SN7 SHORT NOTE 5M

Describe the coronaviruses and the other emerging viral infections.

Microbiology · 2nd Professional — Para-Clinical

Coronaviruses

Enveloped viruses with a helical nucleocapsid and the largest genome of any RNA virus — single-stranded positive-sense RNA. The name comes from the crown-like fringe of spike (S) glycoprotein seen on electron microscopy
The spike protein determines the receptor and is the vaccine target; SARS-CoV-1 and SARS-CoV-2 bind ACE2, and MERS-CoV binds DPP4
Unusually for an RNA virus it has a proofreading exonuclease, so it mutates more slowly than influenza or HIV — though over a pandemic of that scale variants still emerged

Virus	Emergence and reservoir	Features
Common cold coronaviruses	Endemic worldwide	Mild upper respiratory illness; a significant proportion of common colds
SARS-CoV-1	2002, China; bats through civet cats	Severe acute respiratory syndrome; high mortality but contained and eliminated by isolation and contact tracing, because patients were infectious only after becoming symptomatic
MERS-CoV	2012, Arabian peninsula; bats through dromedary CAMELS	High mortality (about 35%) but limited person-to-person spread; nosocomial outbreaks
SARS-CoV-2	2019; probable bat origin	COVID-19 — a pandemic, driven by substantial pre-symptomatic and asymptomatic transmission, which is precisely why it could not be contained as SARS-CoV-1 was

CLINICAL PEARL

SARS was contained and COVID-19 was not, and the difference was the timing of infectivity. SARS-CoV-1 patients became infectious after they were symptomatic, so isolating symptomatic people interrupted transmission. SARS-CoV-2 spreads before symptoms and from people who never develop them, so the same strategy failed. A single feature of natural history, not virulence or transmissibility alone, determined whether an outbreak could be stopped by classical public health methods.

Covid-19 — Key Points

Transmission — respiratory droplets and aerosols, favoured by crowded, closed and poorly ventilated spaces; and by contaminated surfaces to a lesser extent
Clinical spectrum — from asymptomatic through mild upper respiratory illness to pneumonia, acute respiratory distress syndrome, thrombosis and multi-organ failure. anosmia and ageusia were characteristic early features; "happy hypoxia", with marked hypoxaemia and little breathlessness, was a notable and dangerous presentation
Risk factors for severe disease — age, obesity, diabetes, hypertension, chronic lung, cardiac and kidney disease, and immunosuppression
Diagnosis — RT-PCR on a nasopharyngeal swab is the standard; rapid antigen tests are less sensitive but useful for rapid screening; serology indicates past infection or vaccination
Treatment — supportive care and oxygen; dexamethasone in those requiring oxygen (its mortality benefit was among the most important findings of the pandemic); anticoagulation; and antivirals in selected patients. Antibiotics have no role unless bacterial co-infection is proven
Vaccines — developed with unprecedented speed using mRNA, viral vector and inactivated whole-virus platforms; India produced and deployed Covishield and the indigenous Covaxin on a very large scale
Long COVID — persistent fatigue, breathlessness, cognitive difficulty and other symptoms lasting months, of uncertain mechanism

Other Emerging Viral Infections

Virus	Reservoir and transmission	Features
NIPAH	Fruit bats; through date palm sap, pigs, and person TO person	Outbreaks in KERALA and West Bengal; encephalitis with respiratory illness and very high mortality; requires BSL-4 handling and strict barrier nursing
EBOLA and Marburg	Bats; person to person through body fluids	Viral haemorrhagic fever with high mortality; healthcare workers and those handling bodies are at particular risk; an effective vaccine now exists
ZIKA	AEDES mosquitoes; also sexual and vertical transmission	A mild illness in adults, but causes microcephaly and congenital Zika syndrome, and Guillain-Barré syndrome
Crimean-Congo haemorrhagic fever	Ticks and livestock; person to person including to healthcare workers	Reported from Gujarat and Rajasthan; high mortality
Kyasanur Forest disease	Ticks; monkeys; Western Ghats	Haemorrhagic fever with a biphasic course; a vaccine exists
Hantavirus	Rodent excreta	Haemorrhagic fever with renal syndrome; pulmonary syndrome

Applied Aspects

Most emerging viruses are zoonoses, and their emergence is driven by deforestation, wildlife trade, intensive animal farming, urbanisation and travel — so prevention is ecological and agricultural as much as medical
The "one health" approach — integrating human, animal and environmental health surveillance — is the accepted framework, and India has established programmes along these lines
Suspect Nipah in encephalitis with respiratory features in Kerala, particularly with bat or date palm sap exposure or a cluster of cases, and institute barrier precautions immediately; healthcare workers have died in Indian outbreaks
Barrier precautions protect staff in viral haemorrhagic fevers; nosocomial amplification has been a feature of nearly every outbreak, and safe burial practices matter as much as clinical care
Rapid genomic sequencing and open data sharing allowed the SARS-CoV-2 vaccine to be designed within days of the sequence being published, and this capacity is now part of outbreak preparedness
Notify unusual clusters early; the interval between the first case and recognition determines whether an outbreak is contained or becomes an epidemic, and that interval depends on a clinician thinking something is odd and reporting it

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