIV-uninfected women and 24.4% (10/41) in HIV-infected women. Anogenital Chlamydia trachomatis infection was the most prevalent in both groups of women (20.5% vs 19.5%). There was significant agreement for each STI between self-collected and clinician-collected samples: 91.7%, kappa 0.67, 95% confidence interval (CI) 0.49-0.85 for Chlamydia trachomatis; 99.2%, kappa 0.85, 95% CI 0.57-1.00 for Neisseria gonorrhoeae; 97.7%, kappa 0.39, 95% CI -0.16-0.94 for Trichomonas vaginalis; and 94.7%, kappa 0.51, 95% CI 0.20-0.82 for Mycoplasma genitalium. Women with human papillomavirus had coinfection or multiple infections with other STIs. Risk factors for STIs were being ≤ 25 years old, being employed or a student, reporting a history of STI and having a positive HPV test. A high prevalence of STIs in women in the Tapajós region was found. Cervico-vaginal self-collection is a useful tool for STI screening and can be used in prevention control programs in low-resource settings, such as in northern Brazil.

Clinical and sexual risk correlates of Mycoplasma genitalium in urban pregnant and non-pregnant young women: cross-sectional outcomes using the baseline data from the Women's BioHealth Study.

OBJECTIVE: Research exploring the clinical and sexual risk correlates is essential to define universal standards for screening and management for Mycoplasma genitalium (MG). The objective of this study is to determine the baseline prevalence of MG and associated clinical risks using cross-sectional data. METHODS: Adolescent and young adult women 13-29 years were recruited during clinical visits during which biological specimens were collected for Neisseriagonorrhoeae (NG) and Chlamydia trachomatis (CT) testing to provide vaginal specimens for MG and Trichomonasvaginalis (TV) testing. Demographic, clinical and sexual risk data were collected after obtaining written consent. MG was tested using the Hologic Gen-Probe transcription-mediated amplification-MG analyte-specific reagent assay and TV by the Aptima TV assay. Bivariate analyses were used to evaluate differences in MG prevalence based on pregnancy status, demographic factors, clinical symptoms, concurrent STI and sexual risk behaviour quiz score (maximum score=10). RESULTS: 483 patients with a mean age of 22.4 years (SD 3.6) were enrolled. Most participants were not pregnant (66%) and asymptomatic (59%). MG was the most common STI (MG 16%, TV 9%, CT 8%, NG 1%). Neither pregnancy nor symptoms were predictive of STI positivity. Thirty-five percent of non-pregnant and 45% of pregnant adolescents ≤19 years were positive for any STI. Participants with MG were 3.4 times more likely to be co-infected with other STIs compared with those with other STIs (OR 3.4, 95% CI 1.17 to 10.3, P=0.021). Mean risk quiz scores for STI positive women were six points higher than those who were STI negative (ß=0.63, 95% CI 0.36 to 0.90, P<0.001). There were no differences in risk scores for MG-positive participants compared with other STI positivity. CONCLUSION: MG infection was common, associated with STI co-infection and often asymptomatic, and pregnancy status did not confer protection.

Asymptomatic lymphogranuloma venereum among Nigerian men who have sex with men.

OBJECTIVES: Recent outbreaks of anorectal lymphogranuloma venereum (LGV) among men who have sex with men (MSM) have been characterised by proctocolitis requiring extended antibiotic treatment compared with infections caused by other serovars of Chlamydia trachomatis (CT). We describe the prevalence and clinical features of LGV among Nigerian MSM diagnosed with anorectal CT. METHODS: MSM were recruited for this observational cohort in Lagos, Nigeria, using respondent-driven sampling and screened for HIV and bacterial STIs every three months for up to 18 months. Nucleic acid amplification tests for CT were performed on rectal swab specimens. Prevalent and incident cases of anorectal CT underwent additional testing to identify LGV using novel real-time PCR assays specific for the L-serovars of CT. RESULTS: From April 2014 to July 2016, 420 MSM underwent testing for rectal STIs, of whom 66 (15.7%) had prevalent anorectal CT. Among those without prevalent disease, 68 developed incident infections during 208 person-years of follow-up. Of 134 prevalent and incident cases of anorectal CT, 7 (5.2%) were identified as LGV. None of the seven participants with LGV reported any symptoms. Two of the participants with LGV were simultaneously coinfected with rectal gonorrhoea. HIV coinfection was common among participants with both LGV (n=5, 71%) and non-LGV (n=98, 77%) serovars of CT (P=0.66). CONCLUSIONS: Anorectal LGV was uncommon but present among Nigerian MSM in this study. Consistent screening for L-serovars of CT, or presumptive treatment for LGV in cases with a high suspicion for this diagnosis, could potentially improve patient outcomes and decrease transmission.

A Rapid and Low-Cost PCR Thermal Cycler for Infectious Disease Diagnostics.

