Case Report: First Confirmed Case of Coinfection of SARS-CoV-2 With Choclo orthohantavirus

Abstract

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a major international public health concern. The World Health Organization (WHO) declared the pandemic of coronavirus disease 2019 (COVID-19) on March 11, 2020. In Panama, the first SARS-CoV-2 infection was confirmed on March 9, 2020, and the first fatal case associated to COVID-19 was reported on March 10. This report presents the case of a 44-year-old female who arrived at the hospital with a respiratory failure, five days after the first fatal COVID-19 case, and who was living in a region where hantavirus pulmonary syndrome cases caused by Choclo orthohantavirus (CHOV), are prevalent. Thus, the clinical personnel set a differential diagnosis to determine a respiratory disease caused by the endemic CHOV or the new pandemic SARS-CoV-2. This case investigation describes the first coinfection by SARS-CoV-2 and CHOV worldwide. PCR detected both viruses during early stages of the disease and the genomic sequences were obtained. The presence of antibodies was determined during the patient's hospitalization. After 23 days at the intensive care unit, the patient survived with no sequelae, and antibodies against CHOV and SARS-CoV-2 were still detectable 12 months after the disease. The detection of the coinfection in this patient highlights the importance, during a pandemic, of complementing the testing and diagnosis of the emergent agent, SARS-CoV-2, with other common endemic respiratory pathogens and other zoonotic pathogens, like CHOV, in regions where they are of public health concern.

Keywords: COVID-19; Choclo orthohantavirus; SARS-CoV-2; case report; coinfection; hantavirus pulmonary syndrome.

Figure 1

Timeline: Clinical, epidemiological and laboratory assays of SARS-CoV-2 and CHOV coinfection case. Schematic timeline with events described from top to bottom: molecular and serological laboratory assays for SARS-CoV-2 (light blue) and CHOV (green), type of mechanical ventilation applied to the patient, timeline with the date (year, month, day) and the days of symptoms onset (*) with color coding representing the health institution and clinical management, epidemiological and clinical case description. Abbreviations used in the figure: SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; CHOV, Choclo orthohantavirus; RT-PCR, real time reverse transcription polymerase chain reaction; PCR, polymerase chain reaction; CLIA, chemiluminescent immunoassay; SIA, strip immunoblot assay; PRNT80, 80% plaque reduction neutralization test; Ig, immunoglobulin (A, M and G for this case); ICU, intensive care unit; AMV, advance in mechanical ventilation; COVID-19, coronavirus disease 2019.

Figure 2

Pulmonary images of the patient with HPS and COVID-19. Taken in the intern medicine ward. (A) Posteroanterior chest radiography. Mild peripheral diffuse infiltrate of predominance in both pulmonary bases (black arrows). No cardiomegaly, no pleural effusion. (B) Anteroposterior chest radiography. Increased extent of the radiographic infiltrate in both pulmonary fields (black arrows). No pleural effusion. A rapid progression of the infiltrate is observed in 10 hours of evolution compared to previous radiography. (C) Coronal chest high-resolution simple computed tomography. Scattered multifocal opacities of peripheral predominance in both lungs (white arrows). Isolated consolidated areas (black arrows). (D) Axial chest high-resolution simple computed tomography. Tarnished glass-like opacities in anterior pulmonary location (white arrows) and consolidated areas in posterior pulmonary location (black arrows). Mild bilateral basal posterior pleural effusion (black arrows).

Figure 3

Phylogenetic trees of the SARS-CoV-2 and CHOV sequences from Panama and worldwide. (A) SARS-CoV-2 phylogenetic tree showing 6610 genomes sampled between December 2019 and April 2020, the analysis grouping the sequences in clades (name indicated at the base of each clade branch) was restricted to samples submitted to GISAID until October 2020 (grey: worldwide, blue: Panama). (B) SARS-CoV-2 subtree showing samples from the 19B clade that forms the cluster of transmission associated to the coinfection case (bigger circle with the sample location in blue). The sample locations at the level of health region within Panama are indicated. For acknowledgment table see Supplementary Data . (C) Phylogenetic tree of the orthohantavirus, including CHOV sequence with GenBank accession number OK393713 (blue) with. Maximum likelihood tree was drawn using worldwide reference sequences of orthohantavirus and rooted to Imji virus reference strain, black circles indicates nodes with ultrabootstrap values greater the 50%. All information about GISAID and Genbank accession numbers for the SARS-Cov-2 and orthohantavirus reference sequences, respectively, are listed in Supplementary Data .