Burden of respiratory viral infection in persons with human immunodeficiency virus

Abstract This study was conducted to determine the prevalence of respiratory viral infections (RVI) in persons living with HIV (PLH) admitted with a respiratory complaint using real‐time reverse transcription polymerase chain reaction and primer‐independent next‐generation sequencing (NGS). Of 82 subjects, respiratory viruses were the most common pathogen identified in 27 (33%), followed by fungus and bacteria in 8 (10%) and 4 (5%) subjects, respectively. Among subjects with RVI, 11 (41%) required ICU admission and 16 (59%) required mechanical ventilation. The proportion of respiratory viruses identified, and the associated complicated hospital course highlights the significant role that RVIs play in the lung health of PLH.


| INTRODUC TI ON
Pulmonary complications, including respiratory tract infections, are a major cause of morbidity and mortality among people living with HIV (PLH). 1,2 While bacterial and fungal pathogens have been well -described as important etiologies of opportunistic lung disease, less is known about respiratory viruses in PLH. 3 Studies from antiretroviral therapy (ART)-limited regions revealed a 20-fold higher risk of respiratory viral infections among pediatric and adult PLH compared with HIV-uninfected subjects. 4,5 In these settings, HIV infection was also a risk factor for higher rates of hospitalization, pneumococcal coinfection, and the need for supplemental oxygen in lower respiratory tract influenza infection. [5][6][7] The aim of our study was to determine the prevalence of respiratory viruses in a cohort of PLH hospitalized with a respiratory complaint at a tertiary care center. Secondarily, commercial real-time reverse transcription polymerase chain reaction (rRT-PCR) was compared to pathogen-agnostic next-generation sequencing (NGS) for the detection of viral pathogens in respiratory specimens.

| Screening/enrollment
Of 101 subjects that met criteria for enrollment, 12 refused participation, four were discharged prior to recruitment, two were Spanish-speaking only, and one was decisionally impaired with no available legally authorized representative.
Eighty-two subjects including 49 (60%) men with a mean age of 50 were included in the final analysis (Table 1). Demographic, clinical characteristics, and outcomes were similar between those with and without a respiratory virus with the exception of a significantly higher BMI in the group with a virus. Approximately 1/3 each were current or former smokers, and less than half received an influenza vaccine in the prior season. While more than 70% were prescribed antiretroviral therapy, 39% had plasma HIV RNA levels that were above the limits of detection. More than half of the participants had CD4 cell counts below 200/mm 3 .

| Respiratory virus detection
Thirty-four subjects (41%) were diagnosed with a respiratory infection including 27 (33%) with a respiratory virus detected alone or in combination with other pathogens-including one subject with two viruses detected simultaneously, three with both Pneumocystis jirovecii pneumonia (PJP) and viral coinfection, and 2 (2%) with bacterial/viral coinfection ( Figure S1). Of the seven remaining subjects, PJP was detected in 5 and bacterial pneumonia in 2. Rhinovirus was the most common respiratory viral pathogen detected in 14 subjects (52%), followed by influenza (19%), parainfluenza (11%), coronavirus (7%), and adenovirus (7%). Five respiratory viral infections were identified retrospectively through rRT-PCR testing conducted as part of this study ( Figure S1).
For 29 participants, 39 respiratory samples (29 NP and 10 BAL) were also tested for RNA viruses using NGS ( Figure S2). Three participants had discordant results compared with rRT-PCR testing: One had adenovirus detected by rRT-PCR but not by RNA-based NGS, and two subjects had coronavirus and parainfluenza 4 detected by rRT-PCR but no virus was identified by NGS. NGS did not detect any additional viruses compared to rRT-PCR; however, complete genome sequences were obtained for rhinovirus in three subjects that were genetically distinct from all known rhinoviruses ( Figure S3).

| Clinical outcomes
PLH admitted with a respiratory virus required a high level of care with 41% admitted to the intensive care (ICU) unit and 59% requiring mechanical ventilation. Four subjects with a respiratory virus (15%) were discharged to a higher level of care than on admission, and 3 (11%) died ( Table 1). Subjects who died during hospital admission had a lower mean CD4 (43 cells/µL) and higher HIV viral load (165 962 copies/mL) compared to those who were discharged home or to a rehabilitation facility, but pairwise comparisons were not statistically significant (Table S1).

| D ISCUSS I ON
In this cohort of 82 PLH admitted with a respiratory complaint, respiratory viruses were the most commonly identified respiratory pathogens, more than bacterial and fungal pathogens combined.
Among PLH enrolled in this study, those diagnosed with a respi- Additionally, our characterization of infectious etiologies was molecular-based for viruses but relied on less sensitive methods for the detection of bacteria and PJP. However, in support of these findings, viruses were also the most commonly identified pathogen in community-acquired pneumonia in the EPIC study, which used rigorous microbiologic testing, suggesting that the prevalence of viruses identified in this study is not due to disparate diagnostic sensitivity. 12 We also cannot exclude that viruses identified could represent asymptomatic carriage in the nasopharynx; however, all subjects were symptomatic on admission, and with the exception of four subjects that had concomitant PCP or bacterial infection, no other respiratory pathogens were identified. Lastly, the use of NGS in this study was exploratory and limited to a subset of participants. The limit of detection by the number of reads being sequenced emerged as a constraint of NGS as seen previously. 13,14 Likely for this reason, a coronavirus was identified by RT-PCR, but In conclusion, respiratory viruses were the most common respiratory pathogen identified in admitted PLH. These subjects experienced severe illness as 41% required ICU admission, 59% required mechanical ventilation, and 11% died. Respiratory viral infections represent an important cause of severe illness in PLH admitted with respiratory symptoms. Future research should be directed at understanding if PLH are at increased risk of respiratory viral infections or increased severity compared with HIV-uninfected individuals in the setting of widespread ART availability and in low prevalence HIV settings, and if so, potential mechanisms underlying that increased risk.

CO N FLI C T O F I NTE R E S T
No conflicts of interest to report.

AUTH O R CO NTR I B UTI O N S
Subhashini Sellers: Data curation, Formal analysis, Investigation,

S U PP O RTI N G I N FO R M ATI O N
Additional supporting information may be found online in the Supporting Information section.