The ability to make rapid diagnosis of infectious diseases broadly available in a portable, low-cost format would mark a great step forward in global health. Many molecular diagnostic assays are developed based on using thermal cyclers to carry out polymerase chain reaction (PCR) and reverse-transcription PCR for DNA and RNA amplification and detection, respectively. Unfortunately, most commercial thermal cyclers are expensive and need continuous electrical power supply, so they are not suitable for uses in low-resource settings. We have previously reported a low-cost and simple approach to amplify DNA using vacuum insulated stainless steel thermoses food cans, which we have named it thermos thermal cycler or TTC. Here, we describe the use of an improved set up to enable the detection of viral RNA targets by reverse-transcription PCR (RT-PCR), thus expanding the TTC's ability to identify highly infectious, RNA virus-based diseases in low resource settings. The TTC was successful in demonstrating high-speed and sensitive detection of DNA or RNA targets of sexually transmitted diseases, HIV/AIDS, Ebola hemorrhagic fever, and dengue fever. Our innovative TTC costs less than $200 to build and has a capacity of at least eight tubes. In terms of speed, the TTC's performance exceeded that of commercial thermal cyclers tested. When coupled with low-cost endpoint detection technologies such as nucleic acid lateral-flow assay or a cell-phone-based fluorescence detector, the TTC will increase the availability of on-site molecular diagnostics in low-resource settings.

Point of care diagnostics for sexually transmitted infections: perspectives and advances.

Accurate and inexpensive point-of-care (POC) tests are urgently needed to control sexually transmitted infection epidemics, so that patients can receive immediate diagnoses and treatment. Current POC assays for Chlamydia trachomatis and Neisseria gonorrhoeae perform inadequately and require better assays. Diagnostics for Trichomonas vaginalis rely on wet preparation, with some notable advances. Serological POC assays for syphilis can impact resource-poor settings, with many assays available, but only one available in the U.S. HIV POC diagnostics demonstrate the best performance, with excellent assays available. There is a rapid assay for HSV lesion detection; but no POC serological assays are available. Despite the inadequacy of POC assays for treatable bacterial infections, application of technological advances offers the promise of advancing POC diagnostics for all sexually transmitted infections.

Gene expression profiling of monkeypox virus-infected cells reveals novel interfaces for host-virus interactions.

Monkeypox virus (MPV) is a zoonotic Orthopoxvirus and a potential biothreat agent that causes human disease with varying morbidity and mortality. Members of the Orthopoxvirus genus have been shown to suppress antiviral cell defenses, exploit host cell machinery, and delay infection-induced cell death. However, a comprehensive study of all host genes and virus-targeted host networks during infection is lacking. To better understand viral strategies adopted in manipulating routine host biology on global scale, we investigated the effect of MPV infection on Macaca mulatta kidney epithelial cells (MK2) using GeneChip rhesus macaque genome microarrays. Functional analysis of genes differentially expressed at 3 and 7 hours post infection showed distinctive regulation of canonical pathways and networks. While the majority of modulated histone-encoding genes exhibited sharp copy number increases, many of its transcription regulators were substantially suppressed; suggesting involvement of unknown viral factors in host histone expression. In agreement with known viral dependence on actin in motility, egress, and infection of adjacent cells, our results showed extensive regulation of genes usually involved in controlling actin expression dynamics. Similarly, a substantial ratio of genes contributing to cell cycle checkpoints exhibited concerted regulation that favors cell cycle progression in G1, S, G2 phases, but arrest cells in G2 phase and inhibits entry into mitosis. Moreover, the data showed that large number of infection-regulated genes is involved in molecular mechanisms characteristic of cancer canonical pathways. Interestingly, ten ion channels and transporters showed progressive suppression during the course of infection. Although the outcome of this unusual channel expression on cell osmotic homeostasis remains unknown, instability of cell osmotic balance and membrane potential has been implicated in intracellular pathogens egress. Our results highlight the role of histones, actin, cell cycle regulators, and ion channels in MPV infection, and propose these host functions as attractive research focal points in identifying novel drug intervention sites.

Detection of mycoplasma genitalium in female cervical samples by multitarget real-time PCR.

Mycoplasma genitalum (MG) is associated with variety of urogenital infections such as nongonococcal urethritis (NGU), endometritis and cervicitis. The objective of this study was to demonstrate and evaluate a research polymerase chain reaction (PCR) assay, for the detection of MG in cervical samples of a tested population of women attending gynecology clinics in Bosnia and Herzegovina. The Multitarget Real-Time (MTRT) PCR, utilizing the ABI 7900HT, the sequence detection system, was performed for the detection of MG. Cervical samples (N=97) from females were divided into three types of patient groups: Group 1: patients who had known abnormal clinical cytology reports (N=34); Group 2: patients who reported a history of genitourinary infections (N=22); and Group 3: patients not in either groups 1 or 2 (N=41). Overall, 14,43% (14/97) of those tested were positive for MG. A positive sample was defined as having a cycle threshold cross point (Ct) < 40,0 with a fluorescent detection comparable to the low positive control utilized during the run. This study validated the use of MTRT PCR as a reliable method for the detection of MG in clinical specimens and should facilitate large-scale screening for this organism.

Chlamydia pneumoniae enhances cytokine-stimulated human monocyte matrix metalloproteinases through a prostaglandin E2-dependent mechanism.

Exposure of human monocytes to Chlamydia pneumoniae resulted in a significant enhancement of matrix metalloproteinase (MMP) 1 and 9 production following stimulation with tumor necrosis factor alpha and granulocyte monocyte-colony stimulating factor. The effect of C. pneumoniae on monocyte MMPs was mediated through the induction of prostaglandin E(2). These findings may have implications for atherosclerotic plaque rupture.