Virus World

Purpose

Since the worldwide spread of SARS-CoV-2, different strategies have been followed to combat the pandemic and limit virus transmission. In the meantime, other respiratory viruses continued to circulate, though at decreased rates.

Methods

This study was conducted between June and July 2022, in a hospital in the metropolitan region of Rio Grande do Sul state, in the southernmost state of Brazil. The 337 hospitalized patients included those with respiratory symptoms without delimitation of age. Reverse transcription-quantitative real-time polymerase chain reaction detected 15 different respiratory viruses and confirmed coinfections in the samples. Different statistical tests were applied to evaluate the association between associations of clinical characteristics and coinfection.

Results

Sampling corresponds to 337 selected and 330 patients analyzed. The principal clinical outcome found was hospital discharge in 309 (94%) cases, while 21 (6%) resulted in death. The principal viral agents related to coinfections were Human rhinovirus, Human enterovirus, and Respiratory syncytial virus. The most frequent viral agent detected was SARS-CoV-2, with 60 (18%) infections, followed by 51 (15%) cases of Respiratory syncytial virus B (15%) and 44 (13%) cases of Human rhinovirus 1. Coinfection was mainly observed in children, while adults and the elderly were more affected by a single infection. Analyzing COVID-19 vaccination, 175 (53%) were unvaccinated while the remainder had at least one dose of the vaccine.

Conclusions

This study presents information to update the understanding of viral circulation in the region. Furthermore, the findings clarify the behavior of viral infections and possible coinfections in hospitalized patients, considering different ages and clinical profiles. In addition, this knowledge can help to monitor the population’s clinical manifestations and prevent future outbreaks of respiratory viruses.

Published in Respiratory Research (FEb. 5, 2024):

https://doi.org/10.1186/s12931-024-02708-2 

Saudi scientists have reported that eight ICU patients with a SARS-CoV-2 and MERS coinfection were detected in 2020. Four of the patients were discharged home and 3 died. During the study period from March 14, 2020 to October 19, 2020, there was a total of 67 SARS-CoV-2 ICU admitted patients who underwent simultaneous SARS-CoV-2 and MERS-CoV testing by PCR. Of those patients, 8 (12%) tested positive for both SARS-CoV-2 and MERS-CoV. There were 6 (75%) males, the mean age ± SD was 44.4 ± 11.8 years, and 7 (87.5%) were obese. Of the patients, 7 (87.5%) were non-smokers, 1 (12.5%) had diabetes mellitus, 1 (12.5%) had heart failure, and 1 (12.5%) had been on anti-platelet therapy. The mean hospital length of stay (LOS) was 21.1 ± 11.6 days and the average ICU LOS was 10.9 ± 6.03 days. All patients received supportive therapy and all were treated with corticosteroid. Of all the patients, 4 (50%) were discharged home and 3 (37.5%) died.

Research was published (March 2021) in Travel Medic. and Inf. Diseases:

https://doi.org/10.1016/j.tmaid.2021.102026 

Experts have warned that if Covid-19 cases remain high as flu season begins, the country could face a “twindemic,” with both viruses at high levels. A person has tested positive for both the flu and the coronavirus in Solano County, California, the county health department said. Such co-infection is so far rare and is the first such case to be reported in the county but not the country. At least two such cases have been reported, in Texas and Northern California. Experts have warned that if Covid-19 cases remain high as flu season begins, the U.S. could face a “twindemic,” with both viruses circulating at high levels.  Much of that concern has been focused on health care systems, which could be overwhelmed with a surge of both Covid-19 patients and flu patients. If both viruses begin circulating at high levels, it raises the risk of being infected with both at the same time.

“With the likelihood of both Covid-19 and seasonal flu activity this winter, contracting either disease may weaken your immune system and make you more susceptible to the other disease,” Dr. Bela T. Matyas, Solano County Health Officer, said Thursday in a statement. Little information was provided about the Solano County patient, except that the individual is under 65. The first confirmed case of community spread of Covid-19 in the United States was reported in the county in February.  In March, a Texas doctor reportedly fell ill with both viruses at the same time. And a research letter published in April in the Journal of the American Medical Association noted a case of flu-coronavirus co-infection in Northern California. It's not yet clear how common co-infections will be. "We very much hope that it will not be," Dr. Tara Bouton, an assistant professor of medicine at Boston University School of Medicine. Dr. Peter Chin-Hong, a professor of medicine and infectious disease specialist at the University of California, San Francisco, predicted it's only a matter of time before there are similar cases.

How common it will be "depends on what the flu season is going to look like," Chin-Hong said. “There's nothing that would preclude co-infection. It’s not like Covid comes in and takes out all the flu." It's also not yet clear if patients with co-infection of the flu and Covid-19 will fare worse, Bouton said. "However, there are a few preliminary studies suggesting that this may in fact be the case." That's "all the more reason why people need to do everything they can to prevent that scenario, including getting vaccinated against flu, wearing a mask when appropriate social distancing is not possible, and washing hands," she said.

Background

The COVID-19 pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 virus, emerged in late 2019 and spready globally. Many effects of infection with this pathogen are still unknown, with both chronic and repeated COVID-19 infection producing novel pathologies.

Case presentation

An immunocompromised patient presented with chronic COVID-19 infection. The patient had history of Hodgkin’s lymphoma, treated with chemotherapy and stem cell transplant. During the course of their treatment, eleven respiratory samples from the patient were analyzed by whole-genome sequencing followed by lineage identification. Whole-genome sequencing of the virus present in the patient over time revealed that the patient at various timepoints harboured three different lineages of the virus. The patient was initially infected with the B.1.1.176 lineage before coinfection with BA.1. When the patient was coinfected with both B.1.1.176 and BA.1, the viral populations were found in approximately equal proportions within the patient based on sequencing read abundance. Upon further sampling, the lineage present within the patient during the final two timepoints was found to be BA.2.9. The patient eventually developed respiratory failure and died.

Conclusions

This case study shows an example of the changes that can happen within an immunocompromised patient who is infected with COVID-19 multiple times. Furthermore, this case demonstrates how simultaneous coinfection with two lineages of COVID-19 can lead to unclear lineage assignment by standard methods, which are resolved by further investigation. When analyzing chronic COVID-19 infection and reinfection cases, care must be taken to properly identify the lineages of the virus present.

Key points

We identified the co-infection of the SARS-CoV-2 Omicron and Delta variants in two epidemiologically unrelated patients with chronic kidney disease requiring haemodialysis. Both SARS-CoV-2 variants were co-circulating locally at the time of detection. Amplicon- and probe-based sequencing using short- and long-read technologies identified and quantified Omicron and Delta subpopulations in respiratory samples from the two patients. These findings highlight the importance of genomic surveillance in vulnerable populations.

Preprint available in medRxiv (Feb. 15, 2022):

https://doi.org/10.1101/2022.02.13.22270755