Pathogens in pneumonia-associated respiratory samples from Wuhan prior to SARS-CoV-2 emergence

Unfortunately, today, Wuhan is the early epicenter of the coronavirus disease 2019 (COVID-19) pandemic that broke out in December 2019, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The pandemic continues after more than two years and over 5.8 million deaths.

Study: Total infectome characterization of respiratory infections in pre-COVID-19 Wuhan, China. Image Credit: sleepingpanda/ShutterstockStudy: Total infectome characterization of respiratory infections in pre-COVID-19 Wuhan, China. Image Credit: sleepingpanda/Shutterstock

However, it is only a small part of the global respiratory infection picture. An interesting paper in PLoS Pathogens describes the broad situation with respect to respiratory pathogens that cause acute respiratory infection (ARI) and pneumonia in the city. This provides useful insights into the infectome at baseline and the pathogen profile in people with respiratory disease.


The infectomes of respiratory infection and pneumonia refer to the total number and type of viruses, bacteria, and fungi associated with these diseases. In the current study, the researchers used meta-transcriptomics to identify all microbes present in the respiratory samples simultaneously, identify potentially pathogenic organisms from scratch, and examine the infection-associated viral ribonucleic acid (RNA) that reveals the type of organism and disease association.

What did the study show?

The study included 408 patients with ARI and pneumonia, all of whom presented before the COVID-19 pandemic began. Clinically, 27 were severely ill, and the overall mortality was 0.74%. The meta-transcriptomic analysis was carried out on bronchoalveolar lavage fluid (BALF) samples, characterizing respiratory pathogens, either those already known to be so or potentially novel microbes that have not been characterized so far.

Only the first type was found in this study. About one in three samples contained RNA viruses and a quarter bacteria. Just about one in seven had coinfections with two different species of pathogen. Most of the pathogens belonged to common respiratory pathogens, like the flu virus, rhinovirus, Pseudomonas aeruginosa, and Haemophilus influenzae

More uncommon pathogens were also found, including enterovirus D68 and Chlamydia psittaci. Overall, this unbiased survey strongly indicates that SARS-like viruses were not in circulation during the two years prior to the pandemic.

The seasonal endemic human coronaviruses (hCoV), including HKU1, OC43, 229E, and NL63, were abundant in the study. Surprisingly, a retrospective study of over 600 throat swab specimens from patients with flu-like symptoms during this period also failed to turn up even one case where SARS-CoV-2 infection was present before January 2020.

The results showed a more complex picture containing many more infectious pathogens than with the use of targeted PCR or qPCR. The microbes associated with ARI fall into three epidemiological clusters, namely, the core infectome typical of patients with respiratory infection, occurring annually; the emerging infectome found during ARI outbreaks, in other parts of the world than the region being examined; and sporadic pathogens, uncommon or new.

Core infectome

The core infectome included mostly those respiratory or systemic pathogens that are usually looked for in hospitals, like the flu virus, RSV, Mycoplasma, Klebsiella pneumoniae, Hemophilus influenzae, Pseudomonas aeruginosa, Staphylococcus aureus, and Streptococcus pneumoniae. A single sample contained Chlamydia psittaci, a bird-borne zoonosis.

RNA viruses were present in diversity and abundance, such as rhinoviruses, parainfluenza viruses, and coronaviruses, DNA viruses like herpesviruses were also present but were less abundant. These viral pathogens are often considered less important.

This may be a mistaken assumption, as they are not only abundant and highly prevalent in this subset of patients, but their clinical features may extend beyond respiratory infections, with hCoV OC 43 being the cause of fatal human encephalitis in some cases. These microbes may very well be able to cause opportunistic infections.

Emerging and zoonotic pathogens

The emerging infectome was represented in this survey by one virus, the enterovirus D68, which triggered the source of an unconventional outbreak. This virus had a low prevalence until 2014 but thereafter broke out and spread to over 20 countries, from the USA. The outcomes included severe respiratory illness and even acute flaccid paralysis.

Six cases were found in this study, from June to December 2016, with the strains being closely related as well as to other strains found in China over the same period, indicative of a larger outbreak. The six cases had abundant virus particles, indicating severe infection with actively replicating viral particles.

The zoonotic infectome comprised Chlamydia psittaci alone, which was found at relatively high levels in a patient with pneumonia, breathing distress, and pleural effusion. In the absence of travel history, local exposure is likely.

Importantly, a high level of abundance was observed with several RNA viruses and bacteria, indicative of acute illness. About one in seven cases were caused by two bacterial species, H. influenzae, and P. aeruginosa, and six RNA viruses, including the flu viruses and EV-D68.

The researchers attributed the multiple lineages of the flu viruses and other pathogens found here to their introduction from diverse sources, even imported cases from overseas, since Wuhan is a major city with intense domestic and international traffic, as demonstrated by the rapid and extensive spread of the COVID-19 pandemic.

With the popularization of next-generation sequencing platform in major hospitals, the meta-transcriptomic approach outlined here can be easily integrated into diagnostic practice with much greater speed and significantly more information output than traditional technologies, providing a broad-scale understanding of infectious disease in general.”

Journal reference:
Dr. Liji Thomas

Written by

Dr. Liji Thomas

Dr. Liji Thomas is an OB-GYN, who graduated from the Government Medical College, University of Calicut, Kerala, in 2001. Liji practiced as a full-time consultant in obstetrics/gynecology in a private hospital for a few years following her graduation. She has counseled hundreds of patients facing issues from pregnancy-related problems and infertility, and has been in charge of over 2,000 deliveries, striving always to achieve a normal delivery rather than operative.


